[test-suite] r311413 - [test-suite] Adding the Pathfinder Benchmark
Adrian Prantl via llvm-commits
llvm-commits at lists.llvm.org
Tue Aug 22 07:25:15 PDT 2017
Hal, it looks like this benchmark is failing to build on green dragon because of a warning, could you please take a look?
http://green.lab.llvm.org/green/job/Compiler_Verifiers_GlobalISEL/8407/consoleFull#139682078949ba4694-19c4-4d7e-bec5-911270d8a58c <http://green.lab.llvm.org/green/job/Compiler_Verifiers_GlobalISEL/8407/consoleFull#139682078949ba4694-19c4-4d7e-bec5-911270d8a58c>
/Users/buildslave/jenkins/workspace/Compiler_Verifiers_GlobalISEL/test-suite/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/main.c:175:22: warning: comparison of array 'commandLine' not equal to a null pointer is always true [-Wtautological-pointer-compare]
if ( commandLine != NULL )
^~~~~~~~~~~ ~~~~
<>/Users/buildslave/jenkins/workspace/Compiler_Verifiers_GlobalISEL/test-suite/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/main.c:177:21: error: implicit declaration of function 'YAMLOpen' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
YAMLOpen();
^
/Users/buildslave/jenkins/workspace/Compiler_Verifiers_GlobalISEL/test-suite/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/main.c:181:21: error: implicit declaration of function 'YAMLWriteString' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
YAMLWriteString("Command", commandLine+1);
^
/Users/buildslave/jenkins/workspace/Compiler_Verifiers_GlobalISEL/test-suite/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/main.c:227:5: error: implicit declaration of function 'YAMLClose' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
YAMLClose(); /* works even if YAML logging isn't present */
^
/Users/buildslave/jenkins/workspace/Compiler_Verifiers_GlobalISEL/test-suite/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/main.c:271:9: error: implicit declaration of function 'doMultiSearches' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
doMultiSearches(config);
^
/Users/buildslave/jenkins/workspace/Compiler_Verifiers_GlobalISEL/test-suite/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/main.c:271:9: note: did you mean 'doMultiSearchesQT'?
/Users/buildslave/jenkins/workspace/Compiler_Verifiers_GlobalISEL/test-suite/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchAlgorithms.h:104:6: note: 'doMultiSearchesQT' declared here
void doMultiSearchesQT(Configuration *config);
^
1 warning and 4 errors generated.
> On Aug 21, 2017, at 5:38 PM, Hal Finkel via llvm-commits <llvm-commits at lists.llvm.org> wrote:
>
> Author: hfinkel
> Date: Mon Aug 21 17:38:53 2017
> New Revision: 311413
>
> URL: http://llvm.org/viewvc/llvm-project?rev=311413&view=rev
> Log:
> [test-suite] Adding the Pathfinder Benchmark
>
> PathFinder searches for "signatures" within graphs. Graphs being searched are
> directed and cyclic. Many, but not all nodes within the graph have labels. Any
> given node may have more than one label, and any label may be applied to more
> than one node. A signature is an orderd list of labels. PathFinder searches for
> paths between labels within the signature. PathFinder returns success if there
> is a path from a node with the first label in the signature that passes through
> nodes with each label in order, ultimately reaching a node with the last label
> in the signature. Labeled nodes need not be contiguous on any given path.
>
> At the current time, PathFinder does not do any pathway analysis (e.g. shortest
> path) for discovered signatures. PathFinder simply searches until a signature
> is satisfied or all pathways have been exhausted.
>
> Web: https://mantevo.org/packages/
> Github: https://github.com/Mantevo/PathFinder
>
> When run on an Intel Xeon CPU E5-2699 v4 @ 2.20GHz:
> compile_time: 13.3092
> exec_time: 3.1158
> Maximum resident set size (kbytes): 6256
>
> Patch by Brian Homerding, thanks!
>
> Differential Revision: https://reviews.llvm.org/D36680
>
> Added:
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/CMakeLists.txt
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/COPYING
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/COPYING.LESSER
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/Makefile
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/PathFinder.reference_output
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/README
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/bitfield.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/bitfield.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/configuration.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/configuration.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/gettime.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graph.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graph.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graphGen.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graphGen.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/main.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/medsmall1.adj_list
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/node.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/node.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/parsing.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/parsing.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchAlgorithms.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchAlgorithms.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchDiagram.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchDiagram.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/statistics.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/statistics.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/systemCallMap.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/systemCallMap.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/utils.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/utils.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/vectorUtils.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/vectorUtils.h
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/yaml.c
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/yaml.h
> Modified:
> test-suite/trunk/LICENSE.TXT
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/CMakeLists.txt
> test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Makefile
>
> Modified: test-suite/trunk/LICENSE.TXT
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/LICENSE.TXT?rev=311413&r1=311412&r2=311413&view=diff
> ==============================================================================
> --- test-suite/trunk/LICENSE.TXT (original)
> +++ test-suite/trunk/LICENSE.TXT Mon Aug 21 17:38:53 2017
> @@ -84,6 +84,7 @@ ASC Sequoia: llvm-test/MultiSourc
> llvm-test/MultiSource/Benchmarks/ASC_Sequoia/sphot
> smg2000: llvm-test/MultiSource/Benchmarks/ASCI_Purple/SMG2000
> miniAMR: llvm-test/MultiSource/Benchmarks/DOE-ProxyApps-C/miniAMR
> +Pathfinder: llvm-test/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder
> XSBench: llvm-test/MultiSource/Benchmarks/DOE-ProxyApps-C/XSBench
> HPCCG: llvm-test/MultiSource/Benchmarks/DOE-ProxyApps-C++/HPCCG
> PENNANT: llvm-test/MultiSource/Benchmarks/DOE-ProxyApps-C++/PENNANT
>
> Modified: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/CMakeLists.txt
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/CMakeLists.txt?rev=311413&r1=311412&r2=311413&view=diff
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/CMakeLists.txt (original)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/CMakeLists.txt Mon Aug 21 17:38:53 2017
> @@ -1,2 +1,3 @@
> add_subdirectory(XSBench)
> +add_subdirectory(Pathfinder)
> add_subdirectory(miniAMR)
>
> Modified: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Makefile
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Makefile?rev=311413&r1=311412&r2=311413&view=diff
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Makefile (original)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Makefile Mon Aug 21 17:38:53 2017
> @@ -2,7 +2,7 @@
>
> LEVEL = ../../..
> PARALLEL_DIRS = XSBench \
> - miniAMR
> -
> + miniAMR \
> + Pathfinder
>
> include $(LEVEL)/Makefile.programs
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/CMakeLists.txt
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/CMakeLists.txt?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/CMakeLists.txt (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/CMakeLists.txt Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,4 @@
> +set(PROG PathFinder)
> +list(APPEND LDFLAGS -lm)
> +set(RUN_OPTIONS -x ${CMAKE_CURRENT_SOURCE_DIR}/medsmall1.adj_list)
> +llvm_multisource()
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/COPYING
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/COPYING?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/COPYING (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/COPYING Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,674 @@
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> +
> + <one line to give the program's name and a brief idea of what it does.>
> + Copyright (C) <year> <name of author>
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> + This program is distributed in the hope that it will be useful,
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> +
> +Also add information on how to contact you by electronic and paper mail.
> +
> + If the program does terminal interaction, make it output a short
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> +
> + <program> Copyright (C) <year> <name of author>
> + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
> + This is free software, and you are welcome to redistribute it
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> +
> +The hypothetical commands `show w' and `show c' should show the appropriate
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> +might be different; for a GUI interface, you would use an "about box".
> +
> + You should also get your employer (if you work as a programmer) or school,
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> +
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> +<http://www.gnu.org/philosophy/why-not-lgpl.html>.
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/COPYING.LESSER
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/COPYING.LESSER?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/COPYING.LESSER (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/COPYING.LESSER Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,165 @@
> + GNU LESSER GENERAL PUBLIC LICENSE
> + Version 3, 29 June 2007
> +
> + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
> + Everyone is permitted to copy and distribute verbatim copies
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> +
> +
> + This version of the GNU Lesser General Public License incorporates
> +the terms and conditions of version 3 of the GNU General Public
> +License, supplemented by the additional permissions listed below.
> +
> + 0. Additional Definitions.
> +
> + As used herein, "this License" refers to version 3 of the GNU Lesser
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> + b) Give prominent notice with the combined library that part of it
> + is a work based on the Library, and explaining where to find the
> + accompanying uncombined form of the same work.
> +
> + 6. Revised Versions of the GNU Lesser General Public License.
> +
> + The Free Software Foundation may publish revised and/or new versions
> +of the GNU Lesser General Public License from time to time. Such new
> +versions will be similar in spirit to the present version, but may
> +differ in detail to address new problems or concerns.
> +
> + Each version is given a distinguishing version number. If the
> +Library as you received it specifies that a certain numbered version
> +of the GNU Lesser General Public License "or any later version"
> +applies to it, you have the option of following the terms and
> +conditions either of that published version or of any later version
> +published by the Free Software Foundation. If the Library as you
> +received it does not specify a version number of the GNU Lesser
> +General Public License, you may choose any version of the GNU Lesser
> +General Public License ever published by the Free Software Foundation.
> +
> + If the Library as you received it specifies that a proxy can decide
> +whether future versions of the GNU Lesser General Public License shall
> +apply, that proxy's public statement of acceptance of any version is
> +permanent authorization for you to choose that version for the
> +Library.
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/Makefile
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/Makefile?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/Makefile (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/Makefile Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,6 @@
> +LEVEL = ../../../..
> +
> +PROG = PathFinder
> +LDFLAGS = -lm
> +RUN_OPTIONS = -x $(PROJ_SRC_DIR)/medsmall1.adj_list
> +include $(LEVEL)/MultiSource/Makefile.multisrc
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/PathFinder.reference_output
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/PathFinder.reference_output?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/PathFinder.reference_output (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/PathFinder.reference_output Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,28 @@
> +
> +
> + PathFinder: finding a series of labeled nodes within a
> + two-layer directed, cyclic graph.
> + Copyright (2013) Sandia Corporation
> +
> + Sandia National Laboratories is a multi-program laboratory managed and
> + operated by Sandia Corporation, a wholly owned subsidiary of Lockheed
> + Martin Corporation, for the U.S. Department of Energy's National Nuclear
> + Security Administration under terms of Contract DE-AC04-94AL85000,
> + there is a non-exclusive license for use of this work by or on behalf
> + of the U.S. Government. Export of this program may require a license
> + from the United States Government.
> +
> +
> + 500 functions specified
> + 3463 basic blocks specified
> + 371 total System Call Map elements
> + ...parsing complete.
> +Immediately before parallel
> +
> +
> +44669 found out of 137641 searches. Overall Time: 0:0:0.000
> +
> +
> +Total 44669 legs found
> +
> +exit 0
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/README
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/README?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/README (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/README Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,220 @@
> +**************************************************************************
> +LLVM Test-suite Note:
> +**************************************************************************
> +The original source is located at https://github.com/Mantevo/PathFinder.
> +Beyond this paragraph is the original README contained with the source
> +code. The Makefile refered to within is not utilized within the
> +test-suite. The test-suite builds a serial version (openmp and
> +mpi disabled) with its own cmake and make build system.
> +**************************************************************************
> +
> +PathFinder graph pathway analysis mini-application
> +
> +------------------------------------
> +Contents of this README file:
> +1. PathFinder overview
> +2. PathFinder versions
> +3. Building PathFinder
> +4. Running PathFinder
> +5. PathFinder search algorithm/pseudo code
> +------------------------------------
> +
> +------------------------------------
> +1. PathFinder overview:
> +
> +PathFinder searches for "signatures" within graphs. Graphs being searched are
> +directed and cyclic. Many, but not all nodes within the graph have labels. Any
> +given node may have more than one label, and any label may be applied to more
> +than one node. A signature is an orderd list of labels. PathFinder searches for
> +paths between labels within the signature. PathFinder returns success if there
> +is a path from a node with the first label in the signature that passes through
> +nodes with each label in order, ultimately reaching a node with the last label
> +in the signature. Labeled nodes need not be contiguous on any given path.
> +
> +At the current time, PathFinder does not do any pathway analysis (e.g. shortest
> +path) for discovered signatures. PathFinder simply searches until a signature is
> +satisfied or all pathways have been exhausted.
> +
> +------------------------------------
> +2. PathFinder versions:
> +
> +- PathFinder_ref:
> + reference version: self-contained. Includes serial and OpenMP parallel
> + implementations. MPI is not yet supported.
> +
> +------------------------------------
> +3. Building PathFinder:
> +
> +The standard build is to cd into the 'PathFinder_ref' directory and type 'make'.
> +Doing so builds an OpenMP enabled version of PathFinder (named PathFinder.x). For
> +serial execution, run it with the OMP_NUM_THREADS environment variable set to 1.
> +
> +Alternative build targets:
> + * clean -- removes all .o files
> + * realclean -- removes all .o and .x files
> + * debug -- PathFinder.x+dbg - serial executable with debug information
> + * mpi -- currently not implemented; prints an error message
> +
> +To verify execution, type 'make check' which builds a serial version, runs it
> +against one of the known data sets and compares the results.
> +
> +------------------------------------
> +4. Running PathFinder:
> +
> +The simplest execution is to simply type './PathFinder.x'. This will run
> +PathFinder with a trivial graph (MicroTestData.adj_list in the source
> +directory). It will find 6 legs out of 9 searches, by doing an "exhaustive"
> +search on that graph.
> +
> +An exhaustive search is PathFinder determining if paths exist between any pair
> +of labels for every label existing in the graph. Exhaustive searches are
> +embarrassingly parallel, and can be quite time consuming depending on the size
> +of the graph and number of labels. Running PathFinder exhaustively is done with
> +the -x switch:
> + PathFinder.x -x <data file>
> + e.g. PathFinder.x -x ../scaleData/1kx750.adj_list
> +
> +To search for specific signatures, PathFinder can be run interactively or with
> +a configuration file. To run interactively, use the -i switch:
> + PathFinder.x -i <data file>
> +PathFinder will prompt the operator for a series of labels to define the
> +signature for which PathFinder will search.
> +
> +Multiple data files and multiple signatures can be specified to PathFinder in a
> +configuration file. A python script (config_builder.py) exists to assist the
> +operator in creating a configuration file. A sample configuration file is
> +included in the PathFinder source directory. To run PathFinder with a config
> +file, use the -c switch:
> + PathFinder.x -c <config file>
> + e.g. PathFinder.x -c sampleConfig
> +
> +Typing 'PathFinder -h' will print a help message describing the available
> +execution switches. Sample data files are provided in the 'data' and
> +'generatedData' directories. The python script used to generate representative
> +graph data is in the PathFinder_ref directory. It is named graph_gen.py.
> +
> +YAML output files can be generated by using the -y switch.
> +
> +Sample data sets are included in the "generatedData" and "scaleData"
> +subdirectories. The scaleData files are intended for performance
> +characterization. They are named with the convention:
> + <NodeCount>x<LabelCount>.adj_list
> +For expected results, see scaleData/README
> +
> +------------------------------------
> +5. PathFinder search algorithm / pseudo code
> +
> +PathFinder does a modified depth-first search through the graph. For each
> +signature, PathFinder begins searching from the set of nodes which have the
> +first label in the signature. From these nodes, it finds a path to any node that
> +is labeled with the second label in the signature. This is repeated until a path
> +is found to the last label in the signature. If at any point in the search a
> +path to a label is not found, that search fails.
> +
> +Searches are done recursively. At each node, the target of each edge is checked
> +to see if it is labeled with the next label in the signature. If a match is
> +made, The search continues from the matched node and the subsequent label in the
> +signature. If there are no remaining labels in the signature, the search has
> +succeeded. If no direct edge from the current node matches, then the search
> +continues recursively for the current label along each edge from the current
> +node. If no match exists along any edge, the search fails.
> +
> +Pseudo code:
> +
> +For each file in config file:
> + Parse file into a Graph
> +
> +For each signature in config file:
> + Store for processing
> +
> +For each signature
> +{
> + For each Graph
> + {
> + Make sure the graph contains at least one node labeled with every label
> + in the signature
> +
> + Get set of nodes with signature[0], the first label in signature
> + for each “Start” node
> + {
> + // Recursive procedure to find remaining signature. Requires
> + // current node, the remaining “unfound” signature legs
> + // a result stack of nodes to store path traversed and
> + // a stack of nodes visited so far to detect cycles and
> + // redundant searches
> + Create empty result stack
> + Create empty visited stack
> + success = FindRemainingSignatureFromCurrentNode ( startNode,
> + &signature[1], result, visited )
> + } // end of for each “Start” node
> + } // end of for each Graph
> +} // end of for each Signature
> +
> +
> +// Recursive procedure to find remaining signature.
> +// currentNode – the node whose edges *might* reach the
> +// next label in the signature
> +// signature – an array of pointers to C strings. These strings
> +// are the labels being matched by the nodes being
> +// searched. Each sequential pair of labels is a
> +// “leg” of the search. The last pointer is NULL to
> +// terminate the array.
> +// result – a stack of nodes containing the path currently
> +// traversed to reach this node
> +// visited – a stack of ALL nodes searched during the attempt
> +// to find the current label
> +
> +boolean FindRemainingSignatureFromCurrentNode ( currentNode, signature, result,
> + visited )
> +{
> + If currentNode is in visited
> + return FALSE – we have reached a cycle or a subgraph that has
> + already been searched
> + else
> + push currentNode onto visited stack
> +
> + push currentNode onto result stack
> + For each edge from currentNode
> + {
> + If edge->targetNode->label == signature[0]
> + {
> + If signature[1] != NULL we have more legs in the search
> + Create nextResult for next leg search
> + Create nextVisited for next leg search
> + success = FindRemainingSignatureFromCurrentNode
> + ( edge->targetNode, &signature[1],
> + nextResult, nextVisited )
> + if success
> + result += nextResult
> + delete nextVisited
> + return TRUE, we’ve found the path
> + else
> + continue through edge checking
> + else signature[1] == NULL
> + push edge->targetNode onto result
> + return true, we’ve found the path
> + }
> + else
> + continue through edge checking
> + } // end of for each edge target compared against signature [0]
> +
> + // If we’ve made it this far, none of the edges is a direct
> + // match to the current label, do a deeper search
> + For each edge from current node
> + {
> + success = FindRemainingSignatureFromCurrentNode ( edge->targetNode,
> + &signature[0], result, visited )
> + if success
> + return TRUE, we’ve found the path
> + else
> + continue through edge searching loop
> + }
> +
> + // If we’ve made it this far, we have no path
> + pop currentNode off of result (but not off of visited)
> + return FALSE;
> +} // end of find remaining signature
> +
> +
> +
> +
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/bitfield.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/bitfield.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/bitfield.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/bitfield.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,114 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +#include "bitfield.h"
> +#include "node.h"
> +#include <stdio.h>
> +
> +
> +/* --------
> + * Bitfield is a mask around a character pointer. An array of character
> + * pointers is allocated such that there is a sequence of available bits
> + * equal in length to the number of nodes in a given graph. Bitfield
> + * defines operations that check if a bit corresponding to a node index
> + * is set. This is used by the graph traversal path finding algorithms
> + * to determine if a node has been visited.
> + */
> +
> +
> +/* constructor */
> +Bitfield *Bitfield_new(int bitsNeeded)
> +{
> + int size = (bitsNeeded+7) / 8; /* CHAR_BIT; */
> + Bitfield *new = malloc(sizeof(Bitfield));
> + if ( !new )
> + return(NULL);
> + new->bitfield = calloc(size, sizeof(char));
> + if ( !new->bitfield )
> + {
> + free(new);
> + return(NULL);
> + }
> +
> + new->bitsNeeded = bitsNeeded;
> + return new;
> +}
> +
> +/* destructor */
> +void Bitfield_delete(Bitfield *this)
> +{
> + if ( this )
> + {
> + if ( this->bitfield )
> + free(this->bitfield);
> + free(this);
> + }
> +}
> +
> +/* Returns true if the specified node has been visited */
> +bool Bitfield_nodeVisited(Bitfield *this, struct NodeStruct *node)
> +{
> + int index = node->nodeCount >> 3;
> + char byte = this->bitfield[index];
> + char bit = 1 << (node->nodeCount & 0x07);
> + bool set = byte & bit;
> +
> + this->bitfield[index] |= bit;
> +
> + /* printf ( "Inside Bitfield nodeVisited: Node: %d, index %d, byte %x, bit: %x\n",
> + node->nodeCount, index, byte, bit ); */
> + return(set);
> +}
> +
> +
> +/* Makes a byte-by-byte copy of the "from" bitfield */
> +Bitfield *Bitfield_copy(Bitfield *from)
> +{
> + int i;
> +
> + if ( !from )
> + return(NULL);
> +
> + Bitfield *new = Bitfield_new(from->bitsNeeded);
> + if ( new )
> + {
> + for ( i = 0; i*8 < from->bitsNeeded; ++i )
> + new->bitfield[i] = from->bitfield[i];
> + return(new);
> + }
> + else
> + return(NULL);
> +}
> +
> +
> +void Bitfield_clear(Bitfield *this)
> +{
> + int size = (this->bitsNeeded+7) / 8;
> + memset(this->bitfield, 0, size);
> +}
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/bitfield.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/bitfield.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/bitfield.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/bitfield.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,69 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +#ifndef BITFIELD_H
> +#define BITFIELD_H
> +
> +#include <stdbool.h>
> +#include <stdlib.h>
> +#include <string.h>
> +
> +struct NodeStruct;
> +
> +/* --------
> + * Bitfield is a mask around a character pointer. An array of character
> + * pointers is allocated such that there is a sequence of available bits
> + * equal in length to the number of nodes in a given graph. Bitfield
> + * defines operations that check if a bit corresponding to a node index
> + * is set. This is used by the graph traversal path finding algorithms
> + * to determine if a node has been visited.
> + */
> +
> +typedef struct BitfieldStruct Bitfield;
> +
> +struct BitfieldStruct
> +{
> + int bitsNeeded; /* in BYTES!!! */
> + char *bitfield;
> +};
> +
> +
> +Bitfield *Bitfield_new(int bitsNeeded); /* constructor */
> +void Bitfield_delete(Bitfield *this); /* destructor */
> +
> +/* Returns true if the specified node has been visited */
> +bool Bitfield_nodeVisited(Bitfield *this, struct NodeStruct *node);
> +
> +/* Makes a byte-by-byte copy of the "from" bitfield */
> +Bitfield *Bitfield_copy(Bitfield *from);
> +
> +void Bitfield_clear();
> +
> +#endif
> +
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/configuration.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/configuration.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/configuration.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/configuration.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,69 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * configuration.c
> + *
> + * Created on: October 1, 2013
> + * Author: Brian "Rig" Rigdon
> + */
> +
> +#include <stdio.h>
> + #include "configuration.h"
> +
> + SearchOptions* SearchOptions_new()
> + {
> + SearchOptions *options = malloc(sizeof(SearchOptions));
> + if ( !options )
> + return(NULL);
> + options->searchType = treeSearch;
> + options->multiThreaded = false;
> + options->doStatistics = false;
> + options->writeOutputFile = false;
> + options->outputFile = NULL;
> + options->buildType = endNodesOnly;
> + return(options);
> + }
> +
> + Configuration* Configuration_new()
> + {
> + Configuration *new = malloc(sizeof(Configuration));
> + SearchOptions *options = malloc(sizeof(SearchOptions));
> + if ( !new || !options )
> + {
> + if ( new ) free(new);
> + if ( options ) free(options);
> + return(NULL);
> + }
> + new->graphs = NULL;
> + new->signatures = NULL;
> + new->searchOptions = options;
> + new->qThreadCount = 0;
> + return(new);
> + }
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/configuration.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/configuration.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/configuration.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/configuration.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,80 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +
> +/*
> + * configuration.h
> + *
> + * Created on: October 1, 2013
> + * Author: Brian "Rig" Rigdon
> + */
> +
> +#ifndef CONFIGURATION_H_
> +#define CONFIGURATION_H_
> +
> +#include <stdbool.h>
> +#include "graph.h"
> +#include "graphGen.h"
> +
> +/* I was hoping to avoid this - however because we are dealing with
> + * pointers to arrays of pointers, passing the address of an such
> + * a beast becomes really confusing: Graph *(**pointer)[]
> + * Ergo, I am building a structure to contain all the information
> + * necessary for a given running of this software. For lack of
> + * a better name, we are calling it the "configuration".
> + */
> +
> +/* A simple enum to define which search is to be done */
> +typedef enum { treeSearch, diagramSearch } SearchType;
> +
> +typedef struct SearchOptionsStruct SearchOptions;
> +struct SearchOptionsStruct
> +{
> + SearchType searchType;
> + bool multiThreaded;
> + bool doStatistics;
> + bool writeOutputFile;
> + char *outputFile;
> + BuildType buildType;
> +};
> +
> +SearchOptions * SearchOptions_new();
> +
> +typedef struct ConfigurationStruct Configuration;
> +struct ConfigurationStruct
> +{
> + Graph **graphs; /* a pointer to a NULL terminated array of pointers */
> + Signature *signatures; /* a pointer to a NULL terminated array of Signatures */
> + SearchOptions *searchOptions;
> + int qThreadCount; /* recursion depth to STOP spawning new tasks */
> +};
> +
> +Configuration* Configuration_new();
> +
> +#endif /* CONFIGURATION_H_ */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/gettime.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/gettime.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/gettime.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/gettime.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,43 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +#include <sys/time.h>
> +#ifdef USE_OMP
> +#include <omp.h>
> +#endif
> +
> +extern double currentTime()
> +{
> +#ifdef USE_OMP
> + return omp_get_wtime();
> +#else
> + return 0;
> +#endif
> +}
> +
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graph.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graph.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graph.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graph.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,186 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * graph.c
> + *
> + * Created on: Jan 9, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +/* --------
> + * Graphs are made up of nodes and edges. Nodes hold data and edges
> + * connect nodes to each other. In this representation, edges are
> + * directional (they lead from one node to the next) and may create
> + * looped paths. The data sets from which these graphs are defined
> + * define two-layered graphs. The outer layer may contain one or
> + * more interior nodes. These interior nodes may be linked among each
> + * other. Each containing node may have up to two "entrance" nodes;
> + * that is, an edge goes from the containing node to its entrance node.
> + *
> + * As mentioned above, the graphs are defined in data files. The graph
> + * data structure contains the file name, a count of nodes, a list of
> + * exterior nodes, and structures that assist in the searching through
> + * the graph for "signatures"
> + */
> +
> +#include <stdio.h>
> +#include <stdlib.h>
> +#include <string.h>
> +#include <time.h>
> +#include <math.h>
> +
> +#ifdef USE_OMP
> +#include <omp.h>
> +#endif
> +
> +#include "graph.h"
> +#include "systemCallMap.h"
> +#include "bitfield.h"
> +#include "utils.h"
> +
> +
> +
> +
> +/* -------------------------------------------
> + * Graph Method Definitions
> + *
> + */
> +/* We deleted the code that made a graph singleton. Now we may have
> + * more than one graph. Ergo, the main method (or whatever) will maintain
> + * the graph pointer.
> + */
> +
> +Graph *Graph_new()
> +{
> + Graph *graph= NULL;
> + graph = malloc( sizeof( Graph ));
> + if ( graph )
> + {
> + /* The malloc worked! */
> + graph->fileName = NULL;
> + graph->totalNodes = 0;
> + graph->outerNodes = NULL;
> + graph->searchDiagram = NULL;
> + }
> +
> + return( graph );
> +}
> +
> +/* Destructor - erases current graph, sets singleton to NULL */
> +void Graph_delete( Graph *trash )
> +{
> + SearchDiagram *element;
> + if ( trash )
> + {
> + free( trash->fileName );
> + NodeList_clear( trash->outerNodes, true );
> + if ( trash->searchDiagram ) {
> + for ( element = trash->searchDiagram; element->node != NULL; ++element )
> + {
> + free( element->edgeReferenceArray );
> + }
> + free( trash->searchDiagram );
> + }
> + free( trash );
> + }
> +}
> +
> +bool Graph_addOuterNode( Graph *graph, Node *newOuterNode )
> +{
> + /* a little basic error checking */
> + if ( !graph || !newOuterNode )
> + return (false);
> +
> + /* Is this the first outer node? */
> + if ( graph->outerNodes == NULL ) /* Allocates singletonGraph if it's not there */
> + {
> + graph->outerNodes = NodeList_new();
> + if ( !graph->outerNodes )
> + return( false ); /* the malloc failed */
> + graph->outerNodes->node = newOuterNode;
> + return( true );
> + }
> +
> + /* Otherwise, insert the new node at the tail of the singleton graph */
> + return( NodeList_insertBack( graph->outerNodes, newOuterNode ));
> +}
> +
> +
> +/* Finds a node within the graph. If deep is true, we check interior nodes as well.
> + * If deep is false, we only check to see if the id is an outer node. This does NOT
> + * find the path to the node.
> + */
> +Node *Graph_findNode( Graph *graph, int id, bool deep )
> +{
> + NodeList *nodes;
> + Node *node;
> +
> + for ( nodes = graph->outerNodes; nodes != NULL; nodes = nodes->nextNode )
> + {
> + if ( nodes->node->id == id )
> + return( nodes->node );
> + /* If that wasn't the node, and we're going deep, see if it's there. */
> + if ( deep )
> + {
> + node = Graph_findContainedNode( nodes->node, id );
> + if ( node )
> + return( node );
> + }
> + }
> +
> + return( NULL );
> +}
> +
> +
> +
> +
> +/* Determine if a given node contains the node specified by id. If this problem extended
> + * beyond two layers, this method would be recursive. Returns NULL if node is not contained.
> + * This does NOT find the path to the node.
> + */
> +Node *Graph_findContainedNode( Node *node, int id )
> +{
> + NodeList *nodes;
> +
> + for ( nodes = node->interiorNodes; nodes != NULL; nodes = nodes->nextNode )
> + {
> + if ( nodes->node->id == id )
> + return( nodes->node );
> + }
> +
> + return( NULL );
> +}
> +
> +
> +
> +
> +
> +
> +/* Search Algorithms */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graph.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graph.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graph.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graph.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,101 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +
> +/*
> + * Graph.h
> + *
> + * Created on: Jan 9, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +
> +/* --------
> + * Graphs are made up of nodes and edges. Nodes hold data and edges
> + * connect nodes to each other. In this representation, edges are
> + * directional (they lead from one node to the next) and may create
> + * looped paths. The data sets from which these graphs are defined
> + * define two-layered graphs. The outer layer may contain one or
> + * more interior nodes. These interior nodes may be linked among each
> + * other. Each containing node may have up to two "entrance" nodes;
> + * that is, an edge goes from the containing node to its entrance node.
> + *
> + * As mentioned above, the graphs are defined in data files. The graph
> + * data structure contains the file name, a count of nodes, a list of
> + * exterior nodes, and structures that assist in the searching through
> + * the graph for "signatures"
> + */
> +
> +#ifndef GRAPH_H_
> +#define GRAPH_H_
> +
> +#include <stdbool.h> /* bool is no longer part of the C language */
> +#include "node.h"
> +#include "searchDiagram.h"
> +#include "systemCallMap.h"
> +
> +
> +/* -------------------------------------------
> + * Graph Definitions
> + *
> + */
> +
> +typedef struct GraphStruct Graph;
> +
> +struct GraphStruct
> +{
> + char *fileName; /* the file parsed to give us this graph */
> + int totalNodes; /* Nodes, both outer and interior */
> + NodeList *outerNodes; /* The Linked-List capture of the node data */
> + SearchDiagram *searchDiagram; /* The compressed Node/Edge search structures */
> + SystemCallMap *systemCallMap;
> +};
> +
> +
> +/* "methods" */
> +
> +Graph *Graph_new(); /* Graph constructor */
> +void Graph_delete( Graph *trash ); /* Destructor - erases current graph */
> +bool Graph_addOuterNode( Graph *graph, Node *newOuterNode );
> +/* Finds a node within the graph. If deep is true, we check interior nodes as well.
> + * If deep is false, we only check to see if the id is an outer node. This does NOT
> + * find the path to the node.
> + */
> +Node *Graph_findNode( Graph *graph, int id, bool deep );
> +
> +
> +
> +/* Determine if a given node contains the node specified by id. If this problem extended
> + * beyond two layers, this method would be recursive. Returns NULL if node is not contained.
> + * This does NOT find the path to the node.
> + */
> +Node *Graph_findContainedNode( Node *node, int id );
> +
> +
> +#endif /* GRAPH_H_ */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graphGen.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graphGen.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graphGen.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graphGen.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,195 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * graphGen.c
> + *
> + * Created on: Aug 2, 2013
> + * Author: jbrigdo
> + */
> +
> +#include <stdbool.h>
> +#include <stdio.h>
> +#include "graphGen.h"
> +#include "vectorUtils.h"
> +
> +
> +/* getDuplicateNodeForGraph takes a node from another graph and sees if
> + * a duplicate has previously been created for this graph. If not, it tries
> + * to create and insert a new duplicate. If that fails, we're out of memory.
> + * In that circumstance, we have a significant error condition. It is
> + * time to delete the graph being built and report that error to the
> + * calling method (buildGraphFromPaths).
> + */
> +static Node *getDuplicateNodeForGraph(Graph *graph, Node *from)
> +{
> + Node *newNode = Graph_findNode(graph, from->id, true); /* true == deep search */
> + if ( newNode )
> + return(newNode);
> +
> + /* else */
> + newNode = Node_duplicate(from, graph->totalNodes++ ); /* POST increment */
> + if ( newNode )
> + {
> + Graph_addOuterNode(graph,newNode); /* all nodes are exterior in this graph */
> + newNode->type = exteriorNode;
> + return(newNode);
> + }
> +
> + /* else */
> + Graph_delete(graph); /* Failure is DESTRUCTIVE at this point */
> + return NULL;
> +}
> +
> +
> +Graph *buildGraphFromPaths(NodeVecVec **pathList, BuildType build)
> +{
> + Graph *newGraph = Graph_new();
> + Node *pathNode; /* The node we're looking at in the path */
> + Node *currentNode;
> + Node *nextNode;
> + int i; /* Iterator through the path List array */
> + int j; /* Iterator through each path List */
> + int k; /* Iterator through each path in the path List */
> +
> + if ( !pathList || !newGraph )
> + return(NULL);
> +
> + for ( i = 0; pathList[i] ; ++i )
> + {
> + for (j = 0; j < pathList[i]->contentSize; ++j)
> + {
> + pathNode = pathList[i]->vector[j]->vector[0];
> + currentNode = getDuplicateNodeForGraph(newGraph, pathNode);
> + if ( !currentNode )
> + return(NULL); /* out of memory: crashing! newGraph has already been cleaned up */
> +
> + for ( k = 1; k < pathList[i]->vector[j]->contentSize; ++k /*also incremented below*/ )
> + {
> + if ( build == endNodesOnly )
> + {
> + k = pathList[i]->vector[j]->contentSize - 1;
> + }
> + else if ( build == labeledNodes )
> + {
> + while ( pathList[i]->vector[j]->vector[k]->labelIdx < 0 )
> + ++k;
> + }
> + /* else if ( build == completePath ) no-op */
> +
> + pathNode = pathList[i]->vector[j]->vector[k];
> + nextNode = getDuplicateNodeForGraph(newGraph, pathNode);
> + if ( !nextNode )
> + return(NULL); /* out of memory: crashing! newGraph has already been cleaned up */
> + Node_addEdgeToNode(currentNode, nextNode);
> + // printf ( "Adding edge: %d ==> %d\n", currentNode->id, nextNode->id );
> + currentNode = nextNode;
> + }
> + }
> + }
> +
> + return(newGraph);
> +}
> +
> +
> +/* Write the given graph to a file */
> +bool exportGraph(Graph *graph, char *fileName)
> +{
> + FILE *out = NULL;
> + NodeList *nodes = NULL;
> + EdgeList *edges = NULL;
> + int nodeCount = 0;
> +
> + if ( !graph || !fileName ) /* A little basic error checking */
> + return(false);
> +
> + out = fopen(fileName, "w");
> +
> + if ( !out ) /* A little more basic error checking */
> + return(false);
> +
> + /* Write out the header */
> + /* ... find out how many functions (outer nodes) the graph holds */
> + for ( nodes = graph->outerNodes; nodes != NULL; nodes = nodes->nextNode )
> + {
> + ++nodeCount;
> + }
> + fprintf(out, "Functions: %d\n", nodeCount);
> + fprintf(out, "Basic blocks: %d\n\n", graph->totalNodes);
> +
> + /* First, write out the graph's outer nodes */
> + for ( nodes = graph->outerNodes; nodes != NULL; nodes = nodes->nextNode )
> + {
> + fprintf(out, "%d ", nodes->node->id);
> + //printf("Node: %d ", nodes->node->id);
> + if ( nodes->node->edges )
> + {
> + nodeCount = 0;
> + /* Wow is this inefficient, but two passes is the easiest way to do it. */
> + for ( edges = nodes->node->edges; edges != NULL; edges = edges->nextEdge )
> + {
> + if ( edges->targetNode->type == exteriorNode )
> + ++nodeCount;
> + }
> + fprintf(out, "%d ", nodeCount);
> + //printf("has %d edges: ", nodeCount);
> + for ( edges = nodes->node->edges; edges != NULL; edges = edges->nextEdge )
> + {
> + if ( edges->targetNode->type == exteriorNode )
> + {
> + fprintf(out, "%d ", edges->targetNodeId);
> + //printf("%d, ", edges->targetNodeId);
> + }
> + }
> + fprintf(out, "\n");
> + //printf("\n");
> + }
> + else
> + {
> + fprintf(out, "0 \n" );
> + //printf(" no edges.\n");
> + }
> + }
> +
> + /* then, for each of the outer nodes, write out its interior nodes (if any) */
> + /* We are skipping this for the time being. This currently is being called with flat graphs. */
> +
> + /* Finally, write out the labels. */
> + fprintf(out, "-------------------------------------------- \nSYSTEM CALLS \n\n");
> +
> + for ( nodes = graph->outerNodes; nodes != NULL; nodes = nodes->nextNode )
> + {
> + if ( nodes->node->label != NULL )
> + fprintf(out, "%d %s \n", nodes->node->id, nodes->node->label );
> + /* If we were worried about interior nodes, we'd need a duplicate loop here. */
> + }
> +
> + return(true);
> +
> +}
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graphGen.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graphGen.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graphGen.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/graphGen.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,52 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * graphGen.h
> + *
> + * Created on: Aug 2, 2013
> + * Author: J. Brian Rigdon
> + */
> +
> +#ifndef GRAPHGEN_H
> +#define GRAPHGEN_H
> +
> +#include "graph.h"
> +
> +typedef enum { endNodesOnly, labeledNodes, completePath } BuildType;
> +
> +Graph *buildGraphFromPaths(NodeVecVec **pathList, BuildType build);
> +
> +/* Write the given graph to a file */
> +bool exportGraph(Graph *graph, char *fileName);
> +
> +
> +
> +
> +#endif /* GRAPHGEN_H_ */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/main.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/main.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/main.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/main.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,361 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * main.c
> + *
> + * Created on: Jan 9, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +
> +#include <string.h>
> +#include <stdio.h>
> +#include <stdlib.h>
> +#include <ctype.h>
> +#include <unistd.h>
> +#include <stdbool.h>
> +#include <math.h>
> +#include "parsing.h"
> +#include "utils.h"
> +#include "searchAlgorithms.h"
> +#include "vectorUtils.h"
> +#include "statistics.h"
> +#include "configuration.h"
> +
> +#ifdef QT
> + #include "qThreadSearch.h"
> +#endif /* QT */
> +
> +extern double currentTime();
> +
> +#define helpString "\nUsage: PathFinder.exe [OPTIONS] [<fileName>]\n\n\
> + Operation:\n\
> + -c <config file> use configuration file\n\
> + -i <data file> interactive search of specified data file\n\
> + -x <data file> exhaustive leg search (any label to any label) of data file\n\n\
> + Other:\n\
> + -o <output file> save optimized graph to file\n\
> + -h,u prints this help message.\n\
> + -q <depth> use qthread parallelism (config file only). The depth value\n\
> + specifies how deep in recursion to continue spawning new tasks\n\
> + during searches\n\
> + -y create YAML output\n"
> +
> +/* Forward declarations so that main is the first function we read */
> +void runBatch(char *configFile, Configuration *config);
> +void runInteractively(char *fileName, Configuration *config);
> +void exhaustiveLegSearch(char *fileName, Configuration *config);
> +
> +int main(int argc, char *argv[])
> +{
> + char defaultFile[] = "MicroTestData.adj_list";
> + char *fileName = NULL;
> + Configuration *config = Configuration_new();
> + signed char c;
> + int cFlag = 0; // Why did I make these ints instead of bool? JBR - 10/25/13
> + int iFlag = 0;
> + int xFlag = 0;
> + int tFlag = 0;
> + int dFlag = 0;
> + int oFlag = 0;
> + bool qFlag = 0;
> + int qCount = 0;
> + char commandLine[200];
> + int i;
> +
> + printf ( "\n\n"
> + " PathFinder: finding a series of labeled nodes within a\n"
> + " two-layer directed, cyclic graph.\n"
> + " Copyright (2013) Sandia Corporation\n"
> + "\n"
> + " Sandia National Laboratories is a multi-program laboratory managed and\n"
> + " operated by Sandia Corporation, a wholly owned subsidiary of Lockheed\n"
> + " Martin Corporation, for the U.S. Department of Energy's National Nuclear\n"
> + " Security Administration under terms of Contract DE-AC04-94AL85000,\n"
> + " there is a non-exclusive license for use of this work by or on behalf\n"
> + " of the U.S. Government. Export of this program may require a license \n"
> + " from the United States Government.\n\n\n" );
> +
> + #ifdef DEBUG
> + printf("\tRunning debug build\n\n");
> + #endif
> + #ifdef OPENMP
> + printf("\tRunning Open MP build\n\n");
> + #endif
> + #ifdef QT
> + printf("\tRunning Q Thread build\n\n");
> + #endif
> +
> + if ( !config )
> + {
> + printf("Error: Could not allocation configuration structure.\n\n\t---Exiting\n\n");
> + exit(0);
> + }
> +
> + if ( argc < 2 )
> + {
> + exhaustiveLegSearch(defaultFile, config);
> + }
> + else
> + {
> + while ( (c = getopt(argc, argv, "c:i:x:o:q:huy")) != -1 )
> + {
> + switch (c)
> + {
> + case '?': /* we had a problem */
> + if ( optopt == 'c' )
> + fprintf(stderr, "\tPlease specify configuration file.\n\n");
> + else if ( optopt == 'i' || optopt == 'x' )
> + fprintf(stderr, "\tPlease specify data file.\n\n");
> + else if ( optopt == 'o' )
> + fprintf(stderr, "\tPlease specify output graph data file.\n\n");
> + else if ( optopt == 'q' )
> + fprintf(stderr, "\tPlease specify recursion depth to keep spawning tasks.\n\n");
> + return(1);
> + break; /* Superfluous, I know */
> + case 'h':
> + case 'u':
> + printf ("\n%s\n\n", helpString);
> + return(0); /* Nothing else matters */
> + break; /* Superfluous, I know. */
> + case 'c': /* configuration file */
> + fileName = optarg;
> + cFlag = 1;
> + break;
> + case 'i': /* interactive */
> + fileName = optarg;
> + iFlag = 1;
> + break;
> + case 'x': /* exhaustive leg search */
> + fileName = optarg;
> + xFlag = 1;
> + break;
> + case 'o': /* Save optimized paths in a new graph definition data file */
> + config->searchOptions->outputFile = optarg;
> + config->searchOptions->writeOutputFile = true;
> + oFlag = 1;
> + break;
> + case 's':
> + config->searchOptions->doStatistics = true;
> + break;
> + case 'q':
> + qCount = atoi(optarg);
> + if ( qCount < 1 )
> + qCount = 1;
> + config->qThreadCount = qCount;
> + break;
> + case 'y':
> + if ( commandLine != NULL )
> + {
> + YAMLOpen();
> + commandLine[0] = '\0';
> + for ( i = 0; i < argc; ++i )
> + sprintf(commandLine, "%s %s", commandLine, argv[i] );
> + YAMLWriteString("Command", commandLine+1);
> + }
> + break;
> + default :
> + break;
> + }
> + }
> +
> + /* Debug --* /
> + if (cFlag) printf ("cFlag ");
> + if (iFlag) printf ("iFlag ");
> + if (xFlag) printf ("xFlag ");
> + if (oFlag) printf ("oFlag ");
> + if (fileName) printf ( " - %s", fileName );
> + if (outFile) printf ( " - %s", outFile);
> + printf ("\n");
> + / *-- End Debug */
> +
> + if ( (cFlag+iFlag+xFlag) > 1 )
> + {
> + fprintf(stderr, "-c -i and -x are mutually exclusive, PathFinder can only do one of those.\n\n");
> + return(1);
> + }
> +
> + if ( (cFlag+iFlag+xFlag) == 0 )
> + {
> + fprintf(stderr, "-c (config file) -i (interactive) or -x (exhaustive) must be specified.\n\n");
> + return(1);
> + }
> +
> + if ( oFlag && !xFlag )
> + {
> + fprintf(stderr, "-o (optimized graph output) is only compatible with -x (exhaustive searches).\n\n");
> + return(1);
> + }
> +
> + if ( cFlag )
> + runBatch(fileName, config);
> + else if ( iFlag )
> + runInteractively(fileName, config);
> + else
> + {
> + exhaustiveLegSearch(fileName, config);
> + }
> + }
> +
> + YAMLClose(); /* works even if YAML logging isn't present */
> + return(0); /* zero means no error */
> +}
> +
> +void runBatch(char *configFile, Configuration *config)
> +{
> + bool success;
> + int i;
> + int j;
> + double tick, tock;
> + int hours;
> + int min;
> + double sec;
> +
> + if ( !configFile )
> + {
> + printf("Error: No config file entered.\n\n\t---Exiting---");
> + exit(0);
> + }
> +
> + // printf("config file: %s\n", configFile);
> +
> + tick = currentTime();
> + success = parseConfigFile(configFile, config);
> + tock = currentTime();
> + sec = tock-tick;
> + hours = (int)sec/3600;
> + sec = fmod( sec, 3600.0 );
> + min = (int)sec/60;
> + sec = fmod(sec, 60.0);
> + printf ("\n\nOverall Parse Time: %02d:%02d:%02.3f\n", hours, min, sec);
> +
> + /* Debug --* /
> + for ( i = 0; config->signatures[i] != NULL; ++i );
> + for ( j = 0; config->graphs[j] != NULL; ++j );
> + printf( "%d files, %d signatures \n", j, i );
> + exit(1);
> + / *-- End Debug */
> +
> + if ( success )
> + {
> + #ifdef QT
> + doMultiSearchesQT(config);
> + #else
> + doMultiSearches(config);
> + #endif
> + }
> +
> + printf ("\n\nSearches complete.\n");
> +}
> +
> +
> +void runInteractively(char *fileName, Configuration *config)
> +{
> + char stringBuffer[200];
> + Graph *graph;
> + char *labels[25]; /* Do we need an interactive signature bigger than 25? */
> + NodePtrVec *path = NULL;
> + bool success = false;
> + int i, j;
> + int fullIntSignature[3] = { 0, 0, -1 };
> +
> +
> + graph = parseFile(fileName);
> +
> + if ( !graph )
> + return;
> +
> + while ( 1 )
> + {
> + i = 0;
> + do {
> +
> + printf("\nPlease insert a node label for this signature (\"\" to complete, \"bail\" to exit):\n");
> + gets(stringBuffer);
> +
> + if ( strcmp (stringBuffer, "bail") == 0 )
> + exit(1);
> +
> + if ( strcmp(stringBuffer, "") != 0 )
> + {
> + labels[i] = strdup(stringBuffer);
> + ++i;
> + }
> +
> + } while ( i < 25 && strcmp(stringBuffer, "") != 0 );
> +
> + labels[i] = NULL;
> +
> + /* Debug */
> + printf("\nSignature: ");
> + for ( j = 0; j < i; ++j )
> + {
> + printf("'%s'", labels[j]);
> + if ( j < i-1 )
> + printf(" -> ");
> + else
> + printf("\n\n");
> + }
> + /* end debug */
> +
> + path = NodePtrVec_new(50);
> + success = findLabelPath(graph, (Signature)labels, path, config->searchOptions->searchType);
> +
> + /* Sanity check to verify that a valid path exists */
> + if( success )
> + {
> + /* printStack ( path ); */
> + printf ("Found, resultant path has %d steps.\n", path->contentSize);
> + }
> + else
> + printf("\n\tPath not found for signature.\n");
> +
> + NodePtrVec_delete(path);
> + }
> +
> +}
> +
> +void exhaustiveLegSearch(char *fileName, Configuration *config)
> +{
> + Graph *graph;
> + int found;
> +
> + graph = parseFile(fileName);
> +
> + if ( !graph || !config )
> + return;
> +
> + if ( config->searchOptions->outputFile == NULL )
> + found = findAllPossibleLegs(graph, config->searchOptions->searchType);
> + else
> + found = findAndLogAllPossibleLegs(graph, config->searchOptions);
> + printf("\n\nTotal %d legs found\n\n", found);
> + Graph_delete(graph);
> +}
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/medsmall1.adj_list
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/medsmall1.adj_list?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/medsmall1.adj_list (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/medsmall1.adj_list Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,6153 @@
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>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/node.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/node.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/node.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/node.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,364 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * node.c
> + *
> + * Created on: Feb 1, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +/* --------
> + * Nodes are the basic data structure within the graph. Nodes hold information
> + * regarding their identity (id, label, type, etc.) and information about their
> + * edges (list of edges, number of edges).
> + *
> + * Node.h/.c contains the data definitions for nodes and edges as well as con-
> + * tainers for nodes (NodeList, NodePtrVec) and edges (EdgeList)
> + */
> +
> +#include <stdio.h>
> +#include <stdlib.h>
> +#include <string.h>
> +#include "node.h"
> +#include "graph.h"
> +
> +
> +/* -------------------------------------------
> + * Node Method Definitions
> + *
> + */
> +
> +/* "methods" for nodes */
> +/* Constructor */
> +Node *Node_new(int id, int nodeCount)
> +{
> + Node *node = malloc(sizeof(Node));
> +
> + if ( !node )
> + return(NULL);
> +
> + node->id = id;
> + node->nodeCount = nodeCount; /* index into bitfield - caller must increment! */
> + node->label = NULL;
> + node->labelIdx = -1;
> + node->type = exteriorNode;
> + node->container = NULL;
> + node->interiorNodes = NULL;
> + node->edges = NULL;
> +
> + node->edgeCount = 0;
> + node->entranceCount = 0;
> +
> + return(node);
> +}
> +
> +/* Destructor */
> +void Node_delete(Node *trash)
> +{
> + /* Some basic error checking */
> + if ( !trash ) return;
> +
> + if ( trash->interiorNodes ) /* "true" tells clearNodeList to free the mallocs */
> + NodeList_clear( trash->interiorNodes, true );
> +
> + if ( trash->edges )
> + EdgeList_clear( trash->edges );
> +
> + free( trash );
> +}
> +
> +/* Duplicates node data, BUT NO EDGE INFORMATION */
> +Node *Node_duplicate(Node *from, int newIndex)
> +{
> + Node *copy = malloc(sizeof(Node));
> +
> + if ( !copy || !from )
> + return(NULL);
> +
> + copy->id = from->id;
> + copy->nodeCount = newIndex; /* index into bitfield - caller must increment! */
> + copy->label = from->label;
> + copy->labelIdx = from->labelIdx;
> + copy->type = from->type;
> + copy->container = NULL;
> + copy->interiorNodes = NULL;
> + copy->edges = NULL;
> +
> + copy->edgeCount = 0;
> + copy->entranceCount = 0;
> +
> + return(copy);
> +}
> +
> +/* Identifies the Upper-level node containing inner level node */
> +void Node_setParent(Node *this, Node *parent)
> +{
> + /* Some basic error checking */
> + if ( !this || !parent )
> + return;
> +
> + this->container = parent;
> + this->type = interiorNode;
> +}
> +
> +/* Inserts interior node into parent list */
> +void Node_addInteriorNode(Node *this, Node *interior)
> +{
> + /* some basic error checking */
> + if ( !this || !interior )
> + return;
> +
> + if ( this->interiorNodes == NULL )
> + {
> + this->interiorNodes = NodeList_new();
> + if ( this->interiorNodes == NULL )
> + return; /* malloc failed */
> + this->interiorNodes->node = interior;
> + }
> + else
> + NodeList_insertBack(this->interiorNodes, interior);
> +
> + Node_setParent(interior, this);
> + return;
> +}
> +
> +
> +/* adds an edge from "this" to "node. If an allocation error occurs
> + * this method returns false. If an edge already exists, the method
> + * will NOT add a duplicate edge, and will return true.
> + */
> +bool Node_addEdgeToNode(Node *this, Node *node)
> +{
> + EdgeList *end = NULL;
> + EdgeList *newEdge = NULL;
> +
> + if ( !this || !node )
> + return(false);
> +
> + /* Scream through the list and make sure edge doesn't already exist */
> + for ( end = this->edges; end != NULL; end = end->nextEdge )
> + if ( end->targetNode == node )
> + return true;
> +
> + /* Otherwise, we have a new edge. Insert it at the head of the list */
> + newEdge = EdgeList_new();
> + if ( !newEdge ) /* allocation error */
> + return false;
> + newEdge->targetNode = node;
> + newEdge->targetNodeId = node->id;
> + newEdge->nextEdge = this->edges; /* First time, this is NULL, terminates our list. */
> + this->edges = newEdge;
> + ++this->edgeCount;
> + return(true);
> +}
> +
> +
> +/* -------------------------------------------
> + * NodeList Method Definitions
> + *
> + */
> +
> +/* Constructor */
> +NodeList * NodeList_new()
> +{
> + NodeList *list = malloc(sizeof(NodeList));
> +
> + if ( !list )
> + return(NULL);
> +
> + list->node = NULL;
> + list->nextNode = NULL;
> +
> + return(list);
> +}
> +
> +/* Destructor - also frees the data allocated for nodes if freeMemory is
> + * true (calls their "destructor )
> + */
> +void NodeList_clear(NodeList *trash, bool deleteNodes)
> +{
> + /* Some basic error checking */
> + if ( !trash ) return;
> +
> + if ( trash->nextNode )
> + NodeList_clear(trash->nextNode, deleteNodes);
> +
> + if ( deleteNodes )
> + {
> + Node_delete(trash->node);
> + }
> + free(trash);
> +}
> +
> +/* insertFront modifies the list passed in such that the first element
> + * points to the new node. This is done by duplicating the first element
> + * into a new element, and then modifying the true first element to point
> + * to the node passed and and the created element (which references the
> + * rest of the list).
> + */
> +bool NodeList_insertFront(NodeList *this, Node *newFront)
> +{
> + /* Make a new element that holds the information that used to
> + * be at the front.
> + */
> + NodeList *oldFront = NodeList_new();
> +
> + /* Some basic error checking */
> + if ( !this || !newFront || !oldFront )
> + return(false);
> +
> + /* move the formerly front data to the new element */
> + oldFront->node = this->node;
> + oldFront->nextNode = this->nextNode; /* Now points to the remainder of the list (or NULL) */
> +
> + /* And change the head element to reference the new front node. */
> + this->node = newFront;
> + this->nextNode = oldFront;
> +
> + return(true);
> +}
> +
> +/* Create a new node list element, have it reference the node passed in
> + * and then put it in the back of the list. Returns true on success
> + */
> +bool NodeList_insertBack(NodeList *this, Node *newBack)
> +{
> + NodeList *end;
> + NodeList *newElement;
> +
> + /* Some basic error checking */
> + if ( !this || !newBack )
> + return(false);
> +
> + /* If the node portion of "this" is null,
> + * then we're starting with an empty list.
> + */
> +
> + if ( this->node == NULL )
> + {
> + this->node = newBack;
> + return(true); /* We're done! */
> + }
> +
> + /* Otherwise, we need to find the end of the list */
> + for ( end = this; end->nextNode != NULL; end = end->nextNode )
> + { /* No-op */ }
> +
> + newElement = NodeList_new();
> + if ( !newElement )
> + return(false);
> +
> + newElement->node = newBack;
> + end->nextNode = newElement; /* new nodelist element has a null next */
> +
> + return(true);
> +}
> +
> +
> +
> +
> +
> +/* -------------------------------------------
> + * Edge List Method Definitions
> + *
> + */
> +
> +/* Constructor */
> +EdgeList *EdgeList_new()
> +{
> + EdgeList *newNode = malloc( sizeof( struct EdgeListStruct ));
> + if ( newNode )
> + {
> + newNode->targetNodeId = -1; /* Potentially a bug. what if there's a node named -1? */
> + newNode->targetNode = NULL;
> + newNode->nextEdge = NULL;
> + }
> + return(newNode);
> +}
> +
> +/* Destructor */
> +void EdgeList_clear( EdgeList *this )
> +{
> + /* Some basic error checking */
> + if ( !this )
> + return;
> +
> + if ( this->nextEdge )
> + EdgeList_clear(this->nextEdge);
> +
> + free(this);
> +}
> +
> +/* Insertion Method
> + * It is important to realize that this inserts the edge as an Id, it does
> + * not find or initialize the node specified by that Id. That has to be
> + * done as a separate step later.
> + */
> +bool EdgeList_insertNodeId(EdgeList *this, int targetNodeId)
> +{
> + EdgeList *end;
> + EdgeList *newElement;
> +
> + /* some basic error checking */
> + if ( !this )
> + return(false);
> +
> + /* Check to see if this is the initial insertion into the
> + * Edge list
> + */
> + if ( this->targetNodeId == -1 )
> + {
> + this->targetNodeId = targetNodeId;
> + return(true);
> + }
> +
> + /* Otherwise we find the end of the list and make a new entry */
> + for ( end = this; end->nextEdge != NULL; end = end->nextEdge )
> + { /* No-op */ }
> +
> + newElement = EdgeList_new();
> + if ( !newElement )
> + return(false);
> +
> + newElement->targetNodeId = targetNodeId;
> + end->nextEdge = newElement; /* new edge list element has a null node and next */
> +
> + return(true);
> +}
> +
> +
> +
> +
> +
> +
> +
> +
> +
> +/* Search Algorithms */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/node.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/node.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/node.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/node.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,159 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * node.h
> + *
> + * Created on: Feb 1, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +#ifndef NODE_H_
> +#define NODE_H_
> +
> +
> +
> +
> +/* --------
> + * Nodes are the basic data structure within the graph. Nodes hold information
> + * regarding their identity (id, label, type, etc.) and information about their
> + * edges (list of edges, number of edges).
> + *
> + * Node.h/.c contains the data definitions for nodes and edges as well as con-
> + * tainers for nodes (NodeList, NodePtrVec) and edges (EdgeList)
> + */
> +
> +
> +
> +
> +typedef enum
> +{
> + exteriorNode, /* Default unless Node_setParent is called */
> + interiorNode,
> + entranceNode /* special interior node(s) that begin the interior graph */
> +} NodeType;
> +
> +
> +/* -------------------------------------------
> + * Node Definitions
> + *
> + */
> +
> +
> +
> +typedef struct NodeStruct Node;
> +typedef struct NodeListStruct NodeList;
> +typedef struct EdgeListStruct EdgeList;
> +
> +#include "bitfield.h"
> +#include "vectorUtils.h"
> +#include <stdbool.h>
> +
> +struct NodeStruct
> +{
> + int id; /* id value for the node - typically associated with an address of the basic block */
> + int nodeCount; /* a unique index for this node (0 .. whatever) */
> + char *label;
> + int labelIdx;
> + NodeType type;
> + Node *container; /* if this is an interior node, this points to the outer node containing this one */
> + NodeList *interiorNodes; /* All the nodes contained in this node's subgraph */
> + EdgeList *edges; /* Nodes that can be accessed from this node (includes entrance nodes) */
> +
> + int edgeCount; /* edges from this node to others (DOES NOT INLCUDE INTRANCE NODES) */
> + int entranceCount; /* number of entrance nodes (if any) */
> +};
> +
> +/* "methods" for nodes */
> +
> +Node *Node_new( int id, int nodeCount ); /* Constructor */
> +void Node_delete( Node *trash ); /* Destructor */
> +Node *Node_duplicate(Node *from, int newIndex); /* Duplicates node data, BUT NO EDGE INFORMATION */
> +void Node_setParent( Node *this, Node *parent ); /* Identifies the Upper-level node containing inner level node */
> +void Node_addInteriorNode( Node *this, Node *interior ); /* Inserts interior node into parent list */
> +bool Node_addEdgeToNode(Node *this, Node *node); /* Node* based insertion method */
> +
> +
> +/* -------------------------------------------
> + * Node List Definitions
> + *
> + */
> +
> +struct NodeListStruct
> +{
> + Node *node;
> + NodeList *nextNode;
> +};
> +
> +/* "methods" for NodeLists */
> +
> +NodeList *NodeList_new(); /* Constructor */
> +
> +/* Destructor - also frees the data allocated for nodes if freeMemory is
> + * true (calls their "destructor )
> + */
> +void NodeList_clear( NodeList *trash, bool deleteNodes );
> +
> +/* insertFront modifies the list passed in such that the first element
> + * points to the new node. This is done by duplicating the first element
> + * into a new element, and then modifying the true first element to point
> + * to the node passed and and the created element (which references the
> + * rest of the list).
> + */
> +bool NodeList_insertFront( NodeList *this, Node *newFront );
> +/* Create a new node list element, have it reference the node passed in
> + * and then put it in the back of the list. Returns true on success
> + */
> +bool NodeList_insertBack( NodeList *this, Node *newBack );
> +
> +/* -------------------------------------------
> + * Edge List Definitions
> + *
> + * Edges are processed a little differently than nodes. As soon as a
> + * node is identified, it is created. However, the edges may be
> + * identified prior to the creation of the node to which it references.
> + * Ergo, there's a two pass process - first identifying the edges,
> + * then subsequently setting the pointers to reference them.
> + *
> + * Rather than making a dual structure "Edge" and "EdgeList" pair,
> + * the author is combining the data into a single structure.
> + */
> +
> +struct EdgeListStruct
> +{
> + int targetNodeId;
> + Node *targetNode;
> + EdgeList *nextEdge;
> +};
> +
> +EdgeList *EdgeList_new(); /* Constructor */
> +void EdgeList_clear(EdgeList* this); /* Destructor */
> +bool EdgeList_insertNodeId(EdgeList *this, int targetNodeId); /* Id based insertion method */
> +
> +#endif /* NODE_H_ */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/parsing.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/parsing.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/parsing.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/parsing.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,678 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +
> +/*
> + * graph.c
> + *
> + * Created on: Jan 9, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +#include "parsing.h"
> +#include "graph.h"
> +#include "utils.h"
> +#include "systemCallMap.h"
> +#include "yaml.h"
> +
> +
> +#include <ctype.h>
> +
> +
> +/* buildEntranceList takes an array of integers, and builds a
> + * non-resolved edge list from the array. This is a special
> + * edge list, used only be outer nodes to identify entrance
> + * points into their subgraph. Only the edge data is passed in,
> + * this begins with the second entry (index 1) in the parsed
> + * data array. Likewise the size only counts edges.
> + *
> + * Initially, entrance transitions were handled as a separate
> + * list of edges. After further analysis, however, there is
> + * no operational difference between outer edges and entrance
> + * edges. Ergo, we are modifying this code to put the entrance
> + * edges into the edge list and deprecating the entrance list.
> + * The code is being left in for the time being as comments,
> + * since there are some contextual significances to interior
> + * nodes and entrance edges that may later be required. Otherwise
> + * we could go to a simple flat graph.
> + */
> +void buildEntranceList( Node *outerNode, IntVector *nodeData )
> +{
> + int i;
> + int entranceCount;
> +
> + /* some basic error checking */
> + if ( !outerNode || !nodeData ) return;
> +
> + entranceCount = nodeData->vector[1]; /* count is the first entry, (second of original data); */
> + if ( entranceCount == 0 )
> + return; /* Nothing to see here, folks */
> +
> + if ( entranceCount != nodeData->size-2 )
> + {
> + fprintf ( stderr, "Specified entrance edge length does not match data size for node: %d\n",
> + outerNode->id );
> + }
> +
> + /* Deprecated: outerNode->entranceNodes = EdgeList_new(); */
> + /* Deprecated: if ( outerNode->entranceNodes ) */
> + if ( !outerNode->edges )
> + outerNode->edges = EdgeList_new();
> + if ( outerNode->edges )
> + for ( i = 2; i < nodeData->size; ++i )
> + {
> + /* Deprecated EdgeList_insertBack( outerNode->entranceNodes, edgeData[i] ); */
> + EdgeList_insertNodeId( outerNode->edges, nodeData->vector[i] );
> + ++outerNode->entranceCount;
> + }
> +}
> +
> +
> +/* buildNodeFromData takes the integer array built by the above
> + * method, and creates a node from it. If that node has
> + * edge data, that is also built. The data is in an array,
> + * the size of which is also passed in.
> + */
> +Node *buildNodeFromData( IntVector *nodeData )
> +{
> + int i;
> + int edgeCount;
> +
> + /* some basic error checking */
> + if ( nodeData == NULL || nodeData->size == 0 )
> + return( NULL );
> +
> + Node *node = Node_new( nodeData->vector[0], -1 ); /* Calling method must set index. */
> + if ( !node )
> + return( NULL );
> +
> + /* Currently, the second element in is the edge count */
> + edgeCount = nodeData->vector[1];
> + if ( edgeCount != nodeData->size-2 )
> + {
> + fprintf ( stderr, "Specified edge length does not match data size for node: %d\n",
> + nodeData->vector[0] );
> + }
> +
> + if ( edgeCount > 0 )
> + {
> + node->edges = EdgeList_new();
> + if ( node->edges )
> + for ( i = 2; i < nodeData->size; ++i )
> + {
> + EdgeList_insertNodeId ( node->edges, nodeData->vector[i] );
> + ++node->edgeCount;
> + }
> + }
> +
> + return( node );
> +}
> +
> +
> +/* resolveNodeEdges is the second pass through the graph data
> + * structures. The first pass defines the nodes, and puts the edge
> + * ids in place. The second pass finds the nodes corresponding to
> + * the edge id, and sets the edge pointer to that node. Edges for
> + * outer nodes will only reference other outer nodes. Interior
> + * nodes may have edges to outer nodes or other interior nodes of
> + * their containing node. If an edge references an undefined node
> + * or if an edge goes into the interior of another outer node,
> + * the user will be notified.
> + *
> + * Note: The section that resolves entrance edges has been commented
> + * out because entrance edges are now processed as part of the edge
> + * list.
> + */
> +void resolveNodeEdges( Graph *graph, Node* sourceNode, bool outerNode )
> +{
> + EdgeList *edges;
> + Node *node;
> + bool okSoFar;
> +
> + for ( edges = sourceNode->edges; edges != NULL; edges = edges->nextEdge )
> + {
> + if ( outerNode )
> + {
> + /* We only check for edges to other outer nodes*/
> + node = Graph_findNode( graph, edges->targetNodeId, true ); /* true-> check outer and interior nodes */
> + if ( node )
> + {
> + okSoFar = true;
> + /* Since entrance edges are now part of our edge list, we have to make sure
> + * the link here is appropriate.
> + */
> + if ( node->type == entranceNode || node->type == interiorNode )
> + {
> + if ( node->container != sourceNode )
> + {
> + fprintf( stderr,
> + "resolveNodeEdges: Outer node %d edge to non-contained node: %d\n",
> + sourceNode->id, edges->targetNodeId );
> + fprintf(stderr, "\t%d is type: %s (%d)\n", node->id, node->type == interiorNode ? "interior" : "entrance", (int)node->type);
> + okSoFar = false;
> + }
> + }
> + if ( okSoFar )
> + edges->targetNode = node;
> + }
> + else
> + fprintf( stderr,
> + "resolveNodeEdges: Outer node %d has edge reference to undefined node: %d\n",
> + sourceNode->id, edges->targetNodeId );
> + }
> + else
> + {
> + /* Interior node - the edge can be to an outer node... */
> + node = Graph_findNode( graph, edges->targetNodeId, false ); /* false-> only check outer nodes */
> + if ( node )
> + edges->targetNode = node;
> + else
> + {
> + /* ... or nodes interior to the container of this node */
> + node = Graph_findContainedNode( sourceNode->container, edges->targetNodeId );
> + if ( node )
> + edges->targetNode = node;
> + else
> + {
> + /* we have an undefined node */
> + fprintf( stderr,
> + "resolveNodeEdges: Interior node %d has edge reference to undefined node: %d\n",
> + sourceNode->id, edges->targetNodeId );
> + }
> + }
> + }
> + }
> +
> +}
> +
> +
> +/* pruneLine takes the \r\n off the end of the label. This is an artifact of
> + * the windows file system, not something that was intended to be a part
> + * of the actual label string.
> + */
> +static void pruneLine( char *label )
> +{
> + int i = 0;
> +
> + for ( ; label[i] != '\0'; ++i )
> + {
> + if ( label[i] == '\r' )
> + {
> + label[i] = '\0';
> + return;
> + }
> + if ( label[i] == '\n' )
> + {
> + label[i] = '\0';
> + return;
> + }
> + }
> +}
> +
> +/* parseFile goes through the specified file to build the graph. It
> + * returns a pointer to the graph instance created by the data. Otherwise
> + * it returns NULL if the file is not parsable.
> + */
> +
> +Graph *parseFile( char *fileName )
> +{
> + FILE *inFile;
> + IntVector *fileData = NULL;
> + CharVector *fileString = NULL;
> + Node *newNode = NULL;
> + Node *outerNode = NULL;
> + Node *findNode = NULL;
> + int temp, count;
> + NodeList *outerNodeList = NULL;
> + NodeList *innerNodeList = NULL;
> + Graph *newGraph = NULL;
> + int funcCount = 50; /* used as a default initial size for the system call table */
> + int blockCount = 0;
> + bool systemCallSection = false;
> + int i;
> +
> + /* A little error checking */
> + if ( !fileName )
> + return( NULL );
> +
> +#ifdef PRINT_FILE
> + printf ( "Parsing file %s...\n", fileName );
> +#endif
> +
> + inFile = fopen( fileName, "r" );
> + if ( !inFile )
> + {
> + printf( "Could not open data file: %s (parsing.c:parseFile)\n", fileName );
> + return( NULL );
> + }
> + /* else
> + printf( "Opened %s\n\n", fileName ); */
> +
> + newGraph = Graph_new();
> + if ( !newGraph )
> + return( NULL );
> +
> + newGraph->fileName = strdup( fileName );
> + fileString = CharVector_new( 1024 ); /* allocate our data parsing storage - 1024 is a semi-arbitrary power of 2 */
> +
> + i = 0;
> +
> + /* The first two lines define the number of Functions and basic blocks. */
> + CharVector_getLineFromFile( fileString, inFile );
> + if ( !feof( inFile ) && ( strncmp ( "Functions:", fileString->string, 10 ) == 0 ) )
> + {
> + funcCount = atoi ( fileString->string+10 );
> + printf ( "\t%d functions specified\n", funcCount );
> + YAMLWriteInt("Functions", funcCount);
> + }
> + else
> + {
> + fprintf ( stderr, "Malformed file, Function count not specified in first line\n" );
> + return( NULL );
> + }
> +
> + CharVector_getLineFromFile( fileString, inFile );
> + if ( !feof( inFile ) && ( strncmp ( "Basic blocks:", fileString->string, 13 ) == 0 ) )
> + {
> + blockCount = atoi ( fileString->string+13 );
> + printf ( "\t%d basic blocks specified\n", blockCount );
> + YAMLWriteInt("Basic Blocks", blockCount);
> + }
> + else
> + {
> + fprintf ( stderr, "Malformed file, Function count not specified in first line\n" );
> + return( NULL );
> + }
> +
> + // printf ("Done with header\n");
> +
> + fileData = IntVector_new( 8 ); /* allocate our data parsing storage - 8 is a semi-arbitrary power of 2 */
> +
> + /*
> + * The first section defines the outer nodes. Scan through it to identify the
> + * nodes and to do the first pass of edge definition.
> + */
> + while ( !feof( inFile ) ) /* clumsy use of feof */
> + {
> + CharVector_getLineFromFile( fileString, inFile );
> +
> + if ( feof( inFile ) ) /* that read line was the last line */
> + break;
> +
> + if ( strncmp( "----------", fileString->string, 10 ) == 0 ) /* we have a section break */
> + break;
> +
> + count = IntVector_createFromString ( fileData, fileString->string );
> +
> + if ( count > 0 )
> + {
> + // printf("processing node %d\n", fileData->vector[0] );
> + newNode = buildNodeFromData( fileData );
> + if ( newNode )
> + {
> + Graph_addOuterNode( newGraph, newNode );
> + newNode->nodeCount = newGraph->totalNodes;
> + newGraph->totalNodes += 1;
> + }
> + }
> + IntVector_clear( fileData );
> + }
> +
> + //printf ("Done with outer nodes\n");
> +
> + /* Parse the subsequent sections to get the inner nodes */
> + while ( !feof( inFile ) )
> + {
> + /* The first line will identify the outer node for which the inner nodes are defined. */
> + CharVector_getLineFromFile( fileString, inFile );
> +
> + if ( feof( inFile ) ) /* that fgets was the last line */
> + break;
> +
> + systemCallSection = strncmp( "SYSTEM CALLS", fileString->string, 12) == 0;
> + if ( systemCallSection )
> + break;
> +
> + if ( isdigit( (int)fileString->string[0] ) )
> + temp = atoi( fileString->string ); /* Note: No format error check here... */
> + else
> + temp = -1; /* Man, I hope -1 is never a node id value... */
> + outerNode = Graph_findNode( newGraph, temp, false ); /* false -> only check outer nodes */
> +
> + if ( outerNode == NULL )
> + {
> + fprintf (stderr, "Error in parseFile: Node %d undefined as an outer node\n", temp );
> + break; /* No error recovery - but continue with the program */
> + }
> +
> + /* Now, subsequent lines (up to the section break) identify interior nodes; */
> + while ( !feof( inFile ) )
> + {
> + CharVector_getLineFromFile( fileString, inFile );
> +
> + if ( strncmp( "----------", fileString->string, 10 ) == 0 ) /* we have a section break */
> + break;
> +
> + count = IntVector_createFromString( fileData, fileString->string );
> + if ( count > 0 )
> + {
> + /*
> + * special case: If the node specified is the outerNode, the edge nodes specified
> + * here are the entrance nodes
> + */
> + if ( fileData->vector[0] == outerNode->id )
> + buildEntranceList( outerNode, fileData );
> + else
> + {
> + newNode = buildNodeFromData( fileData );
> + if ( newNode )
> + {
> + Node_addInteriorNode( outerNode, newNode );
> + newNode->nodeCount = newGraph->totalNodes;
> + newGraph->totalNodes += 1;
> + }
> + }
> + }
> + IntVector_clear( fileData );
> + }
> + }
> +
> + //printf ( "Done with interior nodes. On to System Calls\n" );
> +
> + /* All the node mappings have been done, now we build a map of system calls to the
> + * node keys.
> + */
> + newGraph->systemCallMap = SystemCallMap_new( funcCount );
> + if ( newGraph->systemCallMap == NULL )
> + {
> + IntVector_delete( fileData );
> + return( NULL ); /* if we can't build the system call map, we're done. */
> + }
> +
> + if ( systemCallSection )
> + {
> + while ( !feof( inFile ) )
> + {
> + CharVector_getLineFromFile( fileString, inFile );
> +
> + if ( feof( inFile ) ) /* that fgets was the last line */
> + break;
> +
> + if ( isdigit( (int)fileString->string[0] ) )
> + temp = atoi ( fileString->string ); /* get the key */
> + else
> + temp = -1;
> + if ( temp >= 0 ) /* valid key */
> + {
> + /* get the system call name. First, get past the ' ' */
> + for ( i = 0; fileString->string[i] != '\0' && fileString->string[i] != ' '; ++i ) {}
> + if ( fileString->string[i] == ' ' )
> + {
> + ++i;
> + findNode = Graph_findNode( newGraph, temp, true );
> + pruneLine( fileString->string+i );
> + SystemCallMap_insert( newGraph->systemCallMap, fileString->string+i, findNode );
> + }
> + }
> + }
> + } /* ....aaaand we're done parsing the input file. */
> +
> + CharVector_delete(fileString);
> +
> + //printf ( "Done parsing, resolve edges\n" );
> + /* Now that we have all the nodes, resolve all edge definitions */
> + for ( outerNodeList = newGraph->outerNodes;
> + outerNodeList != NULL;
> + outerNodeList = outerNodeList->nextNode )
> + {
> + resolveNodeEdges( newGraph, outerNodeList->node, true ); /* true -> outer node */
> + for ( innerNodeList = outerNodeList->node->interiorNodes;
> + innerNodeList != NULL;
> + innerNodeList = innerNodeList->nextNode )
> + {
> + resolveNodeEdges( newGraph, innerNodeList->node, false ); /* false -> interior node */
> + }
> + }
> +
> +
> + /* How many nodes did we count (outer + interior)?
> + printf ( "\tTotal nodes parsed: %d\n", newGraph->totalNodes ); */
> +
> + /* Debug --* /
> + graphPrettyPrint( newGraph );
> + systemCallMapPrettyPrint( newGraph->systemCallMap );
> + / *-- End Debug */
> +
> + printf( "\t%d total System Call Map elements\n", newGraph->systemCallMap->contentSize );
> + YAMLWriteInt( "System Calls", newGraph->systemCallMap->contentSize );
> +
> + /* Build the search diagram */
> + newGraph->searchDiagram = SearchDiagram_build( newGraph->outerNodes, newGraph->totalNodes );
> +
> + printf ( "\t...parsing complete.\n" );
> + return( newGraph );
> +}
> +
> +
> +
> +
> +/* parseSignature takes a space delimited string and turns it
> + * into a "signature" - a packed array of c-string pointers with
> + * a NULL pointer to signify completion.
> + */
> +char **parseSignature( char *data )
> +{
> + int i = 0;
> + int labelCount = 0; // Used to be 1. The algorithm depends on a terminating space, so it counts based on the END of the label.
> + int copiedLabels = 0;
> + char **labels = NULL;
> + char *debug = NULL;
> +
> + /* A little error checking */
> + if ( !data )
> + return NULL;
> +
> + /* First, scream through the array counting labels */
> + for( i = 0; data[i] != '\0'; ++i )
> + {
> + if ( data[i] == ' ' )
> + {
> + ++labelCount;
> + data[i] = '\0';
> + }
> + }
> +
> + /* Now, allocate the array and make copies */
> + labels = (char **)malloc( (labelCount+1) * sizeof(char*) );
> + i = 0;
> + if ( labels )
> + {
> + for ( copiedLabels = 0; copiedLabels < labelCount; ++copiedLabels )
> + {
> + debug = &data[i];
> + labels[copiedLabels] = strdup( &data[i] );
> + while ( data[i] != '\0' )
> + {
> + /* advance to the end of this label */
> + ++i;
> + }
> + ++i; /* advance beyond the \0 to the start of the next label */
> + }
> + labels[labelCount] = NULL; /* terminate the array */
> + }
> +
> + /* Debug print out * /
> + printf ( "\nSignature: ");
> + for ( i = 0; labels[i] != NULL; ++i )
> + {
> + printf ( "%s ", labels[i] );
> + }
> + /* end Debug */
> +
> + return labels;
> +}
> +
> +
> +
> +
> +
> +/* parseConfigFile reads the data file names and desired search
> + * signatures from the config file. It returns a packed array
> + * of Graph pointers populated corresponding to the data files.
> + * Also, it returns a packed array of pointers to signatures.
> + * (Signatures are themselves packed arrays to C-Strings.) These
> + * packed arrays are terminated with a NULL pointer. They
> + * are returned in the "graphs" and "signatures" parameters
> + * which should be references to the desired pointers. See main.c.
> + */
> +bool parseConfigFile( char *configFileName, Configuration *config )
> +{
> + char data[1000];
> + FILE *configFile = NULL;
> + int fileNum = -1;
> + int sigNum = -1;
> + int i = 0;
> +
> + configFile = fopen( configFileName, "r" );
> + if ( !configFile )
> + {
> + printf( "Could not open %s\n", configFileName );
> + return( NULL );
> + }
> + else
> + printf( "Opened %s\n\n", configFileName );
> +
> + fgets ( data, 1000, configFile );
> + if ( feof( configFile ) || ( strncmp ( "Pathfinder Configuration", data, 24 ) != 0 ) )
> + {
> + printf( "Error in config file: doesn't start with \"Pathfinder Configuration\"\n" );
> + return false;
> + }
> +
> + fgets ( data, 1000, configFile );
> + if ( feof( configFile ) || ( strncmp ( "files", data, 5 ) != 0 ) )
> + {
> + printf( "Error in config file: second line is not file count\n" );
> + return false;
> + }
> + fileNum = atoi( &data[6] );
> + if ( fileNum == 0 )
> + {
> + printf( "No files to parse, exiting.\n" );
> + return false;
> + }
> +
> + fgets ( data, 1000, configFile );
> + if ( feof( configFile ) || ( strncmp ( "signatures", data, 10 ) != 0 ) )
> + {
> + printf( "Error in config file: third line is not signature count\n" );
> + return false;
> + }
> + sigNum = atoi( &data[11] );
> + if ( sigNum == 0 )
> + {
> + printf( "No signatures to search, exiting.\n" );
> + return false;
> + }
> +
> + fgets ( data, 1000, configFile );
> + if ( feof( configFile ) || ( strncmp ( "search type", data, 11 ) != 0 ) )
> + {
> + printf( "Error in config file: third line is not signature count\n" );
> + return false;
> + }
> + if ( strncmp( &data[12], "tree", 4 ) == 0 )
> + config->searchOptions->searchType = treeSearch;
> + else
> + config->searchOptions->searchType = diagramSearch;
> +
> + config->graphs = (Graph **)malloc( (fileNum+1) * sizeof( Graph* ) );
> + if ( !config->graphs )
> + {
> + printf ( "Could not allocate graph storage. Exiting\n" );
> + return false;
> + }
> +
> + for ( i = 0; i < fileNum; ++i )
> + {
> + fgets ( data, 1000, configFile );
> + if ( feof( configFile ) || ( strncmp ( "file ", data, 5 ) != 0 ) ) /* note the ' ' */
> + {
> + printf( "Error in config file: mismatch of file count\n" );
> + return false;
> + }
> +
> + /* strip the \n from the file name. */
> + pruneLine( &data[5] );
> + config->graphs[i] = parseFile( &data[5] );
> + if ( !config->graphs[i] )
> + {
> + /* the file did not parse */
> + printf( "Error parsing %s", &data[5] );
> + free( config->graphs );
> + return false;
> + }
> + }
> + config->graphs[fileNum] = NULL;
> +
> + config->signatures = (Signature *)malloc( (sigNum+1) * sizeof( Signature ) );
> + if ( !config->signatures )
> + {
> + printf ( "Could not allocate signature storage. Exiting\n" );
> + return false;
> + }
> +
> + for ( i = 0; i < sigNum; ++i )
> + {
> + fgets ( data, 1000, configFile );
> + if ( feof( configFile ) || ( strncmp ( "signature ", data, 10 ) != 0 ) ) /* note the ' ' */
> + {
> + printf( "Error in config file: mismatch of signature count\n" );
> + return false;
> + }
> +
> + /* strip the \n from the file name. */
> + pruneLine( &data[10] );
> + config->signatures[i] = parseSignature( &data[10] );
> + if ( !config->signatures[i] )
> + {
> + /* the file did not parse */
> + printf( "Error parsing %s", &data[10] );
> + free( config->graphs ); /* Insufficient! Should call a destructor on each */
> + free( config->signatures );
> + return false;
> + }
> + }
> + config->signatures[sigNum] = NULL;
> +
> + return true;
> +}
> +
> +
> +
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/parsing.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/parsing.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/parsing.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/parsing.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,114 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +
> +/*
> + * parsing.h
> + *
> + * Created on: Jan 9, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +/* --------
> + * This pair of files contains the utility data types and methods for
> + * parsing data files into graphs. It also defines a "configuration"
> + * for a given run of PathFinder. The configuration holds all the info
> + * corresponding to the run - graphs, signatures, search types.
> + */
> +
> +#ifndef PARSING_H_
> +#define PARSING_H_
> +
> +#include "vectorUtils.h"
> +
> +/* Since we're parsing into graphs, we need to know what they are... */
> +#include "graph.h"
> +#include "configuration.h"
> +
> +
> +
> +/* buildEntranceList takes an array of integers, and builds a
> + * non-resolved edge list from the array. This is a special
> + * edge list, used only be outer nodes to identify entrance
> + * points into their subgraph.
> + */
> +void buildEntranceList( Node *outerNode, IntVector *nodeData );
> +
> +
> +/* buildNodeFromData takes the integer array built by the above
> + * method, and creates a node from it. If that node has
> + * edge data, that is also built. The data is in an array,
> + * the size of which is also passed in.
> + */
> +Node *buildNodeFromData( IntVector *nodeData );
> +
> +
> +/* resolveNodeEdges is the second pass through the graph data
> + * structures. The first pass defines the nodes, and puts the edge
> + * ids in place. The second pass finds the nodes corresponding to
> + * the edge id, and sets the edge pointer to that node. Edges for
> + * outer nodes will only reference other outer nodes. Interior
> + * nodes may have edges to outer nodes or other interior nodes of
> + * their containing node. If an edge references an undefined node
> + * or if an edge goes into the interior of another outer node,
> + * the user will be notified.
> + */
> +void resolveNodeEdges( Graph *graph, Node *sourceNode, bool outerNode );
> +
> +
> +
> +/* parseFile goes through the specified file to build the graph. It
> + * returns true if everything goes as planned. Any errors will cause
> + * false to be returned. The built graph can be accessed via
> + * Graph_the().
> + */
> +
> +Graph *parseFile( char *fileName );
> +
> +/* parseSignature takes a space delimited string and turns it
> + * into a "signature" - a packed array of c-string pointers with
> + * a NULL pointer to signify completion. As with our edge parser
> + * the code depends on a space character to terminate the line.
> + */
> +char **parseSignature( char *data );
> +
> +/* parseConfigFile reads the data file names and desired search
> + * signatures from the config file. It returns a packed array
> + * of Graph pointers populated corresponding to the data files.
> + * Also, it returns a packed array of pointers to signatures.
> + * (Signatures are themselves packed arrays to C-Strings.) These
> + * packed arrays are terminated with a NULL pointer. They
> + * are returned in the "graphs" and "signatures" parameters
> + * which should be references to the desired pointers. See main.c.
> + */
> +bool parseConfigFile( char *configFileName, Configuration *config );
> +
> +
> +
> +#endif /* PARSING_H_ */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchAlgorithms.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchAlgorithms.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchAlgorithms.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchAlgorithms.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,667 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> + /*
> + * searchAlgorithms.c
> + *
> + * Created on: Jun 18, 2013
> + * Author: jbrigdo
> + */
> +
> +#include <stdbool.h>
> +#include <stdio.h>
> +#include <stdlib.h>
> +#include <string.h>
> +#include <time.h>
> +#include <math.h>
> +
> +#ifdef USE_OMP
> +#include <omp.h>
> +#endif
> +
> +#include "searchAlgorithms.h"
> +#include "vectorUtils.h"
> +#include "utils.h"
> +#include "graphGen.h"
> +#include "statistics.h"
> +
> +
> +extern double currentTime();
> +
> +static Stats *globalStats = NULL;
> +
> +
> +
> +void doMultiSearches(Configuration *config)
> +{
> + NodePtrVec *result;
> + bool success;
> + Graph *graph;
> + Signature signature;
> + int i;
> + int j;
> + char *debug;
> + double tick, tock;
> + int hours;
> + int min;
> + double sec;
> +
> + tick = currentTime();
> + result = NodePtrVec_new(64); /* 64 is an arbitrary size */
> +
> + for ( i = 0; config->signatures[i] != NULL; ++i )
> + {
> + signature = config->signatures[i];
> + /* Debug --* /
> + printf ("\n\nSignature (");
> + for ( k = 0; signature[k] != NULL; ++k )
> + {
> + debug = signature[k];
> + printf("%s", signature[k]);
> + if ( signature[k+1] != NULL )
> + printf(" ");
> + else
> + printf("):\n");
> + }
> + / *-- End Debug */
> + // printf("Signature %d:\n", i);
> + for ( j = 0; config->graphs[j] != NULL; ++j )
> + {
> + graph = config->graphs[j];
> + result->contentSize = 0; /* clear last search's result */
> + // printf("\t checking file %s... ", graph->fileName);
> + fflush(stdout);
> + success = findLabelPath(graph, signature, result, config->searchOptions->searchType);
> + if ( success )
> + {}// printf("Found!\n");
> + else
> + {}// printf("Not found. Bummer.\n");
> + }
> + }
> +
> + tock = currentTime();
> + sec = tock-tick;
> + hours = (int)sec/3600;
> + sec = fmod( sec, 3600.0 );
> + min = (int)sec/60;
> + sec = fmod(sec, 60.0);
> + printf ("\n\nOverall Search Time: %02d:02%d:%05.2f\n", hours, min, sec);
> +
> +}
> +
> +/* findNextLabel is a recursive method that determines if a path exists between a
> + * specific node and the label that is at the start of the label array argument. The
> + * label array is an array of char pointers that is terminated with a NULL pointer. The
> + * first pointer is the "current" label.
> + *
> + * The node's edge nodes are checked against the current label. If none of them match, then
> + * this method recurses with each edge node and the current label.
> + *
> + * If an edge matches, then we are beginning a search for the next "leg" of the labels.
> + * We recurse with that specific edge and the "next" label. That is the [1] element of
> + * the label array. This starts the search along the next leg - at this point we have
> + * to start a new "result" vector, because we check that vector for loops. It MAY be the
> + * case that the next path segment passes through nodes already traversed in a previous
> + * leg. A new "result" vector will solve that.
> + *
> + * If the next element in the labels list is NULL, the matching edge signifies the end of
> + * our search! VICTORY!
> + *
> + * If we reach the last edge with out a match (directly or recursively) we return a false
> + * list.
> + */
> +
> +bool findNextLabel( Node *node, Signature labels, NodePtrVec *result, Bitfield *visited ) /* NodePtrVec *visited ) */
> +{
> + EdgeList *edge;
> + bool success = false;
> + NodePtrVec *nextLegResult = NULL;
> + /* NodePtrVec *nextLegVisited = NULL; */
> + Bitfield *nextLegVisited = NULL;
> +
> +
> + /* A little basic error checking */
> + if ( !node || !labels || !result|| !visited )
> + {
> + return( false );
> + }
> +
> + /* If this node is already in the vector, we have found a loop. return false. */
> +
> + if ( Bitfield_nodeVisited( visited, node ) )
> + return( false );
> +
> + /* put this node on the result vector to show that we've been here */
> + NodePtrVec_push( result, node );
> +
> + /* Check this node's edges to see if there's a match */
> + /* Note: We have a NodePtrVec holding the set of nodes with this label. It
> + * may be more optimal to see if a given edge node is in that set
> + * rather than doing a bunch of inefficient strcmp calls. Another approach
> + * would be to have unique hash values for each label, and thereby be
> + * able to compare those. However for the initial version of this code,
> + * keeping things simple and straightforward, we're doing the string
> + * compare.
> + */
> +
> + for ( edge = node->edges; edge != NULL; edge = edge->nextEdge )
> + {
> +
> + // string based:
> + if ( edge->targetNode->label && strcmp( edge->targetNode->label, labels[0] ) == 0 )
> + // index based: if ( edge->targetNode->labelIdx == labelIdxs[0] )
> + {
> + if ( labels[1] != NULL ) /* more steps in the signature */
> + {
> + nextLegResult = NodePtrVec_new( 50 ); /* arbitrary size, malloc success checked in recursion */
> + nextLegVisited = Bitfield_new(visited->bitsNeeded);
> +
> + success = findNextLabel( edge->targetNode, &labels[1], nextLegResult, nextLegVisited );
> + /* NodePtrVec_delete( nextLegVisited ); */
> + Bitfield_delete( nextLegVisited );
> + if ( success )
> + {
> + NodePtrVec_appendVectors( result, nextLegResult, true );
> + NodePtrVec_delete( nextLegResult );
> + return( true );
> + }
> +
> + }
> + else /* We have exhausted the signature - ultimate victory! */
> + {
> + /* Register this edge node as being the final node */
> + NodePtrVec_push( result, edge->targetNode );
> + return( true );
> + }
> + }
> + }
> +
> +
> + /* IF we made it here, we need to continue through the tree, seeing if any of our
> + * edge nodes have a connection to a labeled node.
> + */
> + for ( edge = node->edges; edge != NULL; edge = edge->nextEdge )
> + {
> + success = findNextLabel( edge->targetNode, labels, result, visited );
> + if ( success )
> + return( true ); /* this edge has a path to the ultimate signature path */
> + }
> +
> +
> + /* and, if we make it here, we have failed. */
> + NodePtrVec_pop( result ); /* take current node off the result vector */
> + return false;
> +}
> +
> +
> +
> +/* A method to custom-store our results */
> +static void logStats(NodePtrVec *result)
> +{
> + if ( !result ) return;
> + if ( !globalStats )
> + globalStats = Stats_new();
> + Stats_logPath(globalStats, result);
> +}
> +
> +static void printStats()
> +{
> + int i;
> +
> + if ( globalStats )
> + {
> + Stats_calculate(globalStats);
> +
> + printf ( "\nThis graph has %f average nodes between labels.\nStandard deviation: %f, total paths: %d\n\n",
> + globalStats->averageLength, globalStats->standardDeviation, globalStats->pathLengths->size );
> + printf ("\tShortest Path: %d, Longest Path: %d\n", globalStats->minLength, globalStats->maxLength);
> + for ( i = globalStats->minLength; i <= globalStats->maxLength; ++i )
> + {
> + if ( globalStats->histogram[i] != 0 )
> + printf ("\tlength %d appeared %d times\n", i, globalStats->histogram[i] );
> + }
> +
> + }
> +}
> +
> +
> +/* A method to custom-store our results */
> +
> +/* At some point, we will want to use the FullPath argument and pass it along to
> + * buildGraphFromPaths. Until then, however, we're only going to build the most
> + * minimal graph possible.
> + */
> +static void logResult(NodeVecVec *storage, NodePtrVec *result, SearchOptions *options)
> +{
> + NodePtrVec *tips = NodePtrVec_new(2);
> + if ( !storage || !result || !tips ) return;
> +
> + /* We log the stats here, because the storage method below may not hold
> + * the entire path.
> + */
> + if ( !options->multiThreaded && options->doStatistics ) /* statistics are not thread-safe yet */
> + logStats(result);
> +
> + /* Ultimately we may want to log more than the ends... */
> + /* Future: if ( options->buildType == endNodesOnly ) { */
> + NodePtrVec_push(tips, result->vector[0]);
> + NodePtrVec_push(tips, result->vector[result->contentSize-1]);
> + if ( !NodeVecVec_insert(storage, tips) ) /* makes a copy of tips, so we need to... */
> + {
> + printf("CrashAndBURN!!!\n\n");
> + fflush(stdout);
> + }
> + NodePtrVec_delete(tips); /* ... free the mallocs! */
> +}
> +
> +
> +
> +/* findAndRecordAllPaths is almost exactly like findNextLabel. It differs only in that it
> + * 1) doesn't stop with the first discovery of the specified path and 2) records the discovered
> + * path. To do this, it doesn't create a new result vector for
> + */
> +
> +void findAndRecordAllPaths( Node *node, Signature labels, int *labelIdxs,
> + NodePtrVec *result, Bitfield *visited, NodeVecVec *storage,
> + SearchOptions *options )
> +{
> + EdgeList *edge;
> + /* NodePtrVec *nextLegVisited = NULL; */
> + Bitfield *nextLegVisited = NULL;
> +
> +
> + /* A little basic error checking */
> + if ( !node || !labels || !labelIdxs || !result|| !visited )
> + {
> + return;
> + }
> +
> + /* If this node is already in the vector, we have found a loop. return false. */
> +/*
> + if ( NodePtrVec_findReverse( visited, node ) )
> + return( false );
> + else
> + NodePtrVec_push( visited, node );
> +*/
> + if ( Bitfield_nodeVisited( visited, node ) )
> + return;
> +
> + /* put this node on the result vector to show that we've been here */
> + NodePtrVec_push( result, node );
> +
> + /* Check this node's edges to see if there's a match */
> + /* Note: We have a NodePtrVec holding the set of nodes with this label. It
> + * may be more optimal to see if a given edge node is in that set
> + * rather than doing a bunch of inefficient strcmp calls. Another approach
> + * would be to have unique hash values for each label, and thereby be
> + * able to compare those. However for the initial version of this code,
> + * keeping things simple and straightforward, we're doing the string
> + * compare.
> + */
> +
> + for ( edge = node->edges; edge != NULL; edge = edge->nextEdge )
> + {
> +
> + // string based:
> + if ( edge->targetNode->label && strcmp( edge->targetNode->label, labels[0] ) == 0 )
> + // index based: if ( edge->targetNode->labelIdx == labelIdxs[0] )
> + {
> + // strcmp based:
> + if ( labels[1] != NULL ) /* more steps in the signature */
> + // index based: if ( labelIdxs[1] != -1 ) /* more steps in the signature */
> + {
> + nextLegVisited = Bitfield_new(visited->bitsNeeded);
> + findAndRecordAllPaths(edge->targetNode, &labels[1], &labelIdxs[1], result,
> + nextLegVisited, storage, options );
> + Bitfield_delete(nextLegVisited);
> + }
> + else /* We have exhausted the signature - ultimate victory! */
> + {
> + /* Register this edge node as being the final node */
> + // printf ("\tFound!\n");
> + NodePtrVec_push(result, edge->targetNode);
> + Bitfield_nodeVisited(visited, edge->targetNode);/* Mark it as visited */
> + logResult(storage, result, options); // <<<--- here's where I record it
> + NodePtrVec_pop(result);
> + }
> + }
> + }
> +
> +
> + /* IF we made it here, we need to continue through the tree, seeing if any of our
> + * edge nodes have a connection to a labeled node.
> + */
> + for ( edge = node->edges; edge != NULL; edge = edge->nextEdge )
> + {
> + findAndRecordAllPaths(edge->targetNode, labels, labelIdxs, result, visited, storage, options);
> + }
> +
> + NodePtrVec_pop( result ); /* take current node off the result vector */
> + return;
> +}
> +
> +
> +
> +/* findLabelPath takes an array of labels, determines if there are nodes associated
> + * with the labels (each label search will return a NodePtrVec*), and determine if
> + * paths exist passing through the set of labels. This returns the first FOUND
> + * path, not the optimal one. We could do that in a future iteration of the code
> + * by keeping track of all paths found, and going with the shortest.
> + *
> + * The labels passed in is an array of char pointers. The array is null terminated -
> + * i.e. the last valid entry in the array is followed by a pointer with NULL in it.
> + */
> +bool findLabelPath( Graph *graph, Signature labels, NodePtrVec *result, SearchType searchType )
> +{
> + NodePtrVec *startNodes = NULL; /* set of nodes with the first label - potential path start nodes */
> + int i;
> + bool found = false; /* stopping as soon as we can find a path to a final node */
> + /* NodePtrVec *visited = NodePtrVec_new( 50 ); /-* arbitrary size *-/ */
> + Bitfield *visited = Bitfield_new(graph->totalNodes);
> +
> +
> + /* some basic error checking */
> + if ( !graph || !labels || !labels[0] || !labels[1] || !result || !visited )
> + return( false );
> +
> + /* Un-comment to short-circuit searches for non-represented signatures. -->* /
> + if ( !SystemCallMap_signatureRepresented( graph->systemCallMap, labels ) )
> + {
> + //printf( "%s %s invalid signature labels for graph.\n", labels[0], labels[1] );
> + return( false );
> + }
> + / *<-- end of short-circuit region */
> +
> + startNodes = SystemCallMap_findLabeledNodes( graph->systemCallMap, labels[0] );
> +
> + if ( !startNodes )
> + return( false );
> +
> + /* So, if we've made it this far, we have a valid start label. Now, we need to
> + * iterate through the start nodes and see if they can get to the next label...
> + */
> +
> + for ( i = 0; i < startNodes->contentSize && !found; ++i )
> + {
> + if ( searchType == diagramSearch )
> + {
> + SearchDiagram *element = SearchDiagram_findNode( graph->searchDiagram, startNodes->vector[i] );
> + if ( element )
> + found = SearchDiagram_findSignatureAlongEdges( element->node, element->edgeReferenceArray,
> + &labels[1], result, visited );
> + }
> + else
> + found = findNextLabel( startNodes->vector[i], &labels[1], result, visited );
> + Bitfield_clear( visited );
> +
> + if ( !found && result->contentSize != 0 ) /* If it's not found the result SHOULD be empty, however... */
> + result->contentSize = 0; /* effectively clear the result NodePtrVec */
> + }
> +
> +
> + /* NodePtrVec_delete( visited ); */
> + Bitfield_delete( visited );
> + return( found );
> +}
> +
> +
> +/* findAllPossibleLegs does an exhaustive search through each possible label
> + * pairing to determine which legs are possible. This is a brute-force nxn
> + * approach that builds a signature holding only the second label and then
> + * searches for that signature from the nodes representing the first label.
> + * For the time being, it simply prints out the legs that are possible in
> + * this graph.
> + */
> +int findAllPossibleLegs( Graph *graph, SearchType searchType )
> +{
> + int i, j;
> + int found = 0;
> + int searches = 0;
> + double tick, tock;
> + int hours, min;
> + double sec;
> + char timeStr[50];
> +
> + tick = currentTime();
> + fprintf ( stdout, "Immediately before parallel\n" );
> +
> + //#pragma omp parallel private(i,j) shared(graph) reduction(+:found) reduction(+:searches)
> + //#pragma omp single
> + {
> + //#pragma omp parallel for private(i,j) default(none)
> + #ifdef USE_OMP
> + #pragma omp parallel for private(i,j) shared(graph) reduction(+:found) reduction(+:searches)
> + #pragma omp collapse(2)
> + #endif
> + for ( i = 0; i < graph->systemCallMap->contentSize; ++i )
> + {
> + for ( j = 0; j < graph->systemCallMap->contentSize; ++j )
> + {
> + ++searches;
> + char *fullSignature[3] = { NULL, NULL, NULL };
> + int fullIntSignature[3] = { 0, 0, -1 };
> + fullSignature[0] = graph->systemCallMap->vector[i]->label;
> + fullSignature[1] = graph->systemCallMap->vector[j]->label;
> + fullIntSignature[0] = i;
> + fullIntSignature[1] = j;
> + // NodePtrVec *result = NodePtrVec_new(25);
> +
> + /* findLabelPath does the findNextLabel in the above loops */
> + //#pragma omp task shared(graph, fullSignature, found)
> + {
> + NodePtrVec *result = NodePtrVec_new( 25 );
> + if ( findLabelPath( graph, fullSignature, result, searchType ) )
> + {
> +// printStack(result);
> + // logStats(result);
> + ++ found;
> + }
> + else
> + {
> +// printf ( "\n\tPath does not exist %s --/ /-> %s. %d steps.\n", fullSignature[0],
> +// fullSignature[1], result->contentSize );
> + }
> + if ( result )
> + {
> + NodePtrVec_delete( result );
> + }
> + }
> + }
> + //#pragma omp taskwait
> + }
> + }
> +
> +
> + tock = currentTime();
> +
> +
> + sec = tock-tick;
> + hours = (int)sec/3600;
> + sec = fmod( sec, 3600.0 );
> + min = (int)sec/60;
> + sec = fmod( sec, 60.0 );
> + printf ( "\n\n%d found out of %d searches. Overall Time: %d:%d:%2.3f\n",
> + found, searches, hours, min, sec );
> + timeStr[0] = '\0'; /* just in case sprintf doesn't do what we want. */
> + sprintf ( timeStr, "%02d:%02d:%02.3f", hours, min, sec );
> + YAMLWriteInt("Signatures Found", found);
> + YAMLWriteString("Search Time", timeStr);
> +
> +
> + //printStats();
> +
> + return( found );
> +}
> +
> +/*
> + * findAndLogAllPossibleLegs has the same search algorithm as findAllPossibleLegs. However, the requirement
> + * that all the legs be logged requires a more sophisticated means of parallelization in order to do a
> + * reduction of the solutions when all the threads are done.
> + */
> +int findAndLogAllPossibleLegs(Graph *graph, SearchOptions *options)
> +{
> + int i, j, k;
> + int found = 0;
> + int searches = 0;
> + double tick, tock;
> + int hours, min;
> + double sec;
> + int maxThreads = 1;
> + NodeVecVec **lastingResults;
> + Graph *optimizedGraph = NULL;
> + char timeStr[50];
> +
> + /* A little bit of error checking */
> + if ( !graph )
> + return 0;
> +
> + tick = currentTime();
> + fprintf(stdout, "Immediately before parallel\n" );
> +
> + #ifdef USE_OMP
> + #pragma omp parallel private(i,j,k) shared(graph,maxThreads,lastingResults) reduction(+:found) reduction(+:searches)
> + #endif
> + {
> + #ifdef USE_OMP
> + int myThread = omp_get_thread_num();
> + #else
> + int myThread = 0;
> + #endif
> +
> + NodeVecVec *myResults = NULL;
> +
> + #ifdef USE_OMP
> + #pragma omp single
> + #endif
> + {
> + #ifdef USE_OMP
> + maxThreads = omp_get_num_threads();
> + #else
> + maxThreads = 1;
> + #endif
> +
> + options->multiThreaded = maxThreads > 1;
> + /* debug * /printf( "%d total threads, this one is %d\n", maxThreads, myThread ); /* debug */
> + lastingResults = malloc((maxThreads+1) * sizeof(NodeVecVec*) );
> + lastingResults[maxThreads] = 0; /* Null terminated to avoid having to keep track of bitsNeeded */
> + }
> +
> + #ifdef USE_OMP
> + #pragma omp critical
> + #endif
> + {
> + lastingResults[myThread] = NodeVecVec_new(64); /* Arbitrary - multiple of 8, eventually cache line aligned... */
> + myResults = lastingResults[myThread];
> + }
> +
> + #ifdef USE_OMP
> + #pragma omp single
> + #endif
> + {
> + printf ("Immediately before nested for's\n");
> + }
> +
> + #ifdef USE_OMP
> + #pragma omp for
> + #pragma omp collapse(2)
> + #endif
> + for ( i = 0; i < graph->systemCallMap->contentSize; ++i )
> + {
> + for ( j = 0; j < graph->systemCallMap->contentSize; ++j )
> + {
> + ++searches;
> + for (k = 0; k < graph->systemCallMap->vector[i]->nodes->contentSize; ++k)
> + {
> + char *fullSignature[3] = { NULL, NULL, NULL };
> + int fullIntSignature[3] = { 0, 0, -1 };
> + fullSignature[0] = graph->systemCallMap->vector[i]->label;
> + fullSignature[1] = graph->systemCallMap->vector[j]->label;
> + fullIntSignature[0] = i;
> + fullIntSignature[1] = j;
> + NodePtrVec *result = NodePtrVec_new(16);
> + Bitfield *visited = Bitfield_new(graph->totalNodes);
> + /* debug ---> * /
> + printf( "Searching for %s(%d) ~~~> %s\n", fullSignature[0],
> + graph->systemCallMap->vector[i]->nodes->vector[k]->id,
> + fullSignature[1]);
> + /* <-- debug */
> + findAndRecordAllPaths( graph->systemCallMap->vector[i]->nodes->vector[k], &fullSignature[1],
> + &fullIntSignature[1], result, visited, myResults, options );
> + Bitfield_delete(visited);
> + if ( result )
> + NodePtrVec_delete( result );
> + } // end of for (k)... fork? heh.
> + } // end of for (j)
> + } // end of for (i)
> +
> + found = myResults->contentSize;
> + }
> +
> + tock = currentTime();
> + sec = tock-tick;
> + hours = (int)sec/3600;
> + sec = fmod( sec, 3600.0 );
> + min = (int)sec/60;
> + sec = fmod( sec, 60.0 );
> + printf ( "\n\n%d found for %d searches. Overall Time: %d:%d:%2.3f\n",
> + found, searches, hours, min, sec );
> + timeStr[0] = '\0'; /* just in case sprintf doesn't do what we want. */
> + sprintf ( timeStr, "%02d:%02d:%02.3f", hours, min, sec );
> + YAMLWriteInt("Signatures Found", found);
> + YAMLWriteString("Search Time", timeStr);
> +
> + /* debug --> * /
> + printf ("max threads still:%d\n", maxThreads);
> + for ( i = 0; i < maxThreads; ++i )
> + {
> + printf ( "printing out thread %d result - %d long\n", i, lastingResults[i]->contentSize );
> + for ( j = 0; j < lastingResults[i]->contentSize; ++j )
> + {
> + printf("\t");
> + printStack( lastingResults[i]->vector[j] );
> + printf("\n");
> + }
> + }
> + /* <-- debug */
> +
> + /* At some point, we will want to use the FullPath argument and pass it along to
> + * buildGraphFromPaths. Until then, however, we're only going to build the most
> + * minimal graph possible.
> + */
> + if ( options->writeOutputFile && options->outputFile )
> + {
> + optimizedGraph = buildGraphFromPaths(lastingResults, options->buildType);
> + exportGraph(optimizedGraph, options->outputFile);
> + }
> +
> + if ( options->doStatistics && !options->multiThreaded )
> + printStats();
> +
> + return( found );
> +}
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchAlgorithms.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchAlgorithms.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchAlgorithms.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchAlgorithms.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,106 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +
> + /*
> + * searchAlgorithms.h
> + *
> + * Created on: Jun 18, 2013
> + * Author: Brian "Rig" Rigdon
> + */
> +
> +#ifndef SEARCHALGORITHMS_H_
> +#define SEARCHALGORITHMS_H_
> +
> +
> +#include "vectorUtils.h"
> +#include "graph.h"
> +#include "configuration.h"
> +
> +
> +/* findNextLabel is a recursive method that determines if a path exists between a
> + * specific node and the label that is at the start of the label array argument. The
> + * label array is an array of char pointers that is terminated with a NULL pointer. The
> + * first pointer is the "current" label.
> + *
> + * The node's edge nodes are checked against the current label. If none of them match, then
> + * this method recurses with each edge node and the current label.
> + *
> + * If an edge matches, then we are beginning a search for the next "leg" of the labels.
> + * We recurse with that specific edge and the "next" label. That is the [1] element of
> + * the label array. If that element is NULL, the matching edge signifies the end of our
> + * search! VICTORY!
> + *
> + * If we reach the last edge with out a match (directly or recursively) we return a false
> + * list.
> + */
> +
> +bool findNextLabel( Node *node, char *labels[], NodePtrVec *result, Bitfield *visited ); /* NodePtrVec *visited ); */
> +
> +/* findAndRecordAllPaths is almost exactly like findNextLabel. It differs only in that it
> + * 1) doesn't stop with the first discovery of the specified path and 2) records the discovered
> + * path. To do this, it doesn't create a new result vector for
> + */
> +
> +void findAndRecordAllPaths( Node *node, Signature labels, int *labelIdxs,
> + NodePtrVec *result, Bitfield *visited, NodeVecVec *storage,
> + SearchOptions *options );
> +
> +/*
> + * findLabelPath takes an array of labels, determines if there are nodes associated
> + * with the labels (each label search will return a NodePtrVec*), and determine if
> + * paths exist passing through the set of labels.
> + */
> +bool findLabelPath( Graph *graph, Signature labels, NodePtrVec *result, SearchType searchType );
> +
> +/*
> + * findAllPossibleLegs does an exhaustive search through each possible label
> + * pairing to determine which legs are possible. This is a brute-force nxn
> + * approach that builds a signature holding only the second label and then
> + * searches for that signature from the nodes representing the first label.
> + * For the time being, it simply prints out the legs that are possible in
> + * this graph.
> + */
> +int findAllPossibleLegs( Graph *graph, SearchType searchType );
> +
> +/*
> + * findAndLogAllPossibleLegs is a duplicate of the above method, but it
> + * stores the results that are found
> + */
> +
> +int findAndLogAllPossibleLegs( Graph *graph, SearchOptions *options );
> +
> +/* Once the configuration file is parsed, a config structure is created that
> + * specifies the graphs and the signatures to be searched against. This method
> + * does multiple signature searches against multiple files
> + */
> +
> +void doMultiSearchesQT(Configuration *config);
> +
> +#endif /* SEARCHALGORITHMS_H_ */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchDiagram.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchDiagram.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchDiagram.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchDiagram.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,284 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +
> +/*
> + * searchDiagram.c
> + *
> + * Created on: Feb 1, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +#include "searchDiagram.h"
> +#include <string.h>
> +#include <stdlib.h>
> +#include <stdio.h>
> +
> +
> +/* Scream through the diagram to get the element corresponding to this key. This
> + * simply iterates through the entire list, there is no optimization in the search
> + * algorithm.
> + */
> +SearchDiagram *SearchDiagram_findNode ( SearchDiagram *diagram, Node *node )
> +{
> + int idx;
> +
> + /* Do some basic error checking */
> + if ( !diagram )
> + return( NULL );
> +
> + for ( idx = 0; diagram[idx].node != NULL; ++idx )
> + {
> + if ( diagram[idx].node == node ) /* We found it! */
> + return( &diagram[idx] );
> + }
> +
> + /* If we made it here, we couldn't find it. */
> + return( NULL );
> +}
> +
> +
> +
> +/* The meat of this process - the function that creates the search diagram.
> + * It allocates the memory for the array of search diagram elements and
> + * populates them with node data and edgeID arrays. Outer nodes are inserted
> + * into the node array from the lowest addresses and inner nodes are inserted
> + * into the search diagram from the highest. The authors did this to (hopefully)
> + * give a little more efficiency to the searching of the diagram.
> + */
> +SearchDiagram *SearchDiagram_build( NodeList *nodeTree, int nodeCount )
> +{
> + SearchDiagram *diagram = NULL;
> + NodeList *outerNodes = NULL;
> + Node *node = NULL;
> + NodeList *innerNodes = NULL;
> + /* Originally, we speculated that searches would stream through the outer
> + * nodes more than through the interior nodes. (We were wrong.) So we had
> + * this mechanism in place to put the outer nodes at the beginning of the
> + * diagram and the interior nodes at the end. Because we were wrong, this
> + * increases the likelihood of cache misses rather than decreasing it. Ergo
> + * we have replaced the outerIdx and the innerIdx calls.
> + *
> + * So... it turns out that putting the inner nodes near their containing
> + * node actually slows things down - but it's minor (2% - 3 minutes in a
> + * 120 minute run.)
> + int index = 0;
> + */
> + int outerIdx = 0; /* index from the bottom up for outer nodes */
> + int innerIdx = nodeCount-1; /* and from the top down for interior nodes */
> +
> + int edgeCount;
> + EdgeList *edges;
> + SearchDiagram *element; /* for searching in our diagram */
> +
> + /* Do some basic error checking */
> + if ( !nodeTree || nodeCount == 0 )
> + return NULL;
> +
> + /* Allocate an array of SearchDiagram Elements (+1 for a terminus element) */
> + diagram = malloc ( (nodeCount+1) * sizeof(SearchDiagram) );
> + if ( !diagram ) /* malloc failed */
> + return( NULL );
> +
> + diagram[nodeCount].node = NULL;
> + diagram[nodeCount].edgeReferenceArray = NULL;
> +
> + /* Scream through the Nodes and fill in the Search Array allocate space for edges */
> + for ( outerNodes = nodeTree; outerNodes != NULL; outerNodes = outerNodes->nextNode )
> + {
> + node = outerNodes->node;
> + /* This diagram entry needs a key */
> + diagram[outerIdx].node = node;
> + /* How many edges do we need? */
> + edgeCount = node->edgeCount + node->entranceCount;
> + if ( edgeCount > 0 ) /* allocate space for edgeIdArray (+1 for a terminus element) */
> + {
> + diagram[outerIdx].edgeReferenceArray = malloc ( (edgeCount+1) * sizeof(EdgeReferences) );
> + diagram[outerIdx].edgeReferenceArray[edgeCount].edgeTarget = NULL;
> + diagram[outerIdx].edgeReferenceArray[edgeCount].targetNodeEdges = NULL;
> + }
> + else
> + diagram[outerIdx].edgeReferenceArray = NULL;
> +
> + /* What do we do if that malloc fails? */
> +
> + /* increment the outer index: */
> + ++outerIdx;
> +
> + /* Now do the same for this node's interior graph (if present) */
> + for ( innerNodes = node->interiorNodes; innerNodes != NULL; innerNodes = innerNodes->nextNode )
> + {
> + node = innerNodes->node;
> + diagram[innerIdx].node = node;
> + edgeCount = node->edgeCount + node->entranceCount;
> + if ( node->edgeCount > 0 ) /* allocate space for edgeIdArray (+1 for a terminus element) */
> + {
> + diagram[innerIdx].edgeReferenceArray = malloc ( (edgeCount+1) * sizeof(EdgeReferences) );
> + diagram[innerIdx].edgeReferenceArray[edgeCount].edgeTarget = NULL;
> + diagram[innerIdx].edgeReferenceArray[edgeCount].targetNodeEdges = NULL;
> + }
> + else
> + diagram[innerIdx].edgeReferenceArray = NULL;
> +
> + /* Again, what do we do if that malloc fails? */
> +
> + /* decrement the interior index: */
> + --innerIdx;
> + }
> +
> + }
> +
> +
> + /* Check to make sure our counters line up. If they don't, we have a corrupt
> + * graph. That is, there is a mismatch between node definitions and edge lists.
> + * The innerIdx should reference the previous outerIdx location.
> + */
> + if ( outerIdx != innerIdx +1 )
> + {
> + /* Houston, we have a problem */
> + printf ( "Bummer. outerIdx: %d, innerIdx: %d, node count: %d\n", outerIdx, innerIdx, nodeCount );
> + }
> +
> +
> + /* For each node, populate its edge list - edges and entrance nodes (if there) */
> + outerIdx = 0;
> + innerIdx = nodeCount-1;
> + for ( outerNodes = nodeTree; outerNodes != NULL; outerNodes = outerNodes->nextNode )
> + {
> + /* iterate through this node's edges to populate the EdgeIdArray */
> + node = outerNodes->node;
> + for ( edges = node->edges, edgeCount = 0;
> + edges != NULL;
> + edges = edges->nextEdge, ++edgeCount )
> + {
> + element = SearchDiagram_findNode( diagram, edges->targetNode );
> + diagram[outerIdx].edgeReferenceArray[edgeCount].edgeTarget = edges->targetNode;
> + diagram[outerIdx].edgeReferenceArray[edgeCount].targetNodeEdges = element->edgeReferenceArray;
> + }
> + ++outerIdx;
> +
> + /* And then scream through the interior nodes to take care of their edges */
> + for ( innerNodes = node->interiorNodes; innerNodes != NULL; innerNodes = innerNodes->nextNode )
> + {
> + node = innerNodes->node;
> + for ( edges = node->edges, edgeCount = 0;
> + edges != NULL;
> + edges = edges->nextEdge, ++edgeCount )
> + {
> + element = SearchDiagram_findNode( diagram, edges->targetNode );
> + diagram[innerIdx].edgeReferenceArray[edgeCount].edgeTarget = edges->targetNode;
> + diagram[innerIdx].edgeReferenceArray[edgeCount].targetNodeEdges = element->edgeReferenceArray;
> + }
> + --innerIdx;
> + }
> + }
> +
> + return diagram;
> +}
> +
> +
> +
> +bool SearchDiagram_findSignatureAlongEdges ( Node *node, EdgeReferences *edges,
> + char *labels[], NodePtrVec *result, Bitfield *visited )
> +{
> + bool success = false;
> + NodePtrVec *nextLegResult = NULL;
> + Bitfield *nextLegVisited = NULL;
> + int i;
> +
> + /* A little basic error checking */
> + if ( !node || !edges || !labels || !result|| !visited )
> + {
> + return( false );
> + }
> +
> + /* If this node has already been visited, we have found a loop. return false. */
> +
> +/*
> + if ( NodePtrVec_findReverse( visited, node ) )
> + return( false );
> + else
> + NodePtrVec_push( visited, node );
> +*/
> + if ( Bitfield_nodeVisited( visited, node ) )
> + return( false );
> +
> + NodePtrVec_push( result, node );
> +
> + /* Go through the edges once to see if we've found a label match */
> + for ( i = 0; edges[i].edgeTarget != NULL; ++i )
> + {
> + if ( edges[i].edgeTarget->label )
> + {
> + //strcmp based:
> + if ( strcmp( edges[i].edgeTarget->label, labels[0] ) == 0 ) /* match! */
> + // index based: if ( edges[i].edgeTarget->labelIdx == labelIdxs[0] )
> + {
> + if ( labels[1] == NULL ) /* end of the signature, we're DONE */
> + {
> + NodePtrVec_push( result, edges[i].edgeTarget );
> + return( true );
> + }
> + else /* RECURSE TO SEE IF THE REST OF THE SIGNATURE CAN BE FOUND!!! */
> + {
> + nextLegResult = NodePtrVec_new( 50 ); /* arbitrary size, malloc success checked in recursion */
> + nextLegVisited = Bitfield_new(visited->bitsNeeded);
> +
> + success = SearchDiagram_findSignatureAlongEdges ( edges[i].edgeTarget,
> + edges[i].targetNodeEdges,
> + &labels[1], nextLegResult, nextLegVisited );
> + Bitfield_delete( nextLegVisited );
> + if ( success )
> + {
> + NodePtrVec_appendVectors( result, nextLegResult, true );
> + NodePtrVec_delete( nextLegResult );
> + return( true );
> + }
> + }
> + }
> + }
> + }
> +
> + /* IF we made it here, we need to continue through the tree, seeing if any of our
> + * edge nodes have a connection to a labeled node.
> + */
> + for ( i = 0; edges[i].edgeTarget != NULL; ++i )
> + {
> + success = SearchDiagram_findSignatureAlongEdges( edges[i].edgeTarget,
> + edges[i].targetNodeEdges,
> + labels, result, visited );
> + if ( success )
> + return( true ); /* this edge has a path to the ultimate signature path */
> + }
> +
> +
> + /* and, if we make it here, we have failed. */
> + NodePtrVec_pop( result ); /* take current node off the result stack */
> + return false;
> +}
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchDiagram.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchDiagram.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchDiagram.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/searchDiagram.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,93 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * searchDiagram.h
> + *
> + * Created on: Feb 1, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +#ifndef SEARCHDIAGRAM_H_
> +#define SEARCHDIAGRAM_H_
> +
> +#include "node.h"
> +
> +typedef struct SearchDiagramStruct SearchDiagram;
> +typedef struct EdgeReferencesStruct EdgeReferences;
> +
> +struct SearchDiagramStruct
> +{
> + Node *node; /* a reference to the node */
> + EdgeReferences *edgeReferenceArray; /* All the nodes reachable from here */
> +};
> +
> +/* We are creating arrays of SearchDiagram - constructor/destructor would be superfluous */
> +
> +
> +/* The EdgeSearchStruct holds a different representation of
> + * the tree through which we're searching. Our search diagram
> + * will create an array of these for each node in the graph.
> + * Searches will go through the array, looking to match the
> + * search criteria. If the search is unsuccessful, it will
> + * then search the edges of the node. In this array, the first
> + * element is the SEARCH ELEMENT we're comparing against. In
> + * this iteration of the code, we're using the Node pointer
> + * as the search key. The second element is the search edges
> + * contained by that node. The search edges are referenced
> + * directly, no need to go back to the SearchDiagram instance
> + * to get to the edges.
> + */
> +
> +struct EdgeReferencesStruct
> +{
> + Node *edgeTarget; /* The address of the node is how we're defining our search */
> + EdgeReferences *targetNodeEdges; /* pointer to the "to" node's edge references */
> +};
> +
> +/* We are creating arrays of EdgeReferences - constructor/destructor would be superfluous */
> +
> +/* Scream through the diagram to get the element corresponding to this Node* */
> +SearchDiagram *SearchDiagram_findNode ( SearchDiagram *diagram, Node *node );
> +
> +/* The meat of this process - the function that creates the search diagram.
> + * It allocates the memory for the array of search diagram elements and
> + * populates them with node data and edgeID arrays.
> + */
> +SearchDiagram *SearchDiagram_build ( NodeList *nodeTree, int nodeCount );
> +
> +
> +/* And, our search methods. The first calls the second, which is recursive */
> +
> +bool SearchDiagram_findSignatureAlongEdges ( Node *node, EdgeReferences *edges,
> + char *labels[], NodePtrVec *result, Bitfield *visited );
> +
> +
> +
> +#endif /* SEARCHDIAGRAM_H_ */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/statistics.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/statistics.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/statistics.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/statistics.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,238 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * statistics.c
> + *
> + * Created on: Sept 24, 2013
> + * Author: Brian "Rig" Rigdon
> + */
> +
> +#include "statistics.h"
> +#include <math.h>
> +#include <limits.h>
> +
> +HistogramElement *HistogramElement_new(int length)
> +{
> + HistogramElement *new = malloc(sizeof(HistogramElement));
> + if ( !new )
> + return NULL;
> + new->length = length;
> + new->count = 1;
> + new->next = NULL;
> + return(new);
> +}
> +
> +bool HistogramElement_updateList(HistogramElement **head, int length)
> +{
> + HistogramElement **prev = NULL;
> + HistogramElement *current = NULL;
> + HistogramElement *new = NULL;
> + bool histogramInsert = false;
> +
> + prev = head;
> + for ( current = *head; current != NULL; current = current->next )
> + {
> + if ( current->length < length )
> + {
> + prev = ¤t->next;
> + continue; /* iterate down the histogram linked list */
> + }
> + if ( current->length == length )
> + {
> + ++current->count;
> + histogramInsert = true;
> + break;
> + }
> + if ( current->length > length )
> + {
> + /* we are logging a new length, need to allocate and insert */
> + new = HistogramElement_new(length);
> + if ( ! new )
> + return(false);
> + new->next = current;
> + (*prev) = new;
> + histogramInsert = true;
> + break;
> + }
> + }
> +
> + if ( !histogramInsert ) /* this element belongs at the end of the chain */
> + {
> + (*prev) = HistogramElement_new(length);
> + if ( (*prev) == NULL )
> + return(false);
> + }
> +
> + return(true);
> +}
> +
> +Stats *Stats_new()
> +{
> + Stats* new = malloc(sizeof(Stats));
> + if ( new )
> + {
> + new->pathLengths = IntVector_new(16); // Arbitrary, multiple of 8 for vectorization
> + new->averageLength = 0.0;
> + new->standardDeviation = 0.0;
> + new->minLength = INT_MAX;
> + new->maxLength = 0;
> + new->histogram = NULL;
> + if ( new->pathLengths )
> + return(new);
> + else
> + {
> + free(new);
> + return(NULL);
> + }
> + }
> + else
> + return(NULL);
> +}
> +
> +
> +void Stats_delete(Stats* stats)
> +{
> + if ( stats )
> + {
> + if ( stats->pathLengths )
> + free(stats->pathLengths);
> + free(stats);
> + }
> +}
> +
> +
> +bool Stats_logPath(Stats* stats, NodePtrVec* path)
> +{
> +// bool histogramInsert = false;
> +// HistogramElement **prev = NULL;
> +// HistogramElement *hist = NULL;
> +// HistogramElement *new = NULL;
> + int length;
> +
> + if ( !stats || !stats->pathLengths || !path )
> + return(false);
> +
> + length = path->contentSize;
> + if ( length < stats->minLength )
> + stats->minLength = length;
> + if ( length > stats->maxLength )
> + stats->maxLength = length;
> + return ( IntVector_insertEnd(stats->pathLengths, length) );
> +}
> +
> +void Stats_calculate(Stats* stats)
> +{
> + int i;
> + int length;
> + double sum;
> + double diff;
> +
> + /* a little basic error checking */
> + if ( !stats || !stats->pathLengths || stats->pathLengths == 0 )
> + return;
> + stats->histogram = calloc((stats->maxLength+1), sizeof(int));
> + if ( !stats->histogram )
> + return;
> +
> + for ( i = 0; i < stats->pathLengths->size; ++i )
> + {
> + if ( stats->pathLengths->vector[i] > 0 )
> + {
> + length = stats->pathLengths->vector[i];
> + sum += (double)length;
> + /* While we're iterating through the list, let's build our histogram... */
> + /* HistogramElement_updateList(&stats->histogram, length); */
> + stats->histogram[length] += 1;
> + }
> + }
> + if ( i > 0 )
> + stats->averageLength = sum / (double)i;
> +
> + sum = 0.0;
> + for ( i = 0; i < stats->pathLengths->size; ++i )
> + {
> + if ( stats->pathLengths->vector[i] > 0 )
> + {
> + diff = (double)stats->pathLengths->vector[i] - stats->averageLength;
> + sum += diff * diff;
> + }
> + }
> +
> + if ( i > 0 )
> + stats->standardDeviation = sqrt(sum/(double)i);
> +}
> +
> +
> +void testStats()
> +{
> + int i;
> + Stats *test = Stats_new();
> + NodePtrVec bogon;
> +
> + for ( i = 2; i < 10; ++i )
> + {
> + bogon.contentSize = i;
> + Stats_logPath(test,&bogon);
> + }
> +
> + /* Throw in some more silly data */
> + bogon.contentSize = 1;
> + Stats_logPath(test,&bogon);
> + bogon.contentSize = 4;
> + Stats_logPath(test,&bogon);
> + bogon.contentSize = 5;
> + Stats_logPath(test,&bogon);
> + bogon.contentSize = 6;
> + Stats_logPath(test,&bogon);
> + bogon.contentSize = 5;
> + Stats_logPath(test,&bogon);
> + bogon.contentSize = 5;
> + Stats_logPath(test,&bogon);
> + bogon.contentSize = 4;
> + Stats_logPath(test,&bogon);
> + bogon.contentSize = 5;
> + Stats_logPath(test,&bogon);
> + bogon.contentSize = 6;
> + Stats_logPath(test,&bogon);
> + bogon.contentSize = 5;
> + Stats_logPath(test,&bogon);
> + bogon.contentSize = 5;
> + Stats_logPath(test,&bogon);
> +
> + Stats_calculate(test);
> + printf("avg: %f\nstd dev: %f\n", test->averageLength, test->standardDeviation);
> + printf("Histogram:\n");
> + for ( i = test->minLength; i < test->maxLength; ++i )
> + {
> + printf ("\tlength %d appeared %d times\n", i, test->histogram[i] );
> + }
> +
> +}
> +
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/statistics.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/statistics.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/statistics.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/statistics.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,71 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +
> +/*
> + * statistics.h
> + *
> + * Created on: Sept 24, 2013
> + * Author: Brian "Rig" Rigdon
> + */
> +
> +#ifndef STATISTICS_H
> +#define STATISTICS_H
> +
> +#include "vectorUtils.h"
> +
> +typedef struct HistogramElementStruct HistogramElement;
> +struct HistogramElementStruct
> +{
> + int length;
> + int count;
> + struct HistogramElementStruct *next;
> +};
> +
> +HistogramElement *HistogramElement_new(int length);
> +
> +typedef struct StatsStruct Stats;
> +struct StatsStruct
> +{
> + IntVector *pathLengths;
> + int minLength;
> + int maxLength;
> + double averageLength; // does it make sense to say 2.7823 nodes long?
> + double standardDeviation;
> + int *histogram;
> +};
> +
> +Stats *Stats_new();
> +void Stats_delete(Stats* stats);
> +bool Stats_logPath(Stats* stats, NodePtrVec* path);
> +void Stats_calculate(Stats* stats);
> +
> +void testStats();
> +
> +#endif // STATISTICS_H
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/systemCallMap.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/systemCallMap.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/systemCallMap.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/systemCallMap.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,246 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * systemCallMap.c
> + *
> + * Created on: Feb 5, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +#include "systemCallMap.h"
> +#include <string.h>
> +#include <stdio.h>
> +#include <stdlib.h>
> +
> +/* Element constructor */
> +SystemCallMapElement *SystemCallMapElement_new ( char *label, int initialSize )
> +{
> + SystemCallMapElement *element = malloc ( sizeof( SystemCallMapElement ) );
> + if ( element )
> + {
> + element->label = strdup ( label );
> + element->index = -1; /* Set by the insertion algorithm */
> + if ( !element->label )
> + {
> + free( element );
> + return( NULL );
> + }
> + element->nodes = NodePtrVec_new( initialSize );
> + if ( !element->nodes )
> + {
> + free( element->label );
> + free( element );
> + return( NULL );
> + }
> + }
> +
> + return( element );
> +}
> +
> +/* Element destructor */
> +void SystemCallMapElement_delete( SystemCallMapElement *trash )
> +{
> + /* free the mallocs! */
> + if ( trash )
> + {
> + if ( trash->label )
> + free( trash->label );
> + NodePtrVec_delete ( trash->nodes );
> + }
> +}
> +
> +
> +
> +
> +
> +/* Constructor */
> +SystemCallMap *SystemCallMap_new ( int initialSize )
> +{
> + SystemCallMap *map = NULL;
> + SystemCallMapElement **vector = NULL;
> +
> + if ( initialSize <= 0 )
> + return NULL;
> +
> + vector = malloc( initialSize * sizeof( SystemCallMapElement* ) );
> + if ( vector )
> + {
> + map = malloc ( sizeof( SystemCallMap ) );
> + if ( map )
> + {
> + map->allocatedSize = initialSize;
> + map->contentSize = 0;
> + map->vector = vector;
> + }
> + else
> + free( vector );
> + }
> +
> + return map;
> +}
> +
> +/* destructor for an ENTIRE MAP!!! */
> +void SystemCallMap_delete( SystemCallMap *trash )
> +{
> + int i;
> +
> + /* basic error checking */
> + if ( !trash )
> + return;
> +
> + for ( i = 0; i < trash->contentSize; ++i )
> + {
> + SystemCallMapElement_delete( trash->vector[i] );
> + }
> +}
> +
> +
> +
> +/* setter */
> +bool SystemCallMap_insert ( SystemCallMap *map, char *label, Node *node )
> +{
> + int i = 0;
> + SystemCallMapElement *newElement = NULL;
> + bool success = false;
> +
> + /* Some basic error checking */
> + if ( !map || !label || !node )
> + return( false );
> +
> + /* See if this label has already been implemented */
> + for ( i = 0; i < map->contentSize; ++i )
> + {
> + if ( strcmp( label, map->vector[i]->label ) == 0 )
> + {
> + /* found it! */
> + node->label = map->vector[i]->label;
> + node->labelIdx = i;
> + return( NodePtrVec_push( map->vector[i]->nodes, node ) );
> + }
> + }
> +
> + /* If we make it here, we have a new label */
> + if ( map->contentSize == map->allocatedSize )
> + {
> + /* Full up! Need a new vector */
> + map->vector = realloc( map->vector, (map->allocatedSize*2 * sizeof( SystemCallMapElement * )) );
> + if ( map->vector )
> + {
> + map->allocatedSize *= 2;
> + }
> + else
> + return( false );
> + }
> +
> + newElement = SystemCallMapElement_new( label, 8 ); /* arbitrary size of 8 */
> + if ( !newElement )
> + return( false );
> +
> + success = NodePtrVec_push( newElement->nodes, node );
> + if ( !success )
> + SystemCallMapElement_delete( newElement );
> +
> + node->label = newElement->label;
> + node->labelIdx = newElement->index = map->contentSize; /* Does newElement really need the index? */
> + map->vector[map->contentSize] = newElement;
> + map->contentSize += 1;
> +
> + return( true );
> +
> +}
> +
> +
> +
> +/* Finds all nodes associated with a label. */
> +NodePtrVec *SystemCallMap_findLabeledNodes( SystemCallMap *systemCalls, char *label )
> +{
> + int i;
> +
> + /* Debug --> * /
> + printf("Inside SystemCallMap_findLabeledNodes, label: %s\n", label);
> + / *<-- end debug */
> + if ( !systemCalls || !label )
> + return( NULL );
> +
> + for( i = 0; i < systemCalls->contentSize; ++i )
> + {
> + /* Debug -->* /
> + printf("\t...checking against %s...\n", systemCalls->vector[i]->label);
> + / * <-- end debug */
> + if ( strcmp( label, systemCalls->vector[i]->label ) == 0 )
> + return( systemCalls->vector[i]->nodes );
> + }
> +
> + /* Debug --> * /
> + printf("\tleaving SystemCallMap_findLabeledNodes, nothing found.\n");
> + / *<-- end debug */
> + return( NULL );
> +}
> +
> +/* Returns the index of a given label */
> +int SystemCallMap_getLabelIndex( SystemCallMap *map, char *label )
> +{
> + int i;
> +
> + /* See if this label has already been implemented */
> + for ( i = 0; i < map->contentSize; ++i )
> + {
> + if ( strcmp( label, map->vector[i]->label ) == 0 )
> + {
> + return( i );
> + }
> + }
> +
> + /* If we made it here, this label is not represented */
> + return( -1 );
> +}
> +
> +
> +/*
> + * Determines if all the labels in a given signature are represented
> + * within this graph. If not, we know the search will fail. There's
> + * gotta be a better name for this...
> + */
> +bool SystemCallMap_signatureRepresented( SystemCallMap *map, Signature signature )
> +{
> + int i;
> + bool foundByLabel = true;
> +
> + for ( i = 0; signature[i] != NULL && foundByLabel; ++i )
> + {
> + /* if the signature is in the map, its index will be >=0 */
> + if ( SystemCallMap_getLabelIndex( map, signature[i] ) < 0 )
> + foundByLabel = false;
> + }
> +
> + return( foundByLabel );
> +}
> +
> +
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/systemCallMap.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/systemCallMap.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/systemCallMap.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/systemCallMap.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,112 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * systemCallMap.h
> + *
> + * Created on: Feb 5, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +#ifndef SYSTEMCALLMAP_H_
> +#define SYSTEMCALLMAP_H_
> +
> +#include <stdbool.h>
> +#include "node.h"
> +
> +
> +
> +/* A signature is an array of character pointers. Signature arrays
> + * are terminated with a NULL pointer so we don't have to have an
> + * additional datum to contain the length of the array. To make
> + * the code more readable, we are using this typedef:
> + */
> +typedef char **Signature; /* code must be careful to ensure NULL termination */
> +
> +
> +/*
> + * SystemCallMapStruct specifies a label and all the nodes that are associated with
> + * that label. Currently, this is sub-optimal, managing via strcmp. If optimization
> + * is needed, that is left as an exercise for the future. We could see the future
> + * addition of hash values
> + */
> +
> +typedef struct SystemCallMapElementStruct SystemCallMapElement;
> +
> +struct SystemCallMapElementStruct
> +{
> + char *label;
> + int index;
> + NodePtrVec *nodes;
> +};
> +
> +SystemCallMapElement *SystemCallMapElement_new ( char *label, int initialSize ); /* Element constructor */
> +void SystemCallMapElement_delete( SystemCallMapElement *trash ); /* Element destructor */
> +
> +
> +
> +
> +/* The call map is actually a stack (managed like the STL deque) of SystemCallMapElements.
> + * It will insert up to its capacity, and then double its size (allocating a new space, copying
> + * and then freeing the old) when it grows beyond its capacity.
> + */
> +
> +typedef struct SystemCallMapStruct SystemCallMap;
> +
> +struct SystemCallMapStruct
> +{
> + int contentSize;
> + int allocatedSize;
> + SystemCallMapElement **vector; /* a pointer to an array of pointers */
> +};
> +
> +SystemCallMap *SystemCallMap_new( int initialSize );
> +void SystemCallMap_delete( SystemCallMap *trash ); /* destructor for an ENTIRE MAP!!! */
> +
> +/* insert checks to see if there is already an entry for the name passed in. If so,
> + * it appends the node to that map element. If not, a new element is created, the
> + * name is duplicated
> + */
> +bool SystemCallMap_insert ( SystemCallMap *map, char *label, Node *node );
> +
> +
> +/* Finds a list of nodes associated with a label. */
> +NodePtrVec *SystemCallMap_findLabeledNodes( SystemCallMap *systemCalls, char *label );
> +
> +/* Returns the index of a given label */
> +int SystemCallMap_getLabelIndex( SystemCallMap *map, char *label );
> +
> +/*
> + * Determines if all the labels in a given signature are represented
> + * within this graph. If not, we know the search will fail. There's
> + * gotta be a better name for this...
> + */
> +bool SystemCallMap_signatureRepresented( SystemCallMap *map, Signature signature );
> +
> +#endif /* SYSTEMCALLMAP_H_ */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/utils.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/utils.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/utils.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/utils.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,252 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * utils.c
> + *
> + * Created on: Jan 10, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +#include "utils.h"
> +#include <stdio.h>
> +#include <stdlib.h>
> +
> +void edgeListPrettyPrint( EdgeList *edges, int depth, char *header )
> +{
> + int i;
> + for ( i = 0; i < depth; ++i )
> + printf( "\t" );
> + printf( "%s: ", header );
> + for ( ; edges != NULL; edges = edges->nextEdge )
> + printf( " %d,", edges->targetNodeId );
> + printf( "\n" );
> +}
> +
> +
> +void nodeListPrettyPrint( NodeList *nodes, int depth, char *separator, bool multiLine )
> +{
> + int i;
> +
> + if ( !nodes )
> + return;
> +
> + if ( nodes->node )
> + printf( "%d", nodes->node->id );
> + if ( nodes->nextNode )
> + {
> + if ( multiLine )
> + {
> + printf( "\n" );
> + for ( i = 0; i < depth; ++i )
> + {
> + printf( " " );
> + }
> + }
> + printf( "%s", separator );
> + nodeListPrettyPrint( nodes->nextNode, depth + 1, separator, multiLine );
> + }
> + else
> + printf( "\n" );
> +}
> +
> +
> +void graphPrettyPrint ( Graph *graph )
> +{
> + NodeList *outerPtr;
> + NodeList *innerPtr;
> +
> + for ( outerPtr = graph->outerNodes;
> + outerPtr != NULL;
> + outerPtr = outerPtr->nextNode )
> + {
> + printf( "Outer Node: %d, idx: %d, label: %s (%d)\n", outerPtr->node->id,
> + outerPtr->node->nodeCount, outerPtr->node->label ? outerPtr->node->label : "none",
> + outerPtr->node->labelIdx );
> + edgeListPrettyPrint( outerPtr->node->edges, 1, "Edges" );
> + /* Deprecated: edgeListPrettyPrint( outerPtr->node->entranceNodes, 1, "EntranceNodes" ); */
> + for ( innerPtr = outerPtr->node->interiorNodes;
> + innerPtr != NULL;
> + innerPtr = innerPtr->nextNode )
> + {
> + printf( "\tInner Node: %d\n", innerPtr->node->id );
> + edgeListPrettyPrint( innerPtr->node->edges, 2, "Edges" );
> + }
> + }
> +
> + printf ( "\n\n" );
> +}
> +
> +
> +void systemCallMapPrettyPrint( SystemCallMap *map )
> +{
> + SystemCallMapElement *element = NULL;
> + int i = 0;
> + int j = 0;
> +
> + if ( !map )
> + return;
> +
> + for ( i = 0; i < map->contentSize; ++i )
> + {
> + element = map->vector[i];
> + printf( "'%s'\n\t:", element->label );
> + for ( j = 0; element->nodes && j < element->nodes->contentSize; ++j )
> + {
> + printf( "%d", element->nodes->vector[j]->id );
> + if ( j < element->nodes->contentSize-1 )
> + printf( ", " );
> + else
> + printf( "\n\n" );
> + }
> +
> + }
> +
> + printf( "\t%d total System Call Map elements\n", map->contentSize );
> +}
> +
> +bool testGraph()
> +{
> + /* Build it and see if it will get made */
> + Graph *graph = malloc( sizeof( Graph ) );
> + Node *outerNode1 = Node_new( 10, 0 );
> + Node *outerNode2 = Node_new( 20, 1 );
> + Node *innerNode11 = Node_new( 11, 2 );
> + Node *innerNode12 = Node_new( 12, 3 );
> + Node *innerNode21 = Node_new( 21, 4 );
> + Node *innerNode22 = Node_new( 22, 5 );
> + Node *innerNode23 = Node_new( 23, 6 );
> +
> + if ( !graph ) return( false );
> +
> + Graph_addOuterNode( graph, outerNode1 );
> + Graph_addOuterNode( graph, outerNode2 );
> +
> + Node_addInteriorNode( outerNode1, innerNode11 );
> + Node_addInteriorNode( outerNode1, innerNode12 );
> +
> + Node_addInteriorNode( outerNode2, innerNode21 );
> + Node_addInteriorNode( outerNode2, innerNode22 );
> + Node_addInteriorNode( outerNode2, innerNode23 );
> +
> +
> + /* Ok, let's print out the graph and see if it works */
> + graphPrettyPrint( graph );
> +
> + return( true );
> +}
> +
> +void printStack ( NodePtrVec *stack )
> +{
> + if ( !stack ) return;
> + int i;
> + // printf ( "stack size %d out of %d max\n", stack->contentSize, stack->allocatedSize );
> + for ( i = 0; i < stack->contentSize; ++i )
> + {
> + printf("%d", stack->vector[i]->id );
> + fflush(stdout);
> + if ( stack->vector[i]->label )
> + {
> + printf( "(%s)", stack->vector[i]->label );
> + fflush(stdout);
> + }
> + if ( i != stack->contentSize-1 )
> + {
> + printf ( " : " );
> + fflush(stdout);
> + }
> + }
> + printf( "\n" );
> + fflush(stdout);
> +}
> +
> +void testStack()
> +{
> + /* This was written when the stack was storing integers
> + int a, b, c, d, e;
> + printf ( "\n\nTesting stack operations" );
> + NodePtrVec *vector = Stack_new(3);
> + if ( !vector )
> + {
> + printf( "stack allocation failed\n" );
> + return;
> + }
> + Stack_push( vector, 1 );
> + Stack_push( vector, 2 );
> + printStack( vector );
> + Stack_push( vector, 3 );
> + printStack( vector );
> + Stack_push( vector, 4 );
> + printStack( vector );
> +
> + printf ( "\n2 %s in the stack\n", Stack_find( vector, 2 ) ? "is" : "is not" );
> + printf ( "5 %s in the stack\n\n", Stack_find( vector, 5 ) ? "is" : "is not" );
> +
> + printf ( "\n4 %s in the stack\n", Stack_findReverse( vector, 4 ) ? "is" : "is not" );
> + printf ( "45 %s in the stack\n\n", Stack_findReverse( vector, 45 ) ? "is" : "is not" );
> +
> + a = Stack_pop( vector );
> + printStack( vector );
> + b = Stack_pop( vector );
> + c = Stack_pop( vector );
> + d = Stack_pop( vector );
> + e = Stack_pop( vector );
> + printStack( vector );
> + printf ( "%d, %d, %d, %d, %d\n", a, b, c, d, e );
> + */
> +}
> +
> +
> +/* The below code gives compile warnings about the size difference
> + * between pointers and ints. Since this doesn't impact execution,
> + * I am not going to chase down a fix.
> + */
> +void searchDiagramPrettyPrint ( SearchDiagram *diagram )
> +{
> +#if 0
> + SearchDiagram *node;
> + EdgeReferences *edge;
> +
> + for ( node = diagram; node != NULL && node->node != NULL; ++node )
> + {
> + printf ( "Node %x -> %d\n", (unsigned int)node, node->node->id );
> + if ( node->edgeReferenceArray )
> + {
> + printf ( "\t%x\n", (int)node->edgeReferenceArray );
> + for ( edge = node->edgeReferenceArray; edge->edgeTarget != NULL; ++edge )
> + {
> + printf ( "\t\tEdge (target %d) -> %x\n",
> + edge->edgeTarget->id, (int)edge->targetNodeEdges );
> + }
> + }
> +
> + }
> +#endif
> +}
> +
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/utils.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/utils.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/utils.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/utils.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,53 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * utils.h
> + *
> + * Created on: Jan 10, 2013
> + * Author: Brian "Rig" Rigdon, Marcus Smith, Samuel Mulder
> + */
> +
> +#ifndef UTILS_H_
> +#define UTILS_H_
> +
> +#include "graph.h"
> +#include "systemCallMap.h"
> +#include "searchDiagram.h"
> +void edgeListPrettyPrint( EdgeList *edges, int depth, char *header );
> +void nodeListPrettyPrint( NodeList *nodes, int depth, char *separator, bool multiLine );
> +void graphPrettyPrint( Graph *graph );
> +void systemCallMapPrettyPrint( SystemCallMap *map );
> +void printStack ( NodePtrVec *stack );
> +bool testGraph();
> +void testStack();
> +
> +void searchDiagramPrettyPrint ( SearchDiagram *diagram );
> +
> +#endif /* UTILS_H_ */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/vectorUtils.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/vectorUtils.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/vectorUtils.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/vectorUtils.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,563 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * vectorUtils.c
> + *
> + * Created on: Jun 21, 2013
> + * Author: jbrigdo
> + */
> +
> +#include "vectorUtils.h"
> +
> +
> +#include <stdio.h>
> +#include <stdlib.h>
> +#include <string.h>
> +#include <ctype.h>
> +
> +
> +/* --------
> + * IntVector Methods
> + */
> +
> +/* constructor */
> +IntVector *IntVector_new( int size )
> +{
> + IntVector *new = malloc( sizeof(IntVector) );
> + if ( new )
> + {
> + int *vector = malloc ( size * sizeof(int) );
> + if ( vector )
> + {
> + new->vector = vector;
> + new->size = 0;
> + new->allocatedSize = size;
> + return( new );
> + }
> + else
> + {
> + free( new );
> + return( NULL );
> + }
> + }
> + else
> + return( NULL );
> +}
> +
> +/* destructor */
> +void IntVector_delete(IntVector *trash)
> +{
> + if ( trash )
> + {
> + if ( trash->vector )
> + free( trash->vector );
> + free( trash );
> + }
> +}
> +
> +/* inserts a new integer at the tail of the vector */
> +bool IntVector_insertEnd(IntVector *vector, int datum)
> +{
> + int current = 0;
> + int max = 0;
> +
> + /* some basic error checking */
> + if ( !vector )
> + return( false );
> +
> + current = vector->size;
> + max = vector->allocatedSize;
> +
> + if ( current == max ) /* we're full */
> + {
> + vector->vector = realloc( vector->vector, 2*max*sizeof(int) );
> + if ( vector->vector )
> + {
> + vector->allocatedSize = 2*max;
> + }
> + else
> + {
> + fprintf( stderr, "\n\nIntVector_insertEnd failed realloc size = %d\n", current*2 );
> + return( false );
> + }
> + }
> +
> + vector->vector[current] = datum;
> + vector->size += 1;
> + return( true );
> +}
> +
> +/*
> + * A utility method that takes an input string to the next number. If it currently
> + * points to a number, we iterate past that number, past any whitespace or non-number
> + * and point to the first digit character we find. If input currently points a non-
> + * digit character, we find the next digit character and return a pointer to it. If
> + * no non-digit character is found with these rules, we return null.
> + */
> +static char *findNextNumber(char *input)
> +{
> + if ( isdigit( (int)input[0] ) )
> + {
> + /* scream through the string to find a non-digit */
> + ++input;
> + while ( isdigit( (int)input[0] ) && *input != '\0' )
> + ++input;
> + if ( input[0] == '\0' )
> + return( NULL );
> + else
> + /* now find the next digit */
> + while ( !isdigit( (int)input[0] ) && *input != '\0' )
> + ++input;
> + if ( input[0] == '\0' )
> + return(NULL);
> + else
> + return(input);
> + }
> + else
> + {
> + /* find the first digit character */
> + do {
> + if ( input[0] == '\0' )
> + return(NULL);
> + ++input;
> + } while ( !isdigit( (int)input[0] ) );
> + return(input);
> + }
> +}
> +
> +/*
> + * parse space-delimited null-terminated string into an IntVector.
> + * Returns the number of integers collected
> + */
> +int IntVector_createFromString(IntVector *vector, char *inputString)
> +{
> + int dataCount = 0;
> + int datum;
> +
> + /* make sure we have valid pointers passed in*/
> + if ( !vector || !inputString )
> + return(0);
> +
> + /* make sure we're pointing to a digit */
> + if ( !isdigit((int)inputString[0]))
> + {
> + inputString = findNextNumber(inputString);
> + }
> +
> + /* ok, at this point, we know we're pointing at a number */
> + while (inputString) /* set to NULL when there are no more numbers. */
> + {
> + datum = atoi(inputString);
> + inputString = findNextNumber(inputString);
> + if ( !IntVector_insertEnd(vector, datum) )
> + return(0); /* realloc failure */
> + ++dataCount;
> + }
> +
> + return(dataCount);
> +}
> +
> +
> +
> +
> +/* constructor */
> +CharVector *CharVector_new(int size)
> +{
> + CharVector *new = malloc( sizeof(CharVector) );
> + if ( new )
> + {
> + char *string = malloc ( size * sizeof(char) );
> + if ( string )
> + {
> + new->string = string;
> + new->size = 0;
> + new->allocatedSize = size;
> + return( new );
> + }
> + else
> + {
> + free( new );
> + return( NULL );
> + }
> + }
> + else
> + return( NULL );
> +}
> +
> +/* destructor */
> +void CharVector_delete( CharVector *trash )
> +{
> + if ( trash )
> + {
> + if ( trash->string )
> + free( trash->string );
> + free( trash );
> + }
> +}
> +
> +
> +bool CharVector_insertEnd( CharVector *vector, char c )
> +{
> + int size = 0;
> + int max = 0;
> +
> + /* some basic error checking */
> + if ( !vector )
> + return( false );
> +
> + size = vector->size;
> + max = vector->allocatedSize;
> +
> + if ( size == max ) /* we're full */
> + {
> + vector->string = realloc( vector->string, 2*size*sizeof(char) );
> + if ( vector->string )
> + {
> + vector->allocatedSize = size*2;
> + }
> + else
> + {
> + fprintf( stderr, "\n\nIntVector_insertEnd failed realloc size = %d\n", size*2 );
> + return( false );
> + }
> + }
> +
> + vector->string[size] = c;
> + vector->size += 1;
> + return( true );
> +}
> +
> +
> +int CharVector_getLineFromFile( CharVector *vector, FILE *input )
> +{
> + bool notDoneYet = true;
> + char c = '\0';
> +
> + /* Some basic error checking */
> + if ( !vector || !input )
> + return( -1 );
> +
> + vector->size = 0; /* reset the vector prior to filling */
> +
> + /* get to the next digit */
> + do {
> + c = fgetc( input );
> + if ( feof( input ) || c == '\n' )
> + notDoneYet = false;
> + else
> + if ( ! CharVector_insertEnd( vector, c ) )
> + return( -1 ); /* CharVector_insertEnd reached a memory limit. Fail */
> + } while ( notDoneYet );
> +
> + /* make the data a c-string */
> + if ( ! CharVector_insertEnd( vector, '\0' ) )
> + return( -1 ); /* CharVector_insertEnd reached a memory limit. Fail */
> + return( vector->size );
> +}
> +
> +
> +
> +/* -------------------------------------------
> + * Node Pointer Vector Method Definitions
> + *
> + */
> +
> +/* create a new vector allocating specified size */
> +NodePtrVec *NodePtrVec_new( int initialSize )
> +{
> + NodePtrVec *newVector;
> + Node **vector; /* an array of pointers */
> +
> + vector = malloc ( initialSize * sizeof(Node *) );
> + if ( !vector )
> + {
> + printf ( "Malloc failure in NodePtrVec creation\n" );
> + return( NULL );
> + }
> +
> + newVector = malloc ( sizeof(NodePtrVec) );
> + if ( !newVector )
> + {
> + free(vector);
> + printf ( "Malloc failure in NodePtrVec storage creation\n" );
> + return( NULL );
> + }
> +
> + newVector->allocatedSize = initialSize;
> + newVector->contentSize = 0;
> + newVector->vector = vector;
> + return( newVector );
> +}
> +
> +
> +
> +/* destructor */
> +void NodePtrVec_delete( NodePtrVec *trash )
> +{
> + if ( trash )
> + {
> + if ( trash->vector )
> + free(trash->vector);
> + free(trash);
> + }
> +}
> +
> +
> +/* creates duplicate vector (not duplicate nodes!). If exact_copy is true, the
> + * new vector is the same size as the copied one. If false, then only enough
> + * room to hold the copy is allocated.
> + */
> +NodePtrVec *NodePtrVec_copy(NodePtrVec *from, bool exact_copy)
> +{
> + int i;
> +
> + if ( !from )
> + return NULL;
> +
> + NodePtrVec *to = exact_copy ? NodePtrVec_new(from->allocatedSize)
> + : NodePtrVec_new(from->contentSize);
> + if ( !to )
> + return NULL;
> +
> + for ( i = 0; i < from->contentSize; ++i )
> + to->vector[i] = from->vector[i];
> + to->contentSize = from->contentSize;
> + return to;
> +}
> +
> +/* pushes the element if it can. If a memory allocation is required but
> + * fails - false is returned
> + */
> +bool NodePtrVec_push( NodePtrVec *vector, Node *node )
> +{
> + int current;
> + int max;
> +
> + /* some basic error checking */
> + if ( !vector ) return false;
> +
> + current = vector->contentSize;
> + max = vector->allocatedSize;
> +
> + /* see if our vector is full */
> + if ( current == max )
> + {
> + vector->vector = realloc( vector->vector, 2*max * sizeof(Node *) );
> + if ( vector->vector )
> + {
> + vector->allocatedSize = 2*max;
> + }
> + else
> + {
> + printf ( "\n\nNodePtrVec_push failed malloc(%d). Node: %d", 2*max, node->id );
> + if ( node->label )
> + printf ( ", label: %s\n", node->label );
> + else
> + printf ( "\n\n" );
> + return false;
> + }
> + }
> +
> + /* do the actual pushing */
> + vector->vector[current] = node;
> + vector->contentSize += 1;
> +
> + return true;
> +}
> +
> +/* returns the top item and decrements. What do we do to define empty? */
> +Node * NodePtrVec_pop( NodePtrVec *vector )
> +{
> + Node *top = NULL;
> +
> + /* some basic error checking */
> + if ( !vector ) return NULL;
> +
> + if ( vector->contentSize > 0 )
> + {
> + vector->contentSize -= 1;
> + top = vector->vector[vector->contentSize];
> + }
> +
> + return top;
> +}
> +
> +/* Screams through the vector from bottom to top to find the specified element. If found,
> + * returns true.
> + */
> +bool NodePtrVec_find( NodePtrVec *vector, Node *node )
> +{
> + int i;
> +
> + /* some basic error checking */
> + if ( !vector ) return false;
> +
> + for ( i = 0; i < vector->contentSize; ++i )
> + if ( vector->vector[i] == node )
> + return true;
> +
> + return false;
> +}
> +
> +/* Screams through the vector from top to bottom to find the specified element. If found,
> + * returns true. */
> +bool NodePtrVec_findReverse( NodePtrVec *vector, Node *node )
> +{
> + int i;
> +
> + /* some basic error checking */
> + if ( !vector || !vector->vector || !node ) return false;
> +
> + for ( i = vector->contentSize-1; i >= 0; --i )
> + if ( vector->vector[i] == node )
> + return true;
> +
> + return false;
> +}
> +
> +
> +/* Appends the second vector to the first. If the "keepFirst" flag is set, the
> + * entire second vector is appended to the first. Otherwise, the [0] element of
> + * the second vector is skipped. This is useful when the last element of the
> + * first vector is identical to the first element of the second vector, and
> + * we don't want duplication. (And who, really, wants duplication? Really, who
> + * wants duplication?)
> + */
> +void NodePtrVec_appendVectors ( NodePtrVec *first, NodePtrVec *second, bool keepFirst )
> +{
> + int i;
> +
> + /* Some basic error checking */
> + if ( !first || !second )
> + return;
> +
> + if ( keepFirst )
> + i = 0;
> + else
> + i = 1;
> +
> + for ( ; i < second->contentSize; ++i )
> + NodePtrVec_push( first, second->vector[i] );
> +}
> +
> +
> +
> +/* -------------------------------------------
> + * Node Vec Vec Method definitions
> + *
> + * (vector of Node Pointer Vectors )
> + */
> +
> +/* create a new vector allocating specified size */
> +NodeVecVec *NodeVecVec_new( int initialSize )
> +{
> + NodeVecVec *newVector;
> + NodePtrVec **vector; /* an array of pointers */
> +
> + vector = malloc ( initialSize * sizeof(NodePtrVec *) );
> + if ( !vector )
> + {
> + printf ( "Malloc failure in NodeVecVec storage creation\n" );
> + fflush(stdout);
> + return( NULL );
> + }
> +
> + newVector = malloc ( sizeof(NodeVecVec) );
> + if ( !newVector )
> + {
> + free(vector);
> + printf ( "Malloc failure in NodeVecVec creation\n" );
> + fflush(stdout);
> + return( NULL );
> + }
> +
> + newVector->allocatedSize = initialSize;
> + newVector->contentSize = 0;
> + newVector->vector = vector;
> + return( newVector );
> +}
> +
> +
> +
> +/* destructor */
> +void NodeVecVec_delete( NodeVecVec *trash )
> +{
> + int i;
> + if ( trash )
> + {
> + for ( i = 0; i < trash->contentSize; ++i )
> + NodePtrVec_delete(trash->vector[i]);
> + if ( trash->vector )
> + free(trash->vector);
> + free(trash);
> + }
> +}
> +
> +
> +/* pushes a copy of the element if it can. If a memory allocation is required but
> + * fails - false is returned
> + */
> +bool NodeVecVec_insert( NodeVecVec *vector, NodePtrVec *path )
> +{
> + int current;
> + int max;
> + NodePtrVec *copy = NodePtrVec_copy(path,false);
> +
> + /* some basic error checking */
> + if ( !vector || !path || !copy ) return false;
> +
> + current = vector->contentSize;
> + max = vector->allocatedSize;
> +
> + /* see if our vector is full */
> + if ( current == max )
> + {
> + vector->vector = realloc( vector->vector, 2*max * sizeof(Node *) );
> + if ( vector->vector )
> + {
> + vector->allocatedSize = 2*max;
> + }
> + else
> + {
> + printf ( "\n\nNodeVecVec_push failed malloc\n" );
> + fflush(stdout);
> + return false;
> + }
> + }
> +
> + /* do the actual pushing */
> + vector->vector[current] = copy;
> + vector->contentSize += 1;
> +
> + return true;
> +}
> +
> +
> +
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/vectorUtils.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/vectorUtils.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/vectorUtils.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/vectorUtils.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,169 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * vectorUtils.h
> + *
> + * Created on: Jun 21, 2013
> + * Author: J. Brian Rigdon
> + */
> +
> +#ifndef VECTORUTILS_H_
> +#define VECTORUTILS_H_
> +
> +#include <stdio.h>
> +#include <stdbool.h>
> +
> +#include "node.h"
> +
> +/* The IntVector is sort of a C version of std::vector<int> */
> +typedef struct IntVectorStruct IntVector;
> +struct IntVectorStruct
> +{
> + int size; /* number of integers actively stored */
> + int allocatedSize;
> + int *vector;
> +};
> +
> +IntVector *IntVector_new(int size); /* constructor */
> +void IntVector_delete(IntVector *trash); /* destructor */
> +#define IntVector_clear(intVectorPtr) (intVectorPtr->size = 0)
> +#define IntVector_size(intVectorPtr) (intVectorPtr->size)
> +bool IntVector_insertEnd(IntVector *vector, int datum);
> +
> +/*
> + * parse space-delimited null-terminated string into an IntVector.
> + * Returns the number of integers collected
> + */
> +int IntVector_createFromString(IntVector *vector, char *inputString);
> +
> +
> +
> +
> +
> +/* The CharVector is sort of a C version of std::vector<char> */
> +typedef struct CharVectorStruct CharVector;
> +struct CharVectorStruct
> +{
> + int size; /* number of integers actively stored */
> + int allocatedSize;
> + char *string;
> +};
> +
> +CharVector *CharVector_new(int size); /* constructor */
> +void CharVector_delete(CharVector *trash); /* destructor */
> +bool CharVector_insertEnd(CharVector *vector, char c);
> +int CharVector_getLineFromFile(CharVector *vector, FILE *input);
> +
> +
> +
> +
> +
> +
> +/* -------------------------------------------
> + * Node Pointer Vector Definitions
> + *
> + * NodePtrVec are an alternative storage mechanism to the Node Lists.
> + * The Vector is single ended, with a push and a pop. It maintains
> + * a count of contained Node pointers, the maximum allocated size for
> + * the storage and a pointer to the array of Node pointers. When the
> + * contained size reaches the maximum, another piece of memory, we
> + * realloc for twice the size. This is patterned after STL vectors
> + */
> +
> +
> +
> +/* A simple, sized vector class. The vector is initially created with a specified size
> + * even though it holds nothing. Each push increments a counter (pops decrement) until
> + * it reaches its initial size. The next push will be slow, because the vector needs
> + * to grow. At that point, we realloc with DOUBLE the size of the original vector. If
> + * successful, the last datagram is inserted in the end of the vector.
> + */
> +
> +typedef struct NodePtrVecStruct NodePtrVec;
> +
> +struct NodePtrVecStruct
> +{
> + int contentSize; // the number of elements currently in the vector
> + int allocatedSize; // the amount (in sizeof int) currently allocated for this vector
> + Node **vector; // a pointer to the actual data (array of node pointers).
> +};
> +
> +
> +NodePtrVec *NodePtrVec_new(int initialSize); /* create a new vector allocating specified size */
> +void NodePtrVec_delete(NodePtrVec *trash); /* destructor */
> +NodePtrVec *NodePtrVec_copy(NodePtrVec *from, bool exact_copy); /* creates duplicate vector (not duplicate nodes!) */
> +
> +/* pushes the element if it can. If a memory allocation is required but
> + * fails - false is returned
> + */
> +bool NodePtrVec_push(NodePtrVec *vector, Node *node);
> +Node * NodePtrVec_pop(NodePtrVec *vector); /* returns the top item and decrements. If empty, we return -1 */
> +
> +/* Screams through the vector from bottom to top to find the specified element. If found,
> + * returns true.
> + */
> +bool NodePtrVec_find(NodePtrVec *vector, Node *node);
> +
> +/* Screams through the vector from top to bottom to find the specified element. If found,
> + * returns true.
> + */
> +bool NodePtrVec_findReverse(NodePtrVec *vector, Node *node);
> +
> +/* Appends the second vector to the first. If the "keepFirst" flag is set, the
> + * entire second vector is appended to the first. Otherwise, the [0] element of
> + * the second vector is skipped. This is useful when the last element of the
> + * first vector is identical to the first element of the second vector, and
> + * we don't want duplication. (And who, really, wants duplication? Really, who
> + * wants duplication?)
> + */
> +void NodePtrVec_appendVectors(NodePtrVec *first, NodePtrVec *second, bool keepFirst);
> +
> +
> +/* -------------------------------------------
> + * And a vector of Node Pointer Vectors
> + *
> + * Results from the searches are presented as NodePtrVectors. To store a bunch of these
> + * we are defining a vector of these vectors.
> + */
> +
> +typedef struct NodeVecVecStruct NodeVecVec;
> +
> +struct NodeVecVecStruct
> +{
> + int contentSize;
> + int allocatedSize;
> + NodePtrVec **vector;
> +};
> +
> +NodeVecVec *NodeVecVec_new(int initialSize); /* constructor */
> +void NodeVecVec_delete(NodeVecVec* trash); /* destructor */
> +bool NodeVecVec_insert(NodeVecVec* vector, NodePtrVec* path); /* puts a copy of "path" at the end of the vector */
> +
> +#endif /* VECTORUTILS_H_ */
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/yaml.c
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/yaml.c?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/yaml.c (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/yaml.c Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,133 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * yaml.h
> + *
> + * Created on: Jun 21, 2013
> + * Author: J. Brian Rigdon
> + */
> +
> +#include <stdio.h>
> +#include <time.h>
> +#include <stdlib.h>
> +#include "yaml.h"
> +static FILE *output = NULL;
> +
> +/* This file doesn't yet do a true key/element pair clustering the way YAML is
> + * intended to do. It is currently a minimalistic approach to output the most
> + * important data from the run.
> + */
> +
> +/* In case configuration info isn't passed in... */
> +#ifndef CXXFLAGS
> +#define CXXFLAGS "unknown"
> +#endif
> +#ifndef CXXVERSION
> +#define CXXVERSION "unknown"
> +#endif
> +
> +
> +
> +
> +void YAMLOpen()
> +{
> + time_t rawTime;
> + struct tm *timeinfo = NULL;
> + char *fileName = calloc(200, sizeof(char));
> + char *timeStr = calloc(200, sizeof(char));
> +
> +
> + time(&rawTime);
> + timeinfo = localtime(&rawTime);
> +
> + if ( output != NULL || fileName==NULL || timeStr==NULL || timeinfo == NULL )
> + return;
> +
> + sprintf(fileName, "PathFinder_%d-%d-%d_%d-%d-%d.yaml", timeinfo->tm_year+1900, timeinfo->tm_mon+1,
> + timeinfo->tm_mday, timeinfo->tm_hour, timeinfo->tm_min, timeinfo->tm_sec);
> + sprintf(timeStr, "%d/%d/%d, %d:%d:%d", timeinfo->tm_year+1900, timeinfo->tm_mon+1,
> + timeinfo->tm_mday, timeinfo->tm_hour, timeinfo->tm_min, timeinfo->tm_sec);
> + printf("\nWriting YAML: %s\n\n", fileName);
> +
> + /* static data - no need to free(timeinfo); */
> +
> + output = fopen(fileName, "w");
> + if ( output != NULL )
> + {
> + YAMLWriteString("Mini-Application Name", "PathFinder");
> + YAMLWriteString("Mini-Application Version", "1.0.0");
> + YAMLWriteString("Run Date/Time", timeStr);
> + YAMLWriteString("Compiler Version", CXXVERSION);
> + YAMLWriteString("Compiler Flags", CXXFLAGS);
> +
> +#ifdef MPI
> + YAMLWriteString("MPI", "Yes");
> +#else
> + YAMLWriteString("MPI", "No");
> +#endif
> +#ifdef OPENMP
> + YAMLWriteString("OpenMP", "Yes");
> + YAMLWriteString("Open MP Threads", getenv("OMP_NUM_THREADS"));
> +#else
> + YAMLWriteString("OpenMP", "No");
> +#endif
> +
> + }
> +}
> +
> +void YAMLClose()
> +{
> + if ( output!=NULL )
> + fclose(output);
> +}
> +
> +void YAMLWriteString(char *tag, char *data)
> +{
> + if ( output!=NULL )
> + fprintf(output, "%s: %s\n", tag, data);
> +}
> +
> +void YAMLWriteInt(char *tag, int data)
> +{
> + if ( output!=NULL )
> + fprintf(output, "%s: %i\n", tag, data);
> +}
> +
> +void YAMLWriteDouble(char *tag, double data)
> +{
> + if ( output!=NULL )
> + fprintf(output, "%s: %lf\n", tag, data);
> +}
> +
> +void YAMLWriteFloat(char *tag, float data)
> +{
> + if ( output!=NULL )
> + fprintf(output, "%s: %f\n", tag, data);
> +}
> \ No newline at end of file
>
> Added: test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/yaml.h
> URL: http://llvm.org/viewvc/llvm-project/test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/yaml.h?rev=311413&view=auto
> ==============================================================================
> --- test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/yaml.h (added)
> +++ test-suite/trunk/MultiSource/Benchmarks/DOE-ProxyApps-C/Pathfinder/yaml.h Mon Aug 21 17:38:53 2017
> @@ -0,0 +1,47 @@
> +/*************************************************************************
> + *
> + * PathFinder: finding a series of labeled nodes within a
> + * two-layer directed, cyclic graph.
> + * Copyright (2013) Sandia Corporation
> + *
> + * Copyright (2013) Sandia Corporation. Under the terms of Contract
> + * DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government
> + * retains certain rights in this software.
> + *
> + * This file is part of PathFinder.
> + *
> + * PathFinder is free software: you can redistribute it and/or modify
> + * it under the terms of the GNU Lesser General Public License as
> + * published by the Free Software Foundation, either version 3 of the
> + * License, or (at your option) any later version.
> + *
> + * PathFinder is distributed in the hope that it will be useful,
> + * but WITHOUT ANY WARRANTY; without even the implied warranty of
> + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
> + * GNU General Public License for more details.
> + *
> + * You should have received a copy of the GNU General Public License
> + * along with PathFinder. If not, see <http://www.gnu.org/licenses/>.
> + *
> + * Questions? Contact J. Brian Rigdon (jbrigdo at sandia.gov)
> + *
> + */
> +
> +/*
> + * yaml.h
> + *
> + * Created on: Jun 21, 2013
> + * Author: J. Brian Rigdon
> + */
> +
> + #ifndef YAML_H
> + #define YAML_H
> +
> + void YAMLOpen();
> + void YAMLClose();
> + void YAMLWriteString(char *tag, char *data);
> + void YAMLWriteInt(char *tag, int data);
> + void YAMLWriteDouble(char *tag, double data);
> + void YAMLWriteFloat(char *tag, float data);
> +
> + #endif /* YAML_H */
> \ No newline at end of file
>
>
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