[
¥È¥Ã¥×
] [
¿·µ¬
|
°ìÍ÷
|
ñ¸ì¸¡º÷
|
ºÇ½ª¹¹¿·
|
¥Ø¥ë¥×
]
³«»Ï¹Ô:
[[¥Î¡¼¥È/¥Î¡¼¥È]]
**2009-07-03¡¡À¸Ì¿²Ê³Ø·Ï¤Î¥×¥í¥°¥é¥à¤ÎÊÂÎó²½¤ÎÆ°¸þ [#uec93f29]
¤¤¤¯¤Ä¤«¤Î¥Ú¡¼¥¸¤¬ÌÌÇò¤«¤Ã¤¿¤Î¤Ç¡¢¥ê¥ó¥¯¤ò»Ä¤·¤Æ¤ª¤³¤¦~
GPGPU & CHARMM ¤Ç¸¡º÷
-[[March 11, 2009¡¡¡¡Accelerating Life Science and Bioinformatics Applications¡ÄAs if Our Lives Depended on IT:http://www.hpcwire.com/topic/applications/Accelerating-Life-Science-and-Bioinformatics-Applications-41122667.html?viewAll=y]]¡¡¡¡ÆÃ¤ËFloating Point Solutions with GPGPU and Cell Co-Processors¤Î¹à¡£¡¡GPGPU¤ÎÎã¤Ç¤ÏNAMD (NAnoscale Molecular Dynamics), VMD (Visual Molecular Dynamics), and CHARMM (Chemistry at Harvard Macromolecular Mechanics).¡¡¡¡Cell¤ÎÎã¤Ç¤ÏGROMACS (GROningen Machine for Chemical Simulations), a protein folding code that unlocks the mystery of protein assembly and its relationship to cancers, Parkinson's disease and Alzheimer's.¡¡¤¬µó¤²¤é¤ì¤Æ¤¤¤ë
-[[U-Del¤ÎCS³ØÀ¸Project¡¡CISC849 - 011:http://gcl.cis.udel.edu/courses/cisc849011_sp08/project.php]]¡¡[[¥Þ¥Æ¥ê¥¢¥ë¤Ï¤³¤³:http://gcl.cis.udel.edu/courses/cisc849011_sp08/project_wesandnabeel.pdf]]
-[[GPU Computing 3.0:http://www.ece.neu.edu/groups/nucar/GPGPU/GPGPU-2/Luebke.pdf]]¡¡¤Î41¥Ú¡¼¥¸¡¢46¥Ú¡¼¥¸
-U-Del¤ÎJoe Davis¤é¤Î¥Ú¡¼¥¸[[Towards Large-Scale Molecule Dynamics Simulations on Graphics Processors:http://www.imagwiki.org/mediawiki/images/e/e7/08_IMAG_TauferDavis.pdf]]¡¡11¥Ú¡¼¥¸¡¢14¥Ú¡¼¥¸¡¢19¥Ú¡¼¥¸
-[[HaRiken "Harvard/Riken GPGPU Symposium 2008":http://sites.google.com/a/aspuru.com/hariken-08/HaRiken-Abstracts]]
-[[Genome Web ¡Á Genome Technology¡§Not Just for Kids Anymore (September 2007):http://www.genomeweb.com/not-just-kids-anymore-0]]¡¡¡¡VMD, NAMD, CHARMM
-[[SC07 High Performance Computing with CUDA ¡Á Case Study: ¡Á Molecular Dynamics:http://gpgpu.org/static/sc2007/SC07_CUDA_7_NAMD_Phillips.pdf]]
-ËÜ(Springer LNCS) [[Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors:http://www.springerlink.com/content/757u77211847v755/]]
-[[Stream Computing for GPU-Accelerated HPC Applications (April 6th, 2009):http://www.browndeertechnology.com/docs/BDT_GPU_HPC_APPS_20090406.pdf]]
-[[Scalable molecular dynamics with NAMD.:http://www.citeulike.org/user/grondina/article/449842]] J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1781-1802.
-[[2009 Symposium on Application Accelerators in High Performance Computing (SAAHPC'09):http://saahpc.ncsa.illinois.edu/agenda.html]]
-[[Ë̳¤Æ»Âç³Ø Âç³Ø±¡¾ðÊó²Ê³Ø¸¦µæ²Ê À¸Ì¿¿Í´Ö²Ê³ØÀì¹¶¡¡¥Ð¥¤¥ª¥¤¥ó¥Õ¥©¥Þ¥Æ¥£¥¯¥¹¹ÖºÂ ¹½Â¤¥Ð¥¤¥ª¾ðÊó²Ê³Ø¸¦µæ¼¼:http://ibio.jp/index.php]]
IBM Cell & CHARMM¤Ç¸¡º÷
-PPT [[Studying Protein Folding on the Grid: Experiences Using CHARMM on NPACI Resources under Legion:http://legion.virginia.edu/presentations/HPDC-Aug2001.ppt]]
-Paper [[Studying protein folding on the grid: experiences using CHARMM onNPACI resources under Legion:http://ieeexplore.ieee.org/Xplore/login.jsp?url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F7513%2F20446%2F00945172.pdf%3Farnumber%3D945172&authDecision=-203]]
-[[Protein folding with Charmm on Legion:http://www.hoise.com/primeur/01/articles/weekly/AE-PR-04-01-27.html]] San Diego 07 March 2001
-[[Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion:http://www.cs.virginia.edu/papers/Studying_Protein_Folding.pdf]] (CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE, January 2004)
-[[MD Benchmarks for Amber, CHARMM and NAMD:http://ambermd.org/amber8.bench2.html]] (latest update: April, 2005)
NAMD¤Î¥Û¡¼¥à¥Ú¡¼¥¸
-[[NAMD - Scalable Molecular Dynamics:http://www.ks.uiuc.edu/Research/namd/]]~
¤³¤ÎHP¤è¤ê~
NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling. ~
²¿¤»University of Illinois at Urbana Champeign¤À¤«¤é¡£
**2009-06-16 Äɵ ¡Ê¥Þ¥ë¥Á¥³¥¢¤ÈÊÂÎó¥×¥í¥°¥é¥ß¥ó¥°¡Ë [#ucb1d184]
-Sourceforge magazine µ»ö¡¡[[¥½¥Õ¥È¥¦¥§¥¢¹â®²½¤Î¸°¤Ï¡ÖÊÂÎ󲽡ס§¤¤¤ÞÃíÌܤµ¤ì¤ëÊÂÎó²½µ»½Ñ¤òÃΤë:http://sourceforge.jp/magazine/09/05/15/0930226]]¡¡¤Ë¡¢¥Þ¥ë¥Á¥³¥¢´Ä¶¤Ç¤ÎÊÂÎ󥽥եȵ»½Ñ¤ÎɬÍ×À¤òÀ⤯µ»ö¡£
-[[¾ðÊó½èÍý³Ø²ñ»ï¡Ö¾ðÊó½èÍý¡×2008ǯ12·î¹æ¡¡(Vol.49, No.12¡Ë¡ÖÆÃ½¸¡§¡¡¥Þ¥ë¥Á¥³¥¢¤òÀ¸¤«¤¹¤ª¼ê·ÚÊÂÎó¥×¥í¥°¥é¥ß¥ó¥°¡×:http://fw8.bookpark.ne.jp/cm/ipsj/mokuji.asp?category1=Magazine&vol=49&no=12]]¡¡¤Ç¥Þ¥ë¥Á¥³¥¢´Ä¶¤Ç¤ÎÊÂÎ󥽥եȵ»½Ñ¤ÎɬÍ×À¤òµÄÏÀ¤·¤Æ¤¤¤¿¡£
**2007-04-16 [#s72987f3]
¤³¤Î¸¦µæ¤Ï¡¢ÅöÌִ̡ÏÀ¥ì¥Ù¥ë¡×¡£²¿¤«¿·¤·¤¤¤³¤È¤¬½Ð¤Æ¤¯¤ë¤«¤É¤¦¤«¤Ï
¤Þ¤À¤ï¤«¤é¤Ê¤¤¡£
***²¿¤ò¤ä¤ë¤Î¤« [#jdbafa4a]
¤ä¤ê¤¿¤¤¤³¤È¡§¡¡¸½ºß¥³¥ó¥Ô¥å¡¼¥¿¤Ç¡ÊľÎó¤Ë¡Ë½èÍý¤µ¤ì¤Æ¤¤¤ë¤¿¤á¤Ë¡¢»þ´Ö¤¬¤«¤«¤Ã¤Æ¡Öº¤¤ë¡×¤è¤¦¤ÊÌäÂ꤬¤¢¤ë¡£¤½¤ì¤òÊÂÎó¼Â¹Ô¤·¤Æ¡¢Á᤯¤¹¤ë¡£
ÇØ·Ê¡§¡¡(1)¡Ö¥Þ¥ë¥Á¥³¥¢¡×¤Î£Ã£Ð£Õ¤¬¼ê¤´¤í¤ÊÃÍÃʤǼê¤ËÆþ¤ë¤è¤¦¤Ë¤Ê¤Ã¤¿¡£¡Ê£´¥³¥¢¤À¤È£´ÊÂÎó¡¢£¸¥³¥¢¤À¤È£¸ÊÂÎ󡢤«¤±¤ë¡¡£Ã£Ð£Õ¿ô¡Ê£²¤Ä¤È¤«£´¤Ä¤È¤«¡Ë¡Ë~
¡¡¡¡¡¡¡¡(2)Âç³Ø¤Ë¤¢¤ë£Ð£Ã¶µ¼¼¤Î£Ð£Ã¤ò¡¢¶õ¤¤¤Æ¤¤¤ë»þ´Ö¤Ë»È¤Ã¤Æ¡¢ÊÂÎó¼Â¹Ô¤Ç¤¤ë¡£¡Ê£¹£°Âæ»È¤¨¤ì¤Ð£¹£°ÊÂÎó¡Ë
Àè¹Ô¸¦µæ¡§¡¡»³¤Î¤è¤¦¤Ë¤¢¤ë¡£ÊÂÎó½èÍý¤Ï¸Å¤¯¤«¤é¤ÎÏÃÂê¡£~
¡¡¥Ý¥¤¥ó¥È£±¡§¡¡£ÎÂæ¤Î£Ã£Ð£Õ¤¬¤¢¤Ã¤¿¤È¤·¤Æ¤â¡¢¤Ê¤«¤Ê¤«£ÎÇÜ®¤¯¤Ê¤é¤Ê¤¤~
¡¡¡¡¡¡¡¡¡Ê¼Â¤Ïº£¤Þ¤Ç¤ÏÊÂÎó¤Ç²Ô¤°¤è¤ê£Ã£Ð£Õ¥¯¥í¥Ã¥¯¤ò²Ã®¤¹¤ëÊý¤¬´Êñ¤Ç°Â¤«¤Ã¤¿¡Ë~
¡¡¡¡¡¡¡¡¤É¤ì¤À¤±Â®¤¯¤Ê¤ë¤«¤Ï¡¢¥×¥í¥°¥é¥à¤ÎÀ¼Á¤Ë¤è¤ë¡£¤³¤Î¤¢¤¿¤ê¤Î¸¦µæ¤Ï¤¿¤¯¤µ¤ó¤¢¤ë¡£~
¡¡¡¡¡¡¡¡´û¤ËÊÂÎ󲽤µ¤ì¤Æ¤¤¤ë¥×¥í¥°¥é¥à¤â¤¤¤¯¤Ä¤«¡Ê¤«¤Ê¤ê¤¿¤¯¤µ¤ó¡Ë¤¢¤ë¡£~
¡¡¥Ý¥¤¥ó¥È£²¡§¡¡¡ÖÊÂÎ󲽡פϿͼêvs¼«Æ°¤¬¤¢¤ê¡¢¿Í¼ê¤Ï°ìÈ̤ˤÏÂçÊÑ¡£¡Ê¾ÊýÌäÂê¤Ë¤è¤Ã¤Æ¤Ï¼«ÌÀ¤Ê¤â¤Î¤â¿¤¤¡Ë¡¡¼«Æ°²½¤Ïº£¤Ç¤â¸¦µæ¥Í¥¿¡Ê¤¿¤È¤¨¤ÐµÈÅĸ¦¡Ë~
¤â¤¦°ìÅÙ¡Ö¤ä¤ê¤¿¤¤¤³¤È¡×¡§¡¡¤È¤Ë¤«¤¯ÊÂÎó¤Ë¤·¤ÆÂ®¤¯¤Ç¤¤ëÌäÂê¤òÊÂÎó¼Â¹Ô¤·¤Æ¡¢Ìò¤ËΩ¤Ã¤Æ¤ß¤¿¤¤¡£
***´Ä¶¤Ê¤É [#bc6277f8]
´Ä¶¡§¡¡ºòǯÅÙËö¤ËÇã¤Ã¤¿£È£Ð¤Î¥µ¡¼¥Ð¡¼¤Ï£´¥³¥¢¡ß£²£Ã£Ð£Õ¤Ç£¸ÊÂÎó²Äǽ¡£
£Ï£Ó¡§¡¡Linux¤ò¥¤¥ó¥¹¥È¡¼¥ëºÑ¤ß¡£¥×¥í¥»¥¹¥ì¥Ù¥ë¤ÎÊÂÎó½èÍý¤Ï´û¤Ë²Äǽ¡£¸å¤ÇÎã¤ò¼¨¤¹¡£
ÊÂÎó¥ß¥É¥ë¥¦¥§¥¢¡§¡¡¥×¥í¥°¥é¥à¤òÊÂÎóʬ³ä¤·¡¢´Êñ¤Ë¼Â¹Ô¤µ¤»¤é¤ì¤ë¥×¥é¥Ã¥È¥Õ¥©¡¼¥à¡Ê¥ß¥É¥ë¥¦¥§¥¢¡Ë¤¬¤¤¤¯¤Ä¤«¤¢¤ë¡£ÂçÊ̤¹¤ë¤È~
¡¡¡¡¶¦Í¥á¥â¥ê·¿¡ÊÊÑ¿ô¶¦Í·¿¡Ë¥â¥Ç¥ë¡§¡¡¥ß¥É¥ë¥¦¥§¥¢¤È¤·¤ÆOpenMP¤¬Í̾¡£~
¡¡¡¡¥á¥Ã¥»¡¼¥¸¸ò´¹·¿¥â¥Ç¥ë¡§¡¡¥¤¥ó¥¿¡¼¥Õ¥§¡¼¥¹¤È¤·¤ÆMPI¤¬¤¢¤ê¡¢¤½¤Î¼ÂÁõ¤È¤·¤Æ¥Õ¥ê¡¼¤ÎMPICH/MPICH2¤¬¤¢¤ë¡£~
¥â¥Ç¥ë¤È¤·¤ÆÈæ³Ó¤¹¤ë¤È¡¢¶¦Í¥â¥Ç¥ë¤ÏÌ©¤ÊÁê¸ßºîÍѡʺÙγÅÙ¤ÎÊÂÎó¡Ë¤¬²Äǽ¤Ê¤Î¤È¡¢¥³¥ó¥Ñ¥¤¥é¤¬¼«Æ°ÊÂÎ󲽤¹¤ë¤è¤¦¤Ê¤³¤È¤¬²Äǽ¡£¤¿¤È¤¨¤ÐIntel¤Î¥³¥ó¥Ñ¥¤¥é¤Î-parallel¥ª¥×¥·¥ç¥ó¡£¥Ï¡¼¥É¥¦¥§¥¢¤ÎÀ©Ì󤫤éÊÂÎóÅ٤Ϥ½¤ì¤Û¤ÉÂ礤¯¤Ê¤é¤Ê¤¤¡Ê¤»¤¤¤¼¤¤¿ô½½¡Ë~
¥á¥Ã¥»¡¼¥¸¥â¥Ç¥ë¤Ï¥á¥Ã¥»¡¼¥¸¸ò´¹¤Ë»þ´Ö¤¬¤«¤«¤ë¤Î¤ÇÁ¤ÊÁê¸ßºîÍÑ¡ÊÂçγÅÙ¤ÎÊÂÎó¡Ë¤Ë¸þ¤¯¡£¤½¤ÎÂå¤ï¤êÊÂÎóÅÙ¤ÏÂ礤¯½ÐÍè¤ë¡£¡ÊTCP/IP¤ò»È¤¦¤Î¤¬Î®¹Ô¤À¤¬¡¢¤½¤ì¤À¤È¤Û¤È¤ó¤É̵¸Â¤Þ¤Ç²Äǽ¡£À¤³¦Ãæ¤Î¥³¥ó¥Ô¥å¡¼¥¿¤ò¤Ä¤Ê¤°¤³¤È¤â²Äǽ¡£¡Ë¥Í¥Ã¥È¥ï¡¼¥¯ÃÙ±ä¤òû½Ì¤¹¤ë¹©ÉפâÀΤ¢¤Ã¤¿¡ÊMyrinet¤¬Í̾¡Ë¡£¥®¥¬¥Ó¥Ã¥È¥¤¡¼¥µ¤Î¾ì¹ç¡¢Å¾Á÷¤ÏÁᤤ¤¬¥»¥Ã¥È¥¢¥Ã¥×¤Ë»þ´Ö¤¬¤«¤«¤ë¤È¸À¤ï¤ì¤ë¡£~
¤³¤ÎÊդε½Ò¤Ø¤Î¥Ý¥¤¥ó¥¿¤ò¤³¤³¤Ëµó¤²¤ë
-¾ðÊó½èÍý¤Îµ»ö[[¥Þ¥ë¥Á¥³¥¢¤Ë¤ª¤±¤ë¥×¥í¥°¥é¥ß¥ó¥°(<ÆÃ½¸>¥Þ¥ë¥Á¥³¥¢¤Ë¤ª¤±¤ë¥½¥Õ¥È¥¦¥§¥¢):http://ci.nii.ac.jp/naid/10016924240/]]
-[[¥Þ¥ë¥Á¥³¥¢CPU¤Î²¸·Ã¤òµý¼õ¤¹¤ëÊýË¡:http://www.hpc.co.jp/hit/support/multicore.html]]¡¡²¿¤È¤³¤ì¤ÎºÇ½é¤ÎÈæ³Ó¤ÏBLAST¤À¤Ã¤¿
-Àд¬À콤Âç³Ø¤Î¼ø¶È¡¡[[¾ðÊóÅŻҹ©³ØÆÃÊ̲ÊÌÜ· ÆÃ¼ì¹ÖµÁ¡Ê¸å´ü¡Ë:http://hyperion.ie.isenshu-u.ac.jp/ecc/sample/presentation/mitou_1.ppt]]
-¶µ²Ê½ñ¡¡[[¥Þ¥ë¥Á¥³¥¢CPU¤Î¤¿¤á¤ÎÊÂÎó¥×¥í¥°¥é¥ß¥ó¥°¡½ÊÂÎó½èÍý&¥Þ¥ë¥Á¥¹¥ì¥Ã¥ÉÆþÌç (ñ¹ÔËÜ) :http://www.amazon.co.jp/%E3%83%9E%E3%83%AB%E3%83%81%E3%82%B3%E3%82%A2CPU%E3%81%AE%E3%81%9F%E3%82%81%E3%81%AE%E4%B8%A6%E5%88%97%E3%83%97%E3%83%AD%E3%82%B0%E3%83%A9%E3%83%9F%E3%83%B3%E3%82%B0%E2%80%95%E4%B8%A6%E5%88%97%E5%87%A6%E7%90%86-%E3%83%9E%E3%83%AB%E3%83%81%E3%82%B9%E3%83%AC%E3%83%83%E3%83%89%E5%85%A5%E9%96%80-%E5%AE%89%E7%94%B0-%E7%B5%B9%E5%AD%90/dp/4798014621]]~
Amazon¤Ç¤ÎɾȽ¤Ï°¤¤¤ß¤¿¤¤¡¡
-Ãμ±¡§¡¡MPI vs OpenMP = OpenMP¤Ï¥á¥â¥ê¶¦Í·¿¤Î¥Þ¥ë¥Á¥×¥í¥»¥Ã¥µÂбþ¤Î¥ß¥É¥ë¥¦¥§¥¢ vs MPI¤Ï(TCP/IP¤ò»È¤Ã¤¿¡Ë¥á¥Ã¥»¡¼¥¸¥Ñ¥·¥ó¥°·¿¤Î¥ß¥É¥ë¥¦¥§¥¢¡£¥á¥â¥ê¶¦Í·¿¤ÏCPU¿ô¤Ë¾å¸Â¤¢¤ë¤¬¥á¥Ã¥»¡¼¥¸·¿¤ÏÂ礤¯½ÐÍè¤ë¡£¤½¤ÎÂå¤ï¤ê¡¢¥á¥â¥ê¶¦Í·¿¤Ï¥Ç¡¼¥¿¸ò´¹¤¬Â®¤¤¤¬¥á¥Ã¥»¡¼¥¸Êý¤ÏÃÙ¤¤¡£
-[[¥Þ¥ë¥Á¥³¥¢CPU¤Î²¸·Ã¤òµý¼õ¤¹¤ëÊýË¡:http://www.hpc.co.jp/hit/support/multicore.html]]¡¡¤Ë¤è¤ë¤È¡¢
--¡¡1 ¥¤¥ó¥Æ¥ë¥³¥ó¥Ñ¥¤¥é¤Î -parallel ¥ª¥×¥·¥ç¥ó¤ò»È¤Ã¤ÆÊÂÎ󲽤¹¤ëÊýË¡¡Ä¥½¡¼¥¹¥³¡¼¥ÉÊѹ¹ÉÔÍ×
--¡¡2 Intel¤Î¿ôÃͱ黻¥é¥¤¥Ö¥é¥ê¤ò»È¤Ã¤ÆÊÂÎ󲽤¹¤ëÊýË¡¡ÄÊÂÎ󲽤µ¤ì¤¿¥é¥¤¥Ö¥é¥ê¤ò¸Æ¤Ó½Ð¤»¤Ð¹âÀǽ²½
--¡¡3 OpenMP¤ò»È¤Ã¤ÆÊÂÎ󲽤¹¤ëÊýË¡¡ÄÊÂÎ󲽤·¤¿¤¤Éôʬ¤ËOpenMP¥Ç¥£¥ì¥¯¥Æ¥£¥Ö¡Ê»Ø¼¨¹Ô¡Ë¤òÆþ¤ì¤ë
--¡¡4 MPI¤ò»È¤Ã¤ÆÊÂÎ󲽤¹¤ëÊýË¡¡ÄMPI²½¤ÏÆñ°×ÅÙ¤¬¹â¤¤~
Æñ°×ÅÙ¤¬¹â¤¤¤È¸À¤¦Íýͳ¤Ï¡¢¥¤¥ó¥Æ¥ë¥³¥ó¥Ñ¥¤¥é¤À¤È¼«Æ°ÊÂÎ󲽤ò¤·¤Æ¤¯¤ì¤ë¤Î¤ËÂФ·¡¢MPI²½¤Ï¼«Ê¬¤ÇÊÂÎ󲽤·¤Ê¤±¤ì¤Ð¤Ê¤é¤Ê¤¤¤«¤é¡£~
¤½¤ì¤Ç¤â¡¢¤¤¤¯¤Ä¤«¤Î¥Æ¥¥¹¥È¤¬¾Ò²ð¤µ¤ì¤Æ¤¤¤ë¡£~
¡¡¡¡¡¡[[Íý¸¦¤Ç¥¹¥Ñ¥³¥ó¹Ö½¬²ñ¤Ë»È¤Ã¤¿¥Æ¥¥¹¥È:http://accc.riken.jp/HPC/training/text.html]]~
¡¡¡¡¡¡[[¡ÖMPIÊÂÎó¥×¥í¥°¥é¥ß¥ó¥°¡×:http://www.hpc.co.jp/hit/B-DEV/MPI-01.htm]](2001ǯ)~
***¥ì¥Ù¥ë¡Ý£±¤ÎͽÈ÷¼Â¸³~ [#bfbf7f32]
ÀÞ³ÑÇã¤Ã¤¿¥µ¡¼¥Ð¡¼¤Ê¤Î¤Ç¡¢ËÜÅö¤ËÊÂÎó¼Â¹Ô¤Ç¤¤ë¤«»î¤·¤Æ¤ß¤¿¡£~
CPU¤Ç¤Î»Å»ö¤À¤±¡Ê¤Û¤È¤ó¤É¡¢¤À¤¬¡Ë¤ò¤¹¤ë¥×¥í¥°¥é¥à¤òºî¤ë¡£²¿¤Ç¤â¤¤¤¤¤¬¡¢Í¾¤ê¤Ë¼«ÌÀ¤Ê¥×¥í¥°¥é¥à¤À¤È¥³¥ó¥Ñ¥¤¥é¤¬¸¤¤¤Î¤ÇÌ¿Îá¤òºÇŬ²½¡á¾Ê¤¤¤Æ¤·¤Þ¤¦¤Î¤ÇÍ×Ãí°Õ¡£¥×¥í¥°¥é¥à¤Ï~
#include <math.h>
#include <stdio.h>
#include <unistd.h>
#include <string.h>
main(int argc, char **argv) {
int i, maxi;
double x;
char bufin[256];
if (argc !=2) {
fprintf(stderr, "usage: paratest <maxi>. maxi=~~10000000\n");
} else {
maxi = atoi(argv[1]);
if (maxi<=0) {
fprintf(stderr, "maxi <= 0\n");
}
}
for (i=0; i<255; i++) bufin[i]='\0';
x = 0.0;
for (i=0; i<maxi; i++) {
x = x + sin( (double) i/maxi );
}
read(0, bufin, 256);
printf("%s", strcat(bufin, "a"));
fprintf(stderr, "%s", strcat(bufin, "a"));
}
¥³¥ó¥Ñ¥¤¥ë»þ¤Ë-lm¤¬É¬Íס£¡ÊMath Library¤ò»È¤Ã¤Æ¤¤¤ë¤¿¤á¡Ë
¤³¤Î¥×¥í¥°¥é¥à¤ò¥×¥í¥»¥¹¤È¤·¤Æ¡¢ÊÂÎó¼Â¹Ô¤µ¤»¤Æ¤ß¤ë¡£¥·¥§¥ë¥ì¥Ù¥ë¤ÇÊÂÎ󵝯°¡¢¤Ä¤Þ¤êcshell¤Ç¤Î¡Ö&¡×¤ä¡Ö|¡×¤ò»È¤¦¡£ºÇ½é¤Ë¡Ö&¡×¤ò»î¤·¤¿¤¬¡¢½ªÎ»¤¬È½Äꤷ¤Ë¤¯¤¤¤Î¤Ç¡¢¡Ö|¡×¡Ê¥Ñ¥¤¥×¡Ë¤ò»È¤¦¤³¤È¤Ë¤¹¤ë¡£~
·è¤á¤¿¿ô¤Î¥×¥í¥»¥¹¤ò¥Ñ¥¤¥×¤Ç¤Ä¤Ê¤¤¤ÇÊÂÎó¤Ëµ¯Æ°¤¹¤ë¡£ºÇ¸å¤Ë¥Ñ¥¤¥×¤òÄ̤¸¤Æ¥á¥Ã¥»¡¼¥¸¤¬ºÇ¸å¤Î¥×¥í¥»¥¹¤Ë¹Ô¤Ã夤¤Æ¡¢½ªÎ»¤¬¤ï¤«¤ë¡£¤³¤Î¥·¥§¥ë¥¹¥¯¥ê¥×¥È¤Ï~
#!/bin/csh
set N = 100000000
# Case of 8 processes
echo "" | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $ N | pipebody $N | pipebody $N
# Case of 12 processes
#echo "" | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pebody $N | pipebody $N
# Case of 1 process
#echo "" | pipebody $N
¤Î¤è¤¦¤Ë½ñ¤¤¤¿¡£
¤³¤ì¤ò¼Â¹Ô¤µ¤»¤ë»þ¤Ë¡¢¥³¥Þ¥ó¥Étime¤ò»È¤¦¡£ºÇ¶á¤ÎLinux¤Îtime¥³¥Þ¥ó¥É¤Ï¡¢~
The default format string is
%Uuser %Ssystem %Eelapsed %PCPU (%Xtext+%Ddata %Mmax)k
%Iinputs+%Ooutputs (%Fmajor+%Rminor)pagefaults %Wswaps
¤È¤¤¤¦¤³¤È¤Ç¡¢ÀΤʤ¬¤é¤Î real ... user ... sys ... ¤È¤¤¤¦·Á¼°¤Ç¤Ê¤¤¤¬¡¢µÑ¤Ã¤Æ¾ðÊó¤Ïʬ¤«¤ê¤ä¤¹¤¤¡£
·ë²Ì¤Ï¼¡¤Î¤è¤¦¤Ë¤Ê¤Ã¤¿¡£~
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ user system elapsed PCPU~
¥×¥í¥»¥¹£±¤Ä¡§¡¡¡¡ 9.720u 0.028s 0:09.74 100.0% 0+0k 0+0io 0pf+0w~
¥×¥í¥»¥¹£´¤Ä¡§¡¡¡¡38.814u 0.036s 0:09.75 398.3% 0+0k 0+0io 0pf+0w~
¥×¥í¥»¥¹£¸¤Ä¡§¡¡¡¡77.476u 0.020s 0:09.76 793.9% 0+0k 0+0io 0pf+0w~
¥×¥í¥»¥¹£¹¤Ä¡§¡¡¡¡87.301u 0.040s 0:14.62 597.4% 0+0k 0+0io 0pf+0w~
¥×¥í¥»¥¹£±£²¡§¡¡¡¡116.407u 0.028s 0:15.93 730.8% 0+0k 0+0io 0pf+0w~
¥×¥í¥»¥¹£±£¶¡§¡¡¡¡155.189u 0.044s 0:19.54 794.3% 0+0k 0+0io 0pf+0w
¤³¤Î´Ä¶¤Ç¤Ï£±¤Ä¤Î¥×¥í¥»¥¹¤¬¿©¤¦£Ã£Ð£Õ»þ´Ö¤Ï9.72ÉÃÄøÅ٤Ǥ¢¤ê¡¢¥×¥í¥»¥¹¿ô¤ò£±¢Í£´¢Í£¸¤Þ¤ÇÁý¤ä¤·¤¿»þ¤Ëuser time¡Ê¡á¥×¥í¥»¥¹Áí»þ´Ö¡Ë¤Ï38.81Éáá4¡ß9.70Éá¢77.48Éáá8¡ß9.685¤Î¤è¤¦¤ËÁý¤¨¤Æ¤¤¤ë¤¬¡¢elapsed time¡Ê¡áüËö¤Ç¸«¤Æ¤¤¤ë»þ´Ö¡Ë¤Ï£³¤Ä¤È¤â9.74¡Á9.76ÉäǤۤȤó¤ÉÊѤï¤é¤Ê¤¤¡£¤Ä¤Þ¤ê£¸ÊÂÎó¤Þ¤Ç¼Â¸½¤Ç¤¤Æ¤¤¤ë¡£¤½¤Î¤È¤¤ÎCPU percentage (PCPU) ¤Ï398.3% 793.9%¤È¡¢¤Û¤È¤ó¤ÉÊÂÎóÅÙ¤ÈÆ±¤¸Ãͤò¼¨¤·¤Æ¤¤¤ë¡£
¤È¤³¤í¤¬¡¢£¹¥×¥í¥»¥¹¤ò±Û¤¨¤¿¤È¤³¤í¤Ç¡¢£¹¤ÄÌÜ¤Î¥×¥í¥»¥¹¤Ï;¤Ã¤Æ¤·¤Þ¤¤¸å¤«¤é¼Â¹Ô¤µ¤ì¤ë¤ï¤±¤Ç¡¢¼ÂºÝ elapsed time ¤¬¡Ê9.75É䫤é¡Ë14.6Éä˿¤Ó¤Æ¤¤¤ë¡£´°Á´¤Ë£²Çܤˤʤé¤Ê¤¤Íýͳ¤Ï¡¢¤ª¤½¤é¤¯³°Â¦¤Î¥ª¡¼¥Ð¡¼¥Ø¥Ã¥É¤¬¤¢¤ë¤¿¤á¤À¤í¤¦¡£¤½¤·¤Æ¡¢£¹¥×¥í¥»¥¹¢Í£±£²¥×¥í¥»¥¹¢Í£±£¶¥×¥í¥»¥¹¤ÈÁý¤ä¤·¤Æ¤â elapsed time ¤Ï¿¾¯Áý¤¨¤ë¤À¤±¤ÇÇÜÁý¤Ï¤·¤Æ¤¤¤Ê¤¤ 14.6ÉâÍ15.9ÉâÍ19.5Éáʣ±£¶¤Î¾ì¹ç¿¾¯Èù̯¤«¤â¡£Âç¾æÉפ«¤Ê¡©¡Ë
¤È¤¤¤¦¤³¤È¤«¤é¡¢£¸ÊÂÎ󤬼¸½¤µ¤ì¤Æ¤¤¤ë¤é¤·¤¤¤³¤È¤Ïʬ¤«¤Ã¤¿¡£
***¼¡¤Î¥¹¥Æ¥Ã¥× [#yb5bcea8]
¹Í¤¨¤é¤ì¤ëÊý¸þ¤È¤·¤Æ¡¢
-Intel¤Î¥³¥ó¥Ñ¥¤¥é¤Î¼«Æ°ÊÂÎó²½µ¡Ç½¤¬»È¤¨¤ë¤«»î¤·¤¿¾å¤Ç¡¢ËܳÊŪ¤Ê¥×¥í¥°¥é¥à¤òÊÂÎó¼Â¹Ô¤·¤Æ¤ß¤ë¡£¡Ê¤ä¤Ã¤Æ¤ß¤ë¡¢¤È¤¤¤¦¥ì¥Ù¥ë¤Ç¶½Ì£¤¢¤ê¡£¤½¤ÎÄøÅÙ¡Ë
-OpenMP¤òÆþ¤ì¤Æ¡¢¤¤¤¸¤Ã¤Æ¤ß¤ë¡£¡Ê¤ä¤Ã¤Æ¤ß¤ë¤È¤¤¤¦¥ì¥Ù¥ë¤«¤Ê¡£µÈÅĸ¦¤È°ì½ï¤Ë¤ä¤ë¤È¤¤¤¤¤«¤â¡ËOpenMP¤À¤È¥á¥â¥ê¶¦Í·¿¤Î¤ß¤Ê¤Î¤Ç¡¢¼Â½¬¼¼¤ÎPC¤ò·Ò¤°¤È¤¤¤¦Êý¸þ¤Ï̵¤¯¤Ê¤ë¤À¤í¤¦¡£
-MPICH2¤òÆþ¤ì¤Æ¡¢¤¤¤¸¤Ã¤Æ¤ß¤ë¡£
-ÎãÂê¥×¥í¥°¥é¥à¤òÀ¸ÊªÊ¬»Ò²Ê¤«¤é¤â¤é¤¨¤ë²ÄǽÀ¤¬¤¢¤ë¤Î¤Ç¡¢¤½¤ì¤ò»î¤·¤Æ¤ß¤¿¤¤¡£¥¿¥ó¥Ñ¥¯¼Á¤ÎXÀþ²óÀޤˤè¤ë²òÀϤò¤¹¤ë¤¿¤á¤Î¥×¥í¥°¥é¥à¤é¤·¤¤¡£¾ÜºÙ¤Ï¤Þ¤À¡£Ïäˤè¤ë¤È¡¢·×»»¤ÏÃͤòÊѤ¨¤Æ·«¤êÊÖ¤·¤Æ·×»»¤¹¤ë¤À¤±¤Ê¤Î¤Ç¡¢¤½¤ì¤Ê¤é¤ÐÊÂÎ󤨤Îʬ³ä¤Ï¤Û¤Ü¼«ÌÀ¤Î¤Ï¤º¡£
½ªÎ»¹Ô:
[[¥Î¡¼¥È/¥Î¡¼¥È]]
**2009-07-03¡¡À¸Ì¿²Ê³Ø·Ï¤Î¥×¥í¥°¥é¥à¤ÎÊÂÎó²½¤ÎÆ°¸þ [#uec93f29]
¤¤¤¯¤Ä¤«¤Î¥Ú¡¼¥¸¤¬ÌÌÇò¤«¤Ã¤¿¤Î¤Ç¡¢¥ê¥ó¥¯¤ò»Ä¤·¤Æ¤ª¤³¤¦~
GPGPU & CHARMM ¤Ç¸¡º÷
-[[March 11, 2009¡¡¡¡Accelerating Life Science and Bioinformatics Applications¡ÄAs if Our Lives Depended on IT:http://www.hpcwire.com/topic/applications/Accelerating-Life-Science-and-Bioinformatics-Applications-41122667.html?viewAll=y]]¡¡¡¡ÆÃ¤ËFloating Point Solutions with GPGPU and Cell Co-Processors¤Î¹à¡£¡¡GPGPU¤ÎÎã¤Ç¤ÏNAMD (NAnoscale Molecular Dynamics), VMD (Visual Molecular Dynamics), and CHARMM (Chemistry at Harvard Macromolecular Mechanics).¡¡¡¡Cell¤ÎÎã¤Ç¤ÏGROMACS (GROningen Machine for Chemical Simulations), a protein folding code that unlocks the mystery of protein assembly and its relationship to cancers, Parkinson's disease and Alzheimer's.¡¡¤¬µó¤²¤é¤ì¤Æ¤¤¤ë
-[[U-Del¤ÎCS³ØÀ¸Project¡¡CISC849 - 011:http://gcl.cis.udel.edu/courses/cisc849011_sp08/project.php]]¡¡[[¥Þ¥Æ¥ê¥¢¥ë¤Ï¤³¤³:http://gcl.cis.udel.edu/courses/cisc849011_sp08/project_wesandnabeel.pdf]]
-[[GPU Computing 3.0:http://www.ece.neu.edu/groups/nucar/GPGPU/GPGPU-2/Luebke.pdf]]¡¡¤Î41¥Ú¡¼¥¸¡¢46¥Ú¡¼¥¸
-U-Del¤ÎJoe Davis¤é¤Î¥Ú¡¼¥¸[[Towards Large-Scale Molecule Dynamics Simulations on Graphics Processors:http://www.imagwiki.org/mediawiki/images/e/e7/08_IMAG_TauferDavis.pdf]]¡¡11¥Ú¡¼¥¸¡¢14¥Ú¡¼¥¸¡¢19¥Ú¡¼¥¸
-[[HaRiken "Harvard/Riken GPGPU Symposium 2008":http://sites.google.com/a/aspuru.com/hariken-08/HaRiken-Abstracts]]
-[[Genome Web ¡Á Genome Technology¡§Not Just for Kids Anymore (September 2007):http://www.genomeweb.com/not-just-kids-anymore-0]]¡¡¡¡VMD, NAMD, CHARMM
-[[SC07 High Performance Computing with CUDA ¡Á Case Study: ¡Á Molecular Dynamics:http://gpgpu.org/static/sc2007/SC07_CUDA_7_NAMD_Phillips.pdf]]
-ËÜ(Springer LNCS) [[Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors:http://www.springerlink.com/content/757u77211847v755/]]
-[[Stream Computing for GPU-Accelerated HPC Applications (April 6th, 2009):http://www.browndeertechnology.com/docs/BDT_GPU_HPC_APPS_20090406.pdf]]
-[[Scalable molecular dynamics with NAMD.:http://www.citeulike.org/user/grondina/article/449842]] J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1781-1802.
-[[2009 Symposium on Application Accelerators in High Performance Computing (SAAHPC'09):http://saahpc.ncsa.illinois.edu/agenda.html]]
-[[Ë̳¤Æ»Âç³Ø Âç³Ø±¡¾ðÊó²Ê³Ø¸¦µæ²Ê À¸Ì¿¿Í´Ö²Ê³ØÀì¹¶¡¡¥Ð¥¤¥ª¥¤¥ó¥Õ¥©¥Þ¥Æ¥£¥¯¥¹¹ÖºÂ ¹½Â¤¥Ð¥¤¥ª¾ðÊó²Ê³Ø¸¦µæ¼¼:http://ibio.jp/index.php]]
IBM Cell & CHARMM¤Ç¸¡º÷
-PPT [[Studying Protein Folding on the Grid: Experiences Using CHARMM on NPACI Resources under Legion:http://legion.virginia.edu/presentations/HPDC-Aug2001.ppt]]
-Paper [[Studying protein folding on the grid: experiences using CHARMM onNPACI resources under Legion:http://ieeexplore.ieee.org/Xplore/login.jsp?url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F7513%2F20446%2F00945172.pdf%3Farnumber%3D945172&authDecision=-203]]
-[[Protein folding with Charmm on Legion:http://www.hoise.com/primeur/01/articles/weekly/AE-PR-04-01-27.html]] San Diego 07 March 2001
-[[Studying protein folding on the Grid: experiences using CHARMM on NPACI resources under Legion:http://www.cs.virginia.edu/papers/Studying_Protein_Folding.pdf]] (CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE, January 2004)
-[[MD Benchmarks for Amber, CHARMM and NAMD:http://ambermd.org/amber8.bench2.html]] (latest update: April, 2005)
NAMD¤Î¥Û¡¼¥à¥Ú¡¼¥¸
-[[NAMD - Scalable Molecular Dynamics:http://www.ks.uiuc.edu/Research/namd/]]~
¤³¤ÎHP¤è¤ê~
NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling. ~
²¿¤»University of Illinois at Urbana Champeign¤À¤«¤é¡£
**2009-06-16 Äɵ ¡Ê¥Þ¥ë¥Á¥³¥¢¤ÈÊÂÎó¥×¥í¥°¥é¥ß¥ó¥°¡Ë [#ucb1d184]
-Sourceforge magazine µ»ö¡¡[[¥½¥Õ¥È¥¦¥§¥¢¹â®²½¤Î¸°¤Ï¡ÖÊÂÎ󲽡ס§¤¤¤ÞÃíÌܤµ¤ì¤ëÊÂÎó²½µ»½Ñ¤òÃΤë:http://sourceforge.jp/magazine/09/05/15/0930226]]¡¡¤Ë¡¢¥Þ¥ë¥Á¥³¥¢´Ä¶¤Ç¤ÎÊÂÎ󥽥եȵ»½Ñ¤ÎɬÍ×À¤òÀ⤯µ»ö¡£
-[[¾ðÊó½èÍý³Ø²ñ»ï¡Ö¾ðÊó½èÍý¡×2008ǯ12·î¹æ¡¡(Vol.49, No.12¡Ë¡ÖÆÃ½¸¡§¡¡¥Þ¥ë¥Á¥³¥¢¤òÀ¸¤«¤¹¤ª¼ê·ÚÊÂÎó¥×¥í¥°¥é¥ß¥ó¥°¡×:http://fw8.bookpark.ne.jp/cm/ipsj/mokuji.asp?category1=Magazine&vol=49&no=12]]¡¡¤Ç¥Þ¥ë¥Á¥³¥¢´Ä¶¤Ç¤ÎÊÂÎ󥽥եȵ»½Ñ¤ÎɬÍ×À¤òµÄÏÀ¤·¤Æ¤¤¤¿¡£
**2007-04-16 [#s72987f3]
¤³¤Î¸¦µæ¤Ï¡¢ÅöÌִ̡ÏÀ¥ì¥Ù¥ë¡×¡£²¿¤«¿·¤·¤¤¤³¤È¤¬½Ð¤Æ¤¯¤ë¤«¤É¤¦¤«¤Ï
¤Þ¤À¤ï¤«¤é¤Ê¤¤¡£
***²¿¤ò¤ä¤ë¤Î¤« [#jdbafa4a]
¤ä¤ê¤¿¤¤¤³¤È¡§¡¡¸½ºß¥³¥ó¥Ô¥å¡¼¥¿¤Ç¡ÊľÎó¤Ë¡Ë½èÍý¤µ¤ì¤Æ¤¤¤ë¤¿¤á¤Ë¡¢»þ´Ö¤¬¤«¤«¤Ã¤Æ¡Öº¤¤ë¡×¤è¤¦¤ÊÌäÂ꤬¤¢¤ë¡£¤½¤ì¤òÊÂÎó¼Â¹Ô¤·¤Æ¡¢Á᤯¤¹¤ë¡£
ÇØ·Ê¡§¡¡(1)¡Ö¥Þ¥ë¥Á¥³¥¢¡×¤Î£Ã£Ð£Õ¤¬¼ê¤´¤í¤ÊÃÍÃʤǼê¤ËÆþ¤ë¤è¤¦¤Ë¤Ê¤Ã¤¿¡£¡Ê£´¥³¥¢¤À¤È£´ÊÂÎó¡¢£¸¥³¥¢¤À¤È£¸ÊÂÎ󡢤«¤±¤ë¡¡£Ã£Ð£Õ¿ô¡Ê£²¤Ä¤È¤«£´¤Ä¤È¤«¡Ë¡Ë~
¡¡¡¡¡¡¡¡(2)Âç³Ø¤Ë¤¢¤ë£Ð£Ã¶µ¼¼¤Î£Ð£Ã¤ò¡¢¶õ¤¤¤Æ¤¤¤ë»þ´Ö¤Ë»È¤Ã¤Æ¡¢ÊÂÎó¼Â¹Ô¤Ç¤¤ë¡£¡Ê£¹£°Âæ»È¤¨¤ì¤Ð£¹£°ÊÂÎó¡Ë
Àè¹Ô¸¦µæ¡§¡¡»³¤Î¤è¤¦¤Ë¤¢¤ë¡£ÊÂÎó½èÍý¤Ï¸Å¤¯¤«¤é¤ÎÏÃÂê¡£~
¡¡¥Ý¥¤¥ó¥È£±¡§¡¡£ÎÂæ¤Î£Ã£Ð£Õ¤¬¤¢¤Ã¤¿¤È¤·¤Æ¤â¡¢¤Ê¤«¤Ê¤«£ÎÇÜ®¤¯¤Ê¤é¤Ê¤¤~
¡¡¡¡¡¡¡¡¡Ê¼Â¤Ïº£¤Þ¤Ç¤ÏÊÂÎó¤Ç²Ô¤°¤è¤ê£Ã£Ð£Õ¥¯¥í¥Ã¥¯¤ò²Ã®¤¹¤ëÊý¤¬´Êñ¤Ç°Â¤«¤Ã¤¿¡Ë~
¡¡¡¡¡¡¡¡¤É¤ì¤À¤±Â®¤¯¤Ê¤ë¤«¤Ï¡¢¥×¥í¥°¥é¥à¤ÎÀ¼Á¤Ë¤è¤ë¡£¤³¤Î¤¢¤¿¤ê¤Î¸¦µæ¤Ï¤¿¤¯¤µ¤ó¤¢¤ë¡£~
¡¡¡¡¡¡¡¡´û¤ËÊÂÎ󲽤µ¤ì¤Æ¤¤¤ë¥×¥í¥°¥é¥à¤â¤¤¤¯¤Ä¤«¡Ê¤«¤Ê¤ê¤¿¤¯¤µ¤ó¡Ë¤¢¤ë¡£~
¡¡¥Ý¥¤¥ó¥È£²¡§¡¡¡ÖÊÂÎ󲽡פϿͼêvs¼«Æ°¤¬¤¢¤ê¡¢¿Í¼ê¤Ï°ìÈ̤ˤÏÂçÊÑ¡£¡Ê¾ÊýÌäÂê¤Ë¤è¤Ã¤Æ¤Ï¼«ÌÀ¤Ê¤â¤Î¤â¿¤¤¡Ë¡¡¼«Æ°²½¤Ïº£¤Ç¤â¸¦µæ¥Í¥¿¡Ê¤¿¤È¤¨¤ÐµÈÅĸ¦¡Ë~
¤â¤¦°ìÅÙ¡Ö¤ä¤ê¤¿¤¤¤³¤È¡×¡§¡¡¤È¤Ë¤«¤¯ÊÂÎó¤Ë¤·¤ÆÂ®¤¯¤Ç¤¤ëÌäÂê¤òÊÂÎó¼Â¹Ô¤·¤Æ¡¢Ìò¤ËΩ¤Ã¤Æ¤ß¤¿¤¤¡£
***´Ä¶¤Ê¤É [#bc6277f8]
´Ä¶¡§¡¡ºòǯÅÙËö¤ËÇã¤Ã¤¿£È£Ð¤Î¥µ¡¼¥Ð¡¼¤Ï£´¥³¥¢¡ß£²£Ã£Ð£Õ¤Ç£¸ÊÂÎó²Äǽ¡£
£Ï£Ó¡§¡¡Linux¤ò¥¤¥ó¥¹¥È¡¼¥ëºÑ¤ß¡£¥×¥í¥»¥¹¥ì¥Ù¥ë¤ÎÊÂÎó½èÍý¤Ï´û¤Ë²Äǽ¡£¸å¤ÇÎã¤ò¼¨¤¹¡£
ÊÂÎó¥ß¥É¥ë¥¦¥§¥¢¡§¡¡¥×¥í¥°¥é¥à¤òÊÂÎóʬ³ä¤·¡¢´Êñ¤Ë¼Â¹Ô¤µ¤»¤é¤ì¤ë¥×¥é¥Ã¥È¥Õ¥©¡¼¥à¡Ê¥ß¥É¥ë¥¦¥§¥¢¡Ë¤¬¤¤¤¯¤Ä¤«¤¢¤ë¡£ÂçÊ̤¹¤ë¤È~
¡¡¡¡¶¦Í¥á¥â¥ê·¿¡ÊÊÑ¿ô¶¦Í·¿¡Ë¥â¥Ç¥ë¡§¡¡¥ß¥É¥ë¥¦¥§¥¢¤È¤·¤ÆOpenMP¤¬Í̾¡£~
¡¡¡¡¥á¥Ã¥»¡¼¥¸¸ò´¹·¿¥â¥Ç¥ë¡§¡¡¥¤¥ó¥¿¡¼¥Õ¥§¡¼¥¹¤È¤·¤ÆMPI¤¬¤¢¤ê¡¢¤½¤Î¼ÂÁõ¤È¤·¤Æ¥Õ¥ê¡¼¤ÎMPICH/MPICH2¤¬¤¢¤ë¡£~
¥â¥Ç¥ë¤È¤·¤ÆÈæ³Ó¤¹¤ë¤È¡¢¶¦Í¥â¥Ç¥ë¤ÏÌ©¤ÊÁê¸ßºîÍѡʺÙγÅÙ¤ÎÊÂÎó¡Ë¤¬²Äǽ¤Ê¤Î¤È¡¢¥³¥ó¥Ñ¥¤¥é¤¬¼«Æ°ÊÂÎ󲽤¹¤ë¤è¤¦¤Ê¤³¤È¤¬²Äǽ¡£¤¿¤È¤¨¤ÐIntel¤Î¥³¥ó¥Ñ¥¤¥é¤Î-parallel¥ª¥×¥·¥ç¥ó¡£¥Ï¡¼¥É¥¦¥§¥¢¤ÎÀ©Ì󤫤éÊÂÎóÅ٤Ϥ½¤ì¤Û¤ÉÂ礤¯¤Ê¤é¤Ê¤¤¡Ê¤»¤¤¤¼¤¤¿ô½½¡Ë~
¥á¥Ã¥»¡¼¥¸¥â¥Ç¥ë¤Ï¥á¥Ã¥»¡¼¥¸¸ò´¹¤Ë»þ´Ö¤¬¤«¤«¤ë¤Î¤ÇÁ¤ÊÁê¸ßºîÍÑ¡ÊÂçγÅÙ¤ÎÊÂÎó¡Ë¤Ë¸þ¤¯¡£¤½¤ÎÂå¤ï¤êÊÂÎóÅÙ¤ÏÂ礤¯½ÐÍè¤ë¡£¡ÊTCP/IP¤ò»È¤¦¤Î¤¬Î®¹Ô¤À¤¬¡¢¤½¤ì¤À¤È¤Û¤È¤ó¤É̵¸Â¤Þ¤Ç²Äǽ¡£À¤³¦Ãæ¤Î¥³¥ó¥Ô¥å¡¼¥¿¤ò¤Ä¤Ê¤°¤³¤È¤â²Äǽ¡£¡Ë¥Í¥Ã¥È¥ï¡¼¥¯ÃÙ±ä¤òû½Ì¤¹¤ë¹©ÉפâÀΤ¢¤Ã¤¿¡ÊMyrinet¤¬Í̾¡Ë¡£¥®¥¬¥Ó¥Ã¥È¥¤¡¼¥µ¤Î¾ì¹ç¡¢Å¾Á÷¤ÏÁᤤ¤¬¥»¥Ã¥È¥¢¥Ã¥×¤Ë»þ´Ö¤¬¤«¤«¤ë¤È¸À¤ï¤ì¤ë¡£~
¤³¤ÎÊդε½Ò¤Ø¤Î¥Ý¥¤¥ó¥¿¤ò¤³¤³¤Ëµó¤²¤ë
-¾ðÊó½èÍý¤Îµ»ö[[¥Þ¥ë¥Á¥³¥¢¤Ë¤ª¤±¤ë¥×¥í¥°¥é¥ß¥ó¥°(<ÆÃ½¸>¥Þ¥ë¥Á¥³¥¢¤Ë¤ª¤±¤ë¥½¥Õ¥È¥¦¥§¥¢):http://ci.nii.ac.jp/naid/10016924240/]]
-[[¥Þ¥ë¥Á¥³¥¢CPU¤Î²¸·Ã¤òµý¼õ¤¹¤ëÊýË¡:http://www.hpc.co.jp/hit/support/multicore.html]]¡¡²¿¤È¤³¤ì¤ÎºÇ½é¤ÎÈæ³Ó¤ÏBLAST¤À¤Ã¤¿
-Àд¬À콤Âç³Ø¤Î¼ø¶È¡¡[[¾ðÊóÅŻҹ©³ØÆÃÊ̲ÊÌÜ· ÆÃ¼ì¹ÖµÁ¡Ê¸å´ü¡Ë:http://hyperion.ie.isenshu-u.ac.jp/ecc/sample/presentation/mitou_1.ppt]]
-¶µ²Ê½ñ¡¡[[¥Þ¥ë¥Á¥³¥¢CPU¤Î¤¿¤á¤ÎÊÂÎó¥×¥í¥°¥é¥ß¥ó¥°¡½ÊÂÎó½èÍý&¥Þ¥ë¥Á¥¹¥ì¥Ã¥ÉÆþÌç (ñ¹ÔËÜ) :http://www.amazon.co.jp/%E3%83%9E%E3%83%AB%E3%83%81%E3%82%B3%E3%82%A2CPU%E3%81%AE%E3%81%9F%E3%82%81%E3%81%AE%E4%B8%A6%E5%88%97%E3%83%97%E3%83%AD%E3%82%B0%E3%83%A9%E3%83%9F%E3%83%B3%E3%82%B0%E2%80%95%E4%B8%A6%E5%88%97%E5%87%A6%E7%90%86-%E3%83%9E%E3%83%AB%E3%83%81%E3%82%B9%E3%83%AC%E3%83%83%E3%83%89%E5%85%A5%E9%96%80-%E5%AE%89%E7%94%B0-%E7%B5%B9%E5%AD%90/dp/4798014621]]~
Amazon¤Ç¤ÎɾȽ¤Ï°¤¤¤ß¤¿¤¤¡¡
-Ãμ±¡§¡¡MPI vs OpenMP = OpenMP¤Ï¥á¥â¥ê¶¦Í·¿¤Î¥Þ¥ë¥Á¥×¥í¥»¥Ã¥µÂбþ¤Î¥ß¥É¥ë¥¦¥§¥¢ vs MPI¤Ï(TCP/IP¤ò»È¤Ã¤¿¡Ë¥á¥Ã¥»¡¼¥¸¥Ñ¥·¥ó¥°·¿¤Î¥ß¥É¥ë¥¦¥§¥¢¡£¥á¥â¥ê¶¦Í·¿¤ÏCPU¿ô¤Ë¾å¸Â¤¢¤ë¤¬¥á¥Ã¥»¡¼¥¸·¿¤ÏÂ礤¯½ÐÍè¤ë¡£¤½¤ÎÂå¤ï¤ê¡¢¥á¥â¥ê¶¦Í·¿¤Ï¥Ç¡¼¥¿¸ò´¹¤¬Â®¤¤¤¬¥á¥Ã¥»¡¼¥¸Êý¤ÏÃÙ¤¤¡£
-[[¥Þ¥ë¥Á¥³¥¢CPU¤Î²¸·Ã¤òµý¼õ¤¹¤ëÊýË¡:http://www.hpc.co.jp/hit/support/multicore.html]]¡¡¤Ë¤è¤ë¤È¡¢
--¡¡1 ¥¤¥ó¥Æ¥ë¥³¥ó¥Ñ¥¤¥é¤Î -parallel ¥ª¥×¥·¥ç¥ó¤ò»È¤Ã¤ÆÊÂÎ󲽤¹¤ëÊýË¡¡Ä¥½¡¼¥¹¥³¡¼¥ÉÊѹ¹ÉÔÍ×
--¡¡2 Intel¤Î¿ôÃͱ黻¥é¥¤¥Ö¥é¥ê¤ò»È¤Ã¤ÆÊÂÎ󲽤¹¤ëÊýË¡¡ÄÊÂÎ󲽤µ¤ì¤¿¥é¥¤¥Ö¥é¥ê¤ò¸Æ¤Ó½Ð¤»¤Ð¹âÀǽ²½
--¡¡3 OpenMP¤ò»È¤Ã¤ÆÊÂÎ󲽤¹¤ëÊýË¡¡ÄÊÂÎ󲽤·¤¿¤¤Éôʬ¤ËOpenMP¥Ç¥£¥ì¥¯¥Æ¥£¥Ö¡Ê»Ø¼¨¹Ô¡Ë¤òÆþ¤ì¤ë
--¡¡4 MPI¤ò»È¤Ã¤ÆÊÂÎ󲽤¹¤ëÊýË¡¡ÄMPI²½¤ÏÆñ°×ÅÙ¤¬¹â¤¤~
Æñ°×ÅÙ¤¬¹â¤¤¤È¸À¤¦Íýͳ¤Ï¡¢¥¤¥ó¥Æ¥ë¥³¥ó¥Ñ¥¤¥é¤À¤È¼«Æ°ÊÂÎ󲽤ò¤·¤Æ¤¯¤ì¤ë¤Î¤ËÂФ·¡¢MPI²½¤Ï¼«Ê¬¤ÇÊÂÎ󲽤·¤Ê¤±¤ì¤Ð¤Ê¤é¤Ê¤¤¤«¤é¡£~
¤½¤ì¤Ç¤â¡¢¤¤¤¯¤Ä¤«¤Î¥Æ¥¥¹¥È¤¬¾Ò²ð¤µ¤ì¤Æ¤¤¤ë¡£~
¡¡¡¡¡¡[[Íý¸¦¤Ç¥¹¥Ñ¥³¥ó¹Ö½¬²ñ¤Ë»È¤Ã¤¿¥Æ¥¥¹¥È:http://accc.riken.jp/HPC/training/text.html]]~
¡¡¡¡¡¡[[¡ÖMPIÊÂÎó¥×¥í¥°¥é¥ß¥ó¥°¡×:http://www.hpc.co.jp/hit/B-DEV/MPI-01.htm]](2001ǯ)~
***¥ì¥Ù¥ë¡Ý£±¤ÎͽÈ÷¼Â¸³~ [#bfbf7f32]
ÀÞ³ÑÇã¤Ã¤¿¥µ¡¼¥Ð¡¼¤Ê¤Î¤Ç¡¢ËÜÅö¤ËÊÂÎó¼Â¹Ô¤Ç¤¤ë¤«»î¤·¤Æ¤ß¤¿¡£~
CPU¤Ç¤Î»Å»ö¤À¤±¡Ê¤Û¤È¤ó¤É¡¢¤À¤¬¡Ë¤ò¤¹¤ë¥×¥í¥°¥é¥à¤òºî¤ë¡£²¿¤Ç¤â¤¤¤¤¤¬¡¢Í¾¤ê¤Ë¼«ÌÀ¤Ê¥×¥í¥°¥é¥à¤À¤È¥³¥ó¥Ñ¥¤¥é¤¬¸¤¤¤Î¤ÇÌ¿Îá¤òºÇŬ²½¡á¾Ê¤¤¤Æ¤·¤Þ¤¦¤Î¤ÇÍ×Ãí°Õ¡£¥×¥í¥°¥é¥à¤Ï~
#include <math.h>
#include <stdio.h>
#include <unistd.h>
#include <string.h>
main(int argc, char **argv) {
int i, maxi;
double x;
char bufin[256];
if (argc !=2) {
fprintf(stderr, "usage: paratest <maxi>. maxi=~~10000000\n");
} else {
maxi = atoi(argv[1]);
if (maxi<=0) {
fprintf(stderr, "maxi <= 0\n");
}
}
for (i=0; i<255; i++) bufin[i]='\0';
x = 0.0;
for (i=0; i<maxi; i++) {
x = x + sin( (double) i/maxi );
}
read(0, bufin, 256);
printf("%s", strcat(bufin, "a"));
fprintf(stderr, "%s", strcat(bufin, "a"));
}
¥³¥ó¥Ñ¥¤¥ë»þ¤Ë-lm¤¬É¬Íס£¡ÊMath Library¤ò»È¤Ã¤Æ¤¤¤ë¤¿¤á¡Ë
¤³¤Î¥×¥í¥°¥é¥à¤ò¥×¥í¥»¥¹¤È¤·¤Æ¡¢ÊÂÎó¼Â¹Ô¤µ¤»¤Æ¤ß¤ë¡£¥·¥§¥ë¥ì¥Ù¥ë¤ÇÊÂÎ󵝯°¡¢¤Ä¤Þ¤êcshell¤Ç¤Î¡Ö&¡×¤ä¡Ö|¡×¤ò»È¤¦¡£ºÇ½é¤Ë¡Ö&¡×¤ò»î¤·¤¿¤¬¡¢½ªÎ»¤¬È½Äꤷ¤Ë¤¯¤¤¤Î¤Ç¡¢¡Ö|¡×¡Ê¥Ñ¥¤¥×¡Ë¤ò»È¤¦¤³¤È¤Ë¤¹¤ë¡£~
·è¤á¤¿¿ô¤Î¥×¥í¥»¥¹¤ò¥Ñ¥¤¥×¤Ç¤Ä¤Ê¤¤¤ÇÊÂÎó¤Ëµ¯Æ°¤¹¤ë¡£ºÇ¸å¤Ë¥Ñ¥¤¥×¤òÄ̤¸¤Æ¥á¥Ã¥»¡¼¥¸¤¬ºÇ¸å¤Î¥×¥í¥»¥¹¤Ë¹Ô¤Ã夤¤Æ¡¢½ªÎ»¤¬¤ï¤«¤ë¡£¤³¤Î¥·¥§¥ë¥¹¥¯¥ê¥×¥È¤Ï~
#!/bin/csh
set N = 100000000
# Case of 8 processes
echo "" | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $ N | pipebody $N | pipebody $N
# Case of 12 processes
#echo "" | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pipebody $N | pebody $N | pipebody $N
# Case of 1 process
#echo "" | pipebody $N
¤Î¤è¤¦¤Ë½ñ¤¤¤¿¡£
¤³¤ì¤ò¼Â¹Ô¤µ¤»¤ë»þ¤Ë¡¢¥³¥Þ¥ó¥Étime¤ò»È¤¦¡£ºÇ¶á¤ÎLinux¤Îtime¥³¥Þ¥ó¥É¤Ï¡¢~
The default format string is
%Uuser %Ssystem %Eelapsed %PCPU (%Xtext+%Ddata %Mmax)k
%Iinputs+%Ooutputs (%Fmajor+%Rminor)pagefaults %Wswaps
¤È¤¤¤¦¤³¤È¤Ç¡¢ÀΤʤ¬¤é¤Î real ... user ... sys ... ¤È¤¤¤¦·Á¼°¤Ç¤Ê¤¤¤¬¡¢µÑ¤Ã¤Æ¾ðÊó¤Ïʬ¤«¤ê¤ä¤¹¤¤¡£
·ë²Ì¤Ï¼¡¤Î¤è¤¦¤Ë¤Ê¤Ã¤¿¡£~
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ user system elapsed PCPU~
¥×¥í¥»¥¹£±¤Ä¡§¡¡¡¡ 9.720u 0.028s 0:09.74 100.0% 0+0k 0+0io 0pf+0w~
¥×¥í¥»¥¹£´¤Ä¡§¡¡¡¡38.814u 0.036s 0:09.75 398.3% 0+0k 0+0io 0pf+0w~
¥×¥í¥»¥¹£¸¤Ä¡§¡¡¡¡77.476u 0.020s 0:09.76 793.9% 0+0k 0+0io 0pf+0w~
¥×¥í¥»¥¹£¹¤Ä¡§¡¡¡¡87.301u 0.040s 0:14.62 597.4% 0+0k 0+0io 0pf+0w~
¥×¥í¥»¥¹£±£²¡§¡¡¡¡116.407u 0.028s 0:15.93 730.8% 0+0k 0+0io 0pf+0w~
¥×¥í¥»¥¹£±£¶¡§¡¡¡¡155.189u 0.044s 0:19.54 794.3% 0+0k 0+0io 0pf+0w
¤³¤Î´Ä¶¤Ç¤Ï£±¤Ä¤Î¥×¥í¥»¥¹¤¬¿©¤¦£Ã£Ð£Õ»þ´Ö¤Ï9.72ÉÃÄøÅ٤Ǥ¢¤ê¡¢¥×¥í¥»¥¹¿ô¤ò£±¢Í£´¢Í£¸¤Þ¤ÇÁý¤ä¤·¤¿»þ¤Ëuser time¡Ê¡á¥×¥í¥»¥¹Áí»þ´Ö¡Ë¤Ï38.81Éáá4¡ß9.70Éá¢77.48Éáá8¡ß9.685¤Î¤è¤¦¤ËÁý¤¨¤Æ¤¤¤ë¤¬¡¢elapsed time¡Ê¡áüËö¤Ç¸«¤Æ¤¤¤ë»þ´Ö¡Ë¤Ï£³¤Ä¤È¤â9.74¡Á9.76ÉäǤۤȤó¤ÉÊѤï¤é¤Ê¤¤¡£¤Ä¤Þ¤ê£¸ÊÂÎó¤Þ¤Ç¼Â¸½¤Ç¤¤Æ¤¤¤ë¡£¤½¤Î¤È¤¤ÎCPU percentage (PCPU) ¤Ï398.3% 793.9%¤È¡¢¤Û¤È¤ó¤ÉÊÂÎóÅÙ¤ÈÆ±¤¸Ãͤò¼¨¤·¤Æ¤¤¤ë¡£
¤È¤³¤í¤¬¡¢£¹¥×¥í¥»¥¹¤ò±Û¤¨¤¿¤È¤³¤í¤Ç¡¢£¹¤ÄÌÜ¤Î¥×¥í¥»¥¹¤Ï;¤Ã¤Æ¤·¤Þ¤¤¸å¤«¤é¼Â¹Ô¤µ¤ì¤ë¤ï¤±¤Ç¡¢¼ÂºÝ elapsed time ¤¬¡Ê9.75É䫤é¡Ë14.6Éä˿¤Ó¤Æ¤¤¤ë¡£´°Á´¤Ë£²Çܤˤʤé¤Ê¤¤Íýͳ¤Ï¡¢¤ª¤½¤é¤¯³°Â¦¤Î¥ª¡¼¥Ð¡¼¥Ø¥Ã¥É¤¬¤¢¤ë¤¿¤á¤À¤í¤¦¡£¤½¤·¤Æ¡¢£¹¥×¥í¥»¥¹¢Í£±£²¥×¥í¥»¥¹¢Í£±£¶¥×¥í¥»¥¹¤ÈÁý¤ä¤·¤Æ¤â elapsed time ¤Ï¿¾¯Áý¤¨¤ë¤À¤±¤ÇÇÜÁý¤Ï¤·¤Æ¤¤¤Ê¤¤ 14.6ÉâÍ15.9ÉâÍ19.5Éáʣ±£¶¤Î¾ì¹ç¿¾¯Èù̯¤«¤â¡£Âç¾æÉפ«¤Ê¡©¡Ë
¤È¤¤¤¦¤³¤È¤«¤é¡¢£¸ÊÂÎ󤬼¸½¤µ¤ì¤Æ¤¤¤ë¤é¤·¤¤¤³¤È¤Ïʬ¤«¤Ã¤¿¡£
***¼¡¤Î¥¹¥Æ¥Ã¥× [#yb5bcea8]
¹Í¤¨¤é¤ì¤ëÊý¸þ¤È¤·¤Æ¡¢
-Intel¤Î¥³¥ó¥Ñ¥¤¥é¤Î¼«Æ°ÊÂÎó²½µ¡Ç½¤¬»È¤¨¤ë¤«»î¤·¤¿¾å¤Ç¡¢ËܳÊŪ¤Ê¥×¥í¥°¥é¥à¤òÊÂÎó¼Â¹Ô¤·¤Æ¤ß¤ë¡£¡Ê¤ä¤Ã¤Æ¤ß¤ë¡¢¤È¤¤¤¦¥ì¥Ù¥ë¤Ç¶½Ì£¤¢¤ê¡£¤½¤ÎÄøÅÙ¡Ë
-OpenMP¤òÆþ¤ì¤Æ¡¢¤¤¤¸¤Ã¤Æ¤ß¤ë¡£¡Ê¤ä¤Ã¤Æ¤ß¤ë¤È¤¤¤¦¥ì¥Ù¥ë¤«¤Ê¡£µÈÅĸ¦¤È°ì½ï¤Ë¤ä¤ë¤È¤¤¤¤¤«¤â¡ËOpenMP¤À¤È¥á¥â¥ê¶¦Í·¿¤Î¤ß¤Ê¤Î¤Ç¡¢¼Â½¬¼¼¤ÎPC¤ò·Ò¤°¤È¤¤¤¦Êý¸þ¤Ï̵¤¯¤Ê¤ë¤À¤í¤¦¡£
-MPICH2¤òÆþ¤ì¤Æ¡¢¤¤¤¸¤Ã¤Æ¤ß¤ë¡£
-ÎãÂê¥×¥í¥°¥é¥à¤òÀ¸ÊªÊ¬»Ò²Ê¤«¤é¤â¤é¤¨¤ë²ÄǽÀ¤¬¤¢¤ë¤Î¤Ç¡¢¤½¤ì¤ò»î¤·¤Æ¤ß¤¿¤¤¡£¥¿¥ó¥Ñ¥¯¼Á¤ÎXÀþ²óÀޤˤè¤ë²òÀϤò¤¹¤ë¤¿¤á¤Î¥×¥í¥°¥é¥à¤é¤·¤¤¡£¾ÜºÙ¤Ï¤Þ¤À¡£Ïäˤè¤ë¤È¡¢·×»»¤ÏÃͤòÊѤ¨¤Æ·«¤êÊÖ¤·¤Æ·×»»¤¹¤ë¤À¤±¤Ê¤Î¤Ç¡¢¤½¤ì¤Ê¤é¤ÐÊÂÎ󤨤Îʬ³ä¤Ï¤Û¤Ü¼«ÌÀ¤Î¤Ï¤º¡£
¥Ú¡¼¥¸Ì¾: