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Hi, we have a package on DebianMed which has performance issue regarding static build vs dynamic link build (latest gcc) Has only impacted compile option is the static vs dynamic choice, has anyone an idea on where we could investigate or how we could speedup this? For info, executable is quite large 11MB (static) vs 2M (dynamic). Dynamic build exe is linked against: osallou@debiansid:/tmp/ncbi-blast-2.2.25+-src/debian/ncbi-blast+/usr/bin$ ldd /usr/bin/blastx linux-vdso.so.1 => (0x00007fffb01a8000) libblastinput.so => /usr/lib/ncbi-blast+/libblastinput.so (0x00007f06d9572000) libncbi_xloader_blastdb.so => /usr/lib/ncbi-blast+/libncbi_xloader_blastdb.so (0x00007f06d9350000) libncbi_xloader_blastdb_rmt.so => /usr/lib/ncbi-blast+/libncbi_xloader_blastdb_rmt.so (0x00007f06d9127000) libxblastformat.so => /usr/lib/ncbi-blast+/libxblastformat.so (0x00007f06d8edd000) libalign_format.so => /usr/lib/ncbi-blast+/libalign_format.so (0x00007f06d8c32000) libblastdb_format.so => /usr/lib/ncbi-blast+/libblastdb_format.so (0x00007f06d8a1a000) libgene_info.so => /usr/lib/ncbi-blast+/libgene_info.so (0x00007f06d8808000) libxalnmgr.so => /usr/lib/ncbi-blast+/libxalnmgr.so (0x00007f06d856a000) libblastxml.so => /usr/lib/ncbi-blast+/libblastxml.so (0x00007f06d8353000) libxcgi.so => /usr/lib/ncbi-blast+/libxcgi.so (0x00007f06d80c8000) libxhtml.so => /usr/lib/ncbi-blast+/libxhtml.so (0x00007f06d7e48000) libxblast.so => /usr/lib/ncbi-blast+/libxblast.so (0x00007f06d7a36000) libxalgoblastdbindex.so => /usr/lib/ncbi-blast+/libxalgoblastdbindex.so (0x00007f06d77fa000) libcomposition_adjustment.so => /usr/lib/ncbi-blast+/libcomposition_adjustment.so (0x00007f06d75e6000) libxalgodustmask.so => /usr/lib/ncbi-blast+/libxalgodustmask.so (0x00007f06d73dd000) libxalgowinmask.so => /usr/lib/ncbi-blast+/libxalgowinmask.so (0x00007f06d718a000) libseqmasks_io.so => /usr/lib/ncbi-blast+/libseqmasks_io.so (0x00007f06d6f7a000) libseqdb.so => /usr/lib/ncbi-blast+/libseqdb.so (0x00007f06d6cb2000) libblast_services.so => /usr/lib/ncbi-blast+/libblast_services.so (0x00007f06d6aa1000) libxobjutil.so => /usr/lib/ncbi-blast+/libxobjutil.so (0x00007f06d67f5000) libxobjread.so => /usr/lib/ncbi-blast+/libxobjread.so (0x00007f06d64de000) libcreaders.so => /usr/lib/ncbi-blast+/libcreaders.so (0x00007f06d62d5000) libxnetblastcli.so => /usr/lib/ncbi-blast+/libxnetblastcli.so (0x00007f06d60c8000) libxnetblast.so => /usr/lib/ncbi-blast+/libxnetblast.so (0x00007f06d5e1b000) libblastdb.so => /usr/lib/ncbi-blast+/libblastdb.so (0x00007f06d5c06000) libscoremat.so => /usr/lib/ncbi-blast+/libscoremat.so (0x00007f06d59e2000) libtables.so => /usr/lib/ncbi-blast+/libtables.so (0x00007f06d57de000) libncbi_xloader_genbank.so => /usr/lib/ncbi-blast+/libncbi_xloader_genbank.so (0x00007f06d55a1000) libncbi_xreader_id1.so => /usr/lib/ncbi-blast+/libncbi_xreader_id1.so (0x00007f06d537b000) libncbi_xreader_id2.so => /usr/lib/ncbi-blast+/libncbi_xreader_id2.so (0x00007f06d5160000) libncbi_xreader_cache.so => /usr/lib/ncbi-blast+/libncbi_xreader_cache.so (0x00007f06d4f2c000) libxconnect.so => /usr/lib/ncbi-blast+/libxconnect.so (0x00007f06d4c94000) libncbi_xreader.so => /usr/lib/ncbi-blast+/libncbi_xreader.so (0x00007f06d49e5000) libid1.so => /usr/lib/ncbi-blast+/libid1.so (0x00007f06d47cb000) libid2.so => /usr/lib/ncbi-blast+/libid2.so (0x00007f06d457e000) libseqsplit.so => /usr/lib/ncbi-blast+/libseqsplit.so (0x00007f06d4324000) libxcompress.so => /usr/lib/ncbi-blast+/libxcompress.so (0x00007f06d40cf000) libxobjmgr.so => /usr/lib/ncbi-blast+/libxobjmgr.so (0x00007f06d3be3000) libgenome_collection.so => /usr/lib/ncbi-blast+/libgenome_collection.so (0x00007f06d3981000) libseqset.so => /usr/lib/ncbi-blast+/libseqset.so (0x00007f06d3762000) libseqedit.so => /usr/lib/ncbi-blast+/libseqedit.so (0x00007f06d3519000) libseq.so => /usr/lib/ncbi-blast+/libseq.so (0x00007f06d2f16000) libseqcode.so => /usr/lib/ncbi-blast+/libseqcode.so (0x00007f06d2d03000) libsequtil.so => /usr/lib/ncbi-blast+/libsequtil.so (0x00007f06d2af2000) libpub.so => /usr/lib/ncbi-blast+/libpub.so (0x00007f06d28d2000) libmedline.so => /usr/lib/ncbi-blast+/libmedline.so (0x00007f06d26b2000) libbiblio.so => /usr/lib/ncbi-blast+/libbiblio.so (0x00007f06d246a000) libgeneral.so => /usr/lib/ncbi-blast+/libgeneral.so (0x00007f06d220c000) libxser.so => /usr/lib/ncbi-blast+/libxser.so (0x00007f06d1ec0000) libxutil.so => /usr/lib/ncbi-blast+/libxutil.so (0x00007f06d1bea000) libxncbi.so => /usr/lib/ncbi-blast+/libxncbi.so (0x00007f06d180e000) libz.so.1 => /usr/lib/libz.so.1 (0x00007f06d15ed000) libbz2.so.1.0 => /lib/libbz2.so.1.0 (0x00007f06d13dd000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f06d11d8000) libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00007f06d0fc0000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f06d0db8000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f06d0b9b000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f06d0891000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f06d060f000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f06d03f8000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f06d0074000) /lib64/ld-linux-x86-64.so.2 (0x00007f06d97e6000) For a simple "-h" call, here is a benchmark: # Static build" osallou@debiansid:/tmp/ncbi-blast-2.2.25+-src/debian/ncbi-blast+/usr/bin$ time bash -c 'for (( c=1; c<=50; c++ )) ; do ./blastx -h > /dev/null ; done' real 0m0.403s user 0m0.292s sys 0m0.124s # Dynamic build osallou@debiansid:/tmp/ncbi-blast-2.2.25+-src/debian/ncbi-blast+/usr/bin$ time bash -c 'for (( c=1; c<=50; c++ )) ; do blastx -h > /dev/null ; done' real 0m8.002s user 0m4.200s sys 0m3.856s -------- Message original --------
Hi, I quickly build the ncbi-blast+ locally with static build using the debian build process, and indeed, static build binaries are much faster (blastx -h) than dynamically linked ones. I will investigate if there is a way to speedup this. Or if anyone has ideas.... Olivier Le 8/3/11 10:48 AM, Tim Booth a écrit : > time bash -c 'for (( c=1; c<=50; c++ )) ; do ~/tings/ncbi-blast-2.2.25+/bin/blastx -h > /dev/null ; done' -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-REQUEST@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org Archive: http://lists.debian.org/4E3A66F6.7040008@irisa.fr |