{"id":987,"date":"2014-03-19T11:34:31","date_gmt":"2014-03-19T02:34:31","guid":{"rendered":"http:\/\/www.cenav.org\/kdb\/?p=987"},"modified":"2014-04-17T15:08:37","modified_gmt":"2014-04-17T06:08:37","slug":"%e5%88%86%e5%ad%90%e7%b3%bb%e3%82%82%e3%81%ae%e3%81%a5%e3%81%8f%e3%82%8a%e3%82%b7%e3%83%9f%e3%83%a5%e3%83%ac%e3%83%bc%e3%82%b7%e3%83%a7%e3%83%b3%e3%82%bd%e3%83%95%e3%83%88%e3%82%a6%e3%82%a7%e3%82%a2-2","status":"publish","type":"post","link":"https:\/\/www.cenav.org\/kdb\/?p=987","title":{"rendered":"\u5206\u5b50\u7cfb\u3082\u306e\u3065\u304f\u308a\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306e\u6027\u80fd\u8a55\u4fa1\u2015ProteinDF\u2015"},"content":{"rendered":"<h3>\u6982\u8981<\/h3>\n<p>ProteinDF Ver.2014.0 \u306e\u5b9f\u884c\u6027\u80fd\u3092\u3001\u30a2\u30e9\u30cb\u30f3 10\u6b8b\u57fa\u30e2\u30c7\u30eb\u3092\u7528\u3044\u3066\u6e2c\u5b9a\u3057\u305f\u3002\u89e3\u6cd5\u306f\u3001dynamic-replica\u6cd5\u3001distributed\u6cd5\u3001\u30b3\u30ec\u30b9\u30ad\u30fc\u5206\u89e3\uff08CD\uff09\u6cd5\u304c\u5b9f\u88c5\u3055\u308c\u3066\u3044\u308b\u3002\u3053\u308c\u3089\u306e\u3046\u3061CD\u6cd5\u304c\u6700\u3082\u901f\u304f\u3001dynamic-replica\u6cd5\u306b\u6bd4\u307925\u301c80\u500d\u306e\u6027\u80fd\u304c\u78ba\u8a8d\u3055\u308c\u305f\u3002<\/p>\n<h3>\u89e3\u6790\u30e2\u30c7\u30eb<\/h3>\n<p>\u30a2\u30e9\u30cb\u30f3\uff11\uff10\u6b8b\u57fa\u30e2\u30c7\u30eb\uff08ALA10\uff09<\/p>\n<p><a href=\"http:\/\/www.cenav.org\/kdb\/wp-content\/uploads\/2014\/03\/PDF-ALA10-model.png\"><img loading=\"lazy\" class=\"alignnone size-medium wp-image-988\" alt=\"PDF-ALA10-model\" src=\"http:\/\/www.cenav.org\/kdb\/wp-content\/uploads\/2014\/03\/PDF-ALA10-model-560x131.png\" width=\"560\" height=\"131\" srcset=\"https:\/\/www.cenav.org\/kdb\/wp-content\/uploads\/2014\/03\/PDF-ALA10-model-560x131.png 560w, https:\/\/www.cenav.org\/kdb\/wp-content\/uploads\/2014\/03\/PDF-ALA10-model.png 713w\" sizes=\"(max-width: 560px) 100vw, 560px\" \/><\/a><\/p>\n<h3>\u4f7f\u7528\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u30e2\u30b8\u30e5\u30fc\u30eb<\/h3>\n<p>ProteinDF Ver.2014.0<\/p>\n<h3>\u8a08\u7b97\u6761\u4ef6<\/h3>\n<h4>dynamic-replica\u6cd5<\/h4>\n<p>dynamic-replica<br \/>\nlinear_algebra_package = lapack<br \/>\nparallel_processing_type = MS<br \/>\nJ_engine = RI_J<br \/>\nK_engine = conventional<\/p>\n<h4>distributed\u6cd5<\/h4>\n<p>linear_algebra_package = scalapack<br \/>\nparallel_processing_type = MS<br \/>\nJ_engine = RI_J<br \/>\nK_engine = conventional<\/p>\n<h4>CD\u6cd5<\/h4>\n<p>linear_algebra_package = scalapack<br \/>\nparallel_processing_type = MS<br \/>\nJ_engine = CD<br \/>\nK_engine = CD<\/p>\n<h3>\u5b9f\u884c\u74b0\u5883<\/h3>\n<p>FOCUS\u30b9\u30d1\u30b3\u30f3\uff25\u30b7\u30b9\u30c6\u30e0\u3092\u4f7f\u7528<\/p>\n<p>\u30cf\u30fc\u30c9\u30a6\u30a7\u30a2\uff1aCray GreenBlade GB824X (HPC\u5c02\u7528\u30d6\u30ec\u30fc\u30c9\u578b\u30b5\u30fc\u30d0)<br \/>\nCPU\uff1aIntel Xeon E5-2670 v2 (2.5GHz, 25MB L3\u30ad\u30e3\u30c3\u30b7\u30e5, 10\u30b3\u30a2) \u00d72CPU(\u8a0820\u30b3\u30a2)\uff0f\u30ce\u30fc\u30c9<br \/>\n\u30e1\u30e2\u30ea\uff1a 64 GB\uff0f\u30ce\u30fc\u30c9<br \/>\n\u30a4\u30f3\u30bf\u30fc\u30d5\u30a7\u30fc\u30b9\uff1aFDR-InfiniBand (56Gbps) \u00d71\uff0f\u30ce\u30fc\u30c9<br \/>\n\u30aa\u30da\u30ec\u30fc\u30c6\u30a3\u30f3\u30b0\u30b7\u30b9\u30c6\u30e0\uff1aCentOS 6.4 (64bit\u7248)<\/p>\n<p>\u4e26\u5217\u5b9f\u884c\u306f\u3059\u3079\u3066\u30d5\u30e9\u30c3\u30c8\uff2d\uff30\uff29\u306b\u3088\u308b\u3002<\/p>\n<h3>\u8a73\u7d30\u8aac\u660e<\/h3>\n<p>\u4e0b\u56f3\u306f\u3001\u4f7f\u7528\u30b3\u30a2\u6570\uff08#cores\uff09\u306b\u5bfe\u3057\u3066iteration\uff11\u56de\u306b\u8981\u3059\u308b\u6642\u9593\uff08\u5206\uff09\u306e\u69d8\u5b50\u3067\u3042\u308b\u3002\u89e3\u6cd5\u306b\u3088\u3063\u3066\u5b9f\u884c\u6642\u9593\u304c\u5927\u304d\u304f\u7570\u306a\u308b\u305f\u3081\u4e21\u5bfe\u3067\u30d7\u30ed\u30c3\u30c8\u3057\u3066\u3042\u308b\u304c\u3001\u4e26\u5217\u52b9\u7387\u304c\u9ad8\u3044\u5834\u5408\u306b\u306f\u53f3\u4e0b\u304c\u308a\u306e\u76f4\u7dda\u306b\u8fd1\u304f\u306a\u308b\u306f\u305a\u3067\u3042\u308b\u3002dynamic-replica\u6cd5\uff08\u56f3\u4e2ddyn-rep\u3068\u8868\u8a18\uff09\u306f\u3001\u4e0b\u304c\u308a\u65b9\u304c\u7de9\u3084\u304b\u3067\u30b3\u30a2\u6570\u304c\u5927\u304d\u304f\u306a\u3063\u3066\u3082\u3042\u307e\u308a\u901f\u5ea6\u304c\u5909\u308f\u3089\u306a\u3044\u304c\u3001distributed\u6cd5\u306f\u3001\u4e26\u5217\u52b9\u7387\u306b\u95a2\u3057\u3066\u306f\u3084\u3084\u826f\u3044\u3053\u3068\u304c\u5206\u304b\u308b\u3002\u4e00\u65b9\u3001CD\u6cd5\uff08\u56f3\u4e2dCD-SCA\uff09\u306f\u3001\u3053\u308c\u3089\u306b\u6bd4\u3079\u4e00\u6841\u307b\u3069\u9ad8\u901f\u306b\u306a\u3063\u305f\u3002<\/p>\n<p><a href=\"http:\/\/www.cenav.org\/kdb\/wp-content\/uploads\/2014\/03\/PDF-ALA101.png\"><img loading=\"lazy\" class=\"alignnone size-medium wp-image-996\" alt=\"PDF-ALA10\" src=\"http:\/\/www.cenav.org\/kdb\/wp-content\/uploads\/2014\/03\/PDF-ALA101-560x339.png\" width=\"560\" height=\"339\" srcset=\"https:\/\/www.cenav.org\/kdb\/wp-content\/uploads\/2014\/03\/PDF-ALA101-560x339.png 560w, https:\/\/www.cenav.org\/kdb\/wp-content\/uploads\/2014\/03\/PDF-ALA101-1024x620.png 1024w, https:\/\/www.cenav.org\/kdb\/wp-content\/uploads\/2014\/03\/PDF-ALA101.png 1900w\" sizes=\"(max-width: 560px) 100vw, 560px\" \/><\/a><\/p>\n<p>CD\u6cd5\u3068ditributed\u6cd5\u306f200\u30b3\u30a2\u4ee5\u4e0a\u3067\u306f\u30c7\u30c3\u30c9\u30ed\u30c3\u30af\u3092\u8d77\u3053\u3057\u3066\u3044\u308b\u3089\u3057\u304f\u5b9f\u884c\u304c\u9032\u307e\u306a\u304b\u3063\u305f\u3002\u89e3\u6c7a\u3092\u8a66\u307f\u3066\u3044\u308b\u904e\u7a0b\u3067\u3001linear_algebra_package\u306escalapack\u3092lapack\u306b\u5909\u66f4\u3059\u308b\u3068200\u30b3\u30a2\u307e\u3067\u5b9f\u884c\u3059\u308b\u3053\u3068\u304c\u3067\u304d\u3001\u6e2c\u5b9a\u7bc4\u56f2\u5185\u306725\uff5e80\u500d\u3082\u9ad8\u901f\u3067\u3042\u308b\u3053\u3068\u304c\u5206\u304b\u3063\u305f\uff08\u56f3\u4e2dCD-LAP\uff09\u3002<\/p>\n<table width=\"480\" border=\"0\" cellspacing=\"0\" cellpadding=\"0\">\n<tbody>\n<tr>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\"><\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">dyn-rep<\/p>\n<\/td>\n<td colspan=\"2\" valign=\"bottom\" nowrap=\"nowrap\" width=\"160\">\n<p align=\"center\">CD-SCALAPACK<\/p>\n<\/td>\n<td colspan=\"2\" valign=\"bottom\" nowrap=\"nowrap\" width=\"160\">\n<p align=\"center\">CD-LAPACK<\/p>\n<\/td>\n<\/tr>\n<tr>\n<td nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">#cores<\/p>\n<\/td>\n<td nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">Time\/min<\/p>\n<\/td>\n<td nowrap=\"nowrap\" width=\"105\">\n<p align=\"center\">Time\/min<\/p>\n<\/td>\n<td nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">\u500d\u7387<\/p>\n<\/td>\n<td nowrap=\"nowrap\" width=\"105\">\n<p align=\"center\">Time\/min<\/p>\n<\/td>\n<td nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">\u500d\u7387<\/p>\n<\/td>\n<\/tr>\n<tr>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">20<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">23.0<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"105\">\n<p align=\"center\">2.50<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">9.2<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"105\">\n<p align=\"center\">0.88<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">26.0<\/p>\n<\/td>\n<\/tr>\n<tr>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">40<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">18.6<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"105\">\n<p align=\"center\">1.55<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">12.0<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"105\">\n<p align=\"center\">0.48<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">38.4<\/p>\n<\/td>\n<\/tr>\n<tr>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">100<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">15.9<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"105\">\n<p align=\"center\">1.00<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">15.9<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"105\">\n<p align=\"center\">0.27<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">59.6<\/p>\n<\/td>\n<\/tr>\n<tr>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">200<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">15.8<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"105\"><\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">-<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"105\">\n<p align=\"center\">0.20<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">78.9<\/p>\n<\/td>\n<\/tr>\n<tr>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">400<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"80\">\n<p align=\"center\">17.0<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"105\"><\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">-<\/p>\n<\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"105\"><\/td>\n<td valign=\"bottom\" nowrap=\"nowrap\" width=\"55\">\n<p align=\"center\">-<\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3><\/h3>\n","protected":false},"excerpt":{"rendered":"<p>\u6982\u8981 ProteinDF Ver.2014.0 \u306e\u5b9f\u884c\u6027\u80fd\u3092\u3001\u30a2\u30e9\u30cb\u30f3 10\u6b8b\u57fa\u30e2\u30c7\u30eb\u3092\u7528\u3044\u3066\u6e2c\u5b9a\u3057\u305f\u3002\u89e3\u6cd5\u306f\u3001dynamic-replica\u6cd5\u3001distributed\u6cd5\u3001\u30b3\u30ec\u30b9\u30ad\u30fc\u5206\u89e3\uff08CD\uff09\u6cd5\u304c\u5b9f\u88c5\u3055\u308c\u3066\u3044\u308b\u3002\u3053\u308c\u3089 [<a title=\"\u4f1a\u54e1\u767b\u9332\u304c\u5fc5\u8981\u3067\u3059\" href=\"https:\/\/www.cenav.org\/kdb\/?p=987\">\u5168\u6587\u3092\u8aad\u3080<\/a>]<\/p>\n","protected":false},"author":130,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[162,53],"tags":[],"_links":{"self":[{"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=\/wp\/v2\/posts\/987"}],"collection":[{"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=\/wp\/v2\/users\/130"}],"replies":[{"embeddable":true,"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=987"}],"version-history":[{"count":16,"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=\/wp\/v2\/posts\/987\/revisions"}],"predecessor-version":[{"id":1695,"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=\/wp\/v2\/posts\/987\/revisions\/1695"}],"wp:attachment":[{"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=987"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=987"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.cenav.org\/kdb\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=987"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}