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 --------
Sujet: Re: BLAST+ speed & build issues
Date de renvoi : Thu, 4 Aug 2011 09:31:54 +0000 (UTC)
De (renvoi) : debian-...@lists.debian.org
Date : Thu, 04 Aug 2011 11:31:34 +0200
De : Olivier Sallou <olivier.sal...@irisa.fr>
Pour : Tim Booth <ava...@fastmail.fm>
Copie à : debian-...@lists.debian.org, "Aaron M. Ucko" <a...@alum.mit.edu>
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
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