[LLVMbugs] [Bug 3533] New: Add mafft to testsuite

[bugzilla-daemon at cs.uiuc.edu]

http://llvm.org/bugs/show_bug.cgi?id=3533

           Summary: Add mafft to testsuite
           Product: new-bugs
           Version: unspecified
          Platform: PC
               URL: http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-
                    6.624-without-extensions-src.tgz
        OS/Version: Linux
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: new bugs
        AssignedTo: unassignedbugs at nondot.org
        ReportedBy: edwintorok at gmail.com
                CC: llvmbugs at cs.uiuc.edu


I've been looking through the phoronix-testsuite, and found that mafft is quite
easy to compile and run (i.e. simple makefile, no configure).

I compared timings of llvm-gcc (2.5prerelease), and gcc-4.3.3:

gcc -O3:
real    0m19.971s
user    0m19.957s
sys     0m0.012s

llvm-gcc -O3:
real    0m23.793s
user    0m23.785s
sys     0m0.008s

Here is how to build it:
wget
http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.624-without-extensions-src.tgz
wget http://fire-salamander.co.uk/pts-tests/pyruvate_decarboxylase.fasta.bz2
tar xzvf mafft-6.624-without-extensions-src.tgz
bunzip2 pyruvate_decarboxylase.fasta.bz2
cd mafft-6.624-without-extensions/core
make CC="llvm-gcc -O3" -j4
cd ../

time core/pairlocalalign -b 62 -g -0.100 -f -2.00 -h 0.100 -L
<../pyruvate_decarboxylase.fasta
time /core/bfast -b 62 -f -1.53 -h -0.123 -F -l 2.7 -A -X
<../pyruvate_decarboxylase.fasta
time core/dvtditr -F -l 2.7 -z 50 -b 62 -f -1.53 -h -0.123 -I 1 <pre

It is pairlocalalign that is slower on llvm-gcc.

When I'll have some time, I'll try to write a Makefile for the llvm test-suite.


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