{"id":645,"date":"2022-08-03T13:53:32","date_gmt":"2022-08-03T05:53:32","guid":{"rendered":"https:\/\/rayray.moe\/?p=645"},"modified":"2026-02-21T19:12:20","modified_gmt":"2026-02-21T11:12:20","slug":"cp2k-2022-%e7%89%88%e6%9c%ac%e7%9a%84-docker-%e4%b8%8e-singularity-%e5%ae%89%e8%a3%85","status":"publish","type":"post","link":"https:\/\/rayray.moe\/?p=645","title":{"rendered":"CP2K 2022 \u7248\u672c\u7684 docker \u4e0e singularity \u5b89\u88c5"},"content":{"rendered":"<p>\u8fd9\u662f\u4e00\u7bc7\u5173\u4e8ecp2k 2022 \u7248\u672c docker \u955c\u50cf, \u548c\u57fa\u4e8e docker \u955c\u50cf\u8f6c\u6362\u7684 singularity \u6587\u4ef6\u7684\u5b89\u88c5\u8bb0\u5f55.<br \/>\ncp2k 2022 \u7248\u672c\u4e2d\u4e0d\u518d\u6709\u57fa\u4e8e toolchain \u7684 dockerfile, \u800c\u662f\u76f4\u63a5\u4f7f\u7528 docker \u81ea\u52a8\u7f16\u8bd1 toolchain \u4e0e cp2k \u672c\u4f53, \u8fd9\u4f7f\u5176\u7f16\u8bd1\u8fc7\u7a0b\u66f4\u52a0\u65b9\u4fbf.<br \/>\n\u53c2\u8003\u94fe\u63a5:<\/p>\n<ol>\n<li><a href=\"http:\/\/bbs.keinsci.com\/thread-25773-1-1.html\">[CP2K] docker-singularity\u65b9\u6cd5\u5b89\u88c5\u53ef\u968f\u610f\u79fb\u690d\u7684cp2k<\/a><\/li>\n<li><a href=\"https:\/\/github.com\/cp2k\/cp2k\/tree\/master\/tools\/docker\">cp2k-docker-readme<\/a><\/li>\n<li><a href=\"https:\/\/catalog.ngc.nvidia.com\/orgs\/hpc\/containers\/gromacs\">GROMACS-NVIDIA NGC<\/a><\/li>\n<\/ol>\n<h2><a id=\"docker%E7%89%88%E6%9C%AC%E7%9A%84%E5%AE%89%E8%A3%85%E6%96%B9%E6%B3%95\" class=\"anchor\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"><\/span><\/a>docker \u7248\u672c\u7684\u5b89\u88c5\u65b9\u6cd5<\/h2>\n<p>docker \u90e8\u5206\u5b89\u88c5\u8f83\u4e3a\u7b80\u5355, \u53ea\u8981\u53c2\u8003\u5b98\u65b9\u6307\u5357<a href=\"https:\/\/github.com\/cp2k\/cp2k\/tree\/master\/tools\/docker\">cp2k-docker-readme<\/a>\u5373\u53ef. \u9700\u8981\u6ce8\u610f\u7684\u662f\u4e3a\u4e86\u540e\u7eed singularity \u90e8\u5206\u7f16\u8bd1\u6b63\u5e38, \u6211\u4eec\u4f7f\u7528\u7684 cp2k repository \u9700\u8981\u662f git clone \u4e0b\u6765\u7684\u76ee\u5f55, \u5e76\u5207\u6362\u5230\u5bf9\u5e94\u53d1\u884c\u7248\u7248\u672c:<\/p>\n<pre><code class=\"language-bash\">git clone https:\/\/github.com\/cp2k\/cp2k.git\ncd cp2k\ngit checkout 71f6a37\n<\/code><\/pre>\n<p>\u5982\u679c\u4e0b\u8f7d\u7684\u662f\u6e90\u4ee3\u7801, \u53ef\u80fd\u4f1a\u56e0\u4e3a\u6ca1\u6709\u4e0b\u8f7d\u5176\u4ed6 git repository \u800c\u62a5\u9519, \u6b64\u65f6\u9700\u8981\u6309\u7167\u5c4f\u5e55\u6307\u793a clone \u5bf9\u5e94\u7684 repo:<\/p>\n<pre><code class=\"language-bash\">git submodule update --init --recursive\n<\/code><\/pre>\n<p>\u73b0\u5728\u53ef\u4ee5\u5f00\u59cb\u4f7f\u7528 docker build \u4e86. prod_psmp \u5bf9\u5e94\u4e86\u6700\u5e38\u4f7f\u7528\u7684\u7248\u672c.<\/p>\n<pre><code class=\"language-bash\">docker build -f Dockerfile.prod_psmp --build-arg GIT_COMMIT_SHA=$(git rev-parse HEAD) -t cp2k_prod_psmp ..\/..\/\n<\/code><\/pre>\n<p>\u7f51\u7edc\u901f\u5ea6\u597d\u7684\u65f6\u5019, \u7f16\u8bd1\u8fc7\u7a0b\u9700\u8981\u534a\u5c0f\u65f6\u4ee5\u4e0a, \u4f46\u7f51\u7edc\u4e0d\u597d\u7684\u65f6\u5019\u53ef\u80fd\u534a\u5929\u4e5f\u5b8c\u4e8b\u4e0d\u4e86. \u6240\u4ee5\u9009\u62e9\u4e00\u4e2a\u8f83\u597d\u7684\u7f51\u7edc\u73af\u5883\u548c\u65f6\u95f4\u5427.<\/p>\n<p>\u5f53\u5168\u90e8\u7f16\u8bd1\u5b8c\u6210\u540e, \u53ef\u4ee5\u4f7f\u7528\u5b98\u65b9\u6307\u5357\u4e2d\u7684\u65b9\u6cd5\u8bd5\u4e00\u4e0b:<\/p>\n<pre><code class=\"language-bash\">docker run -it -v &quot;$(pwd)&quot;:\/mnt cp2k_prod_psmp mpirun -np 8 cp2k -i test.inp -o test.out\n<\/code><\/pre>\n<p>\u8fd0\u884c\u7a0b\u5e8f, \u4f46\u8bf7\u6ce8\u610f, \u8fd9\u79cd\u65b9\u6cd5\u6bcf\u6b21\u90fd\u4f1a\u65b0\u5efa\u4e00\u4e2a docker \u5bb9\u5668, \u65f6\u95f4\u4e45\u4e86\u5c31\u4f1a\u5806\u7684\u8d8a\u6765\u8d8a\u591a&#8230;<\/p>\n<pre><code class=\"language-bash\">docker ps -a\n<\/code><\/pre>\n<p>\u4f7f\u7528\u5982\u4e0a\u547d\u4ee4\u53ef\u4ee5\u53d1\u73b0\u6bcf\u6b21\u8fd0\u884c\u90fd\u4f1a\u591a\u4e00\u884c\u5bb9\u5668\u6570\u636e, \u6700\u540e\u4f1a\u53d8\u5f97\u4e71\u4f5c\u4e00\u56e2&#8230;.. \u56e0\u6b64\u6211\u4eec\u5e94\u5f53\u9009\u62e9\u5982\u4e0b\u4e24\u79cd\u66ff\u4ee3\u65b9\u6848:<\/p>\n<p>a. \u4f7f\u7528\u4e00\u4e2a\u56fa\u5b9a\u7684\u5de5\u4f5c\u76ee\u5f55, \u7b2c\u4e00\u6b21\u4f7f\u7528 run \u547d\u4ee4\u521b\u5efa, \u4e4b\u540e\u4f7f\u7528 exec \u8fdb\u5165\u5bb9\u5668\u540e\u8fd0\u884c:<\/p>\n<p>\u7b2c\u4e00\u6b21\u8fd0\u884c\u65f6:<\/p>\n<pre><code class=\"language-bash\">cd \/the\/work\/directory\ndocker run -it -v ${PWD}:\/mnt cp2k_prod_psmp \/bin\/bash\n<\/code><\/pre>\n<p>\u9009\u62e9\u5c06\u5f53\u524d\u76ee\u5f55\u6302\u8f7d\u5230\u865a\u62df\u673a\u5185 \/mnt \u7684\u4e3b\u8981\u539f\u56e0\u662f cp2k \u7684\u865a\u62df\u673a\u5df2\u7ecf\u5c06 \/mnt \u6587\u4ef6\u5939\u4f5c\u4e3a\u8d77\u59cb\u76ee\u5f55.<\/p>\n<p>\u4e4b\u540e\u8fd0\u884c\u65f6:<\/p>\n<pre><code class=\"language-bash\">docker ps -a # \u67e5\u770b\u5bf9\u5e94\u7684\u5bb9\u5668 ID\ndocker start 3e15825f13fb # \u8fd9\u91cc\u66ff\u6362\u4e3a\u60f3\u8981\u7684 ID\ndocker exec -it 3e15825f13fb \/bin\/bash\ndocker stop 3e15825f13fb\n<\/code><\/pre>\n<blockquote>\n<p>\u70e6\u8bf7\u6ce8\u610f, \u5982\u679c\u5173\u673a\u524d\u6ca1\u6709\u505c\u6b62 docker \u865a\u62df\u673a\u4e2d\u8fd0\u884c\u7684\u8fdb\u7a0b, \u5173\u673a\u8fc7\u7a0b\u53ef\u80fd\u53d7\u5230\u5f71\u54cd, \u540c\u65f6\u5171\u4eab\u6587\u4ef6\u5939\u53ef\u80fd\u4f1a\u65ad\u5f00, \u8fd9\u4e2a\u5bb9\u5668\u53ef\u80fd\u5c31\u8981\u91cd\u65b0\u505a\u4e86 (\u5e26\u6709\u7a0b\u5e8f\u672c\u4f53\u7684 cp2k-docker \u8fd8\u597d, toolchain \u7248\u672c\u7684\u76f4\u63a5\u5c31\u9700\u8981\u518d\u7f16\u8bd1\u4e00\u6b21\u4e86..)<\/p>\n<\/blockquote>\n<p>b. \u4f7f\u7528\u5b98\u65b9\u6307\u5357\u7684\u65b9\u6cd5, \u4f46\u662f\u6dfb\u52a0 &#8211;rm \u53c2\u6570, \u6bcf\u6b21\u8fd0\u884c\u540e\u76f4\u63a5\u5220\u9664\u5bb9\u5668, \u4e16\u754c\u90fd\u5b89\u9759\u4e86:<\/p>\n<pre><code class=\"language-bash\">cd \/the\/work\/directory\ndocker run -it --rm -v &quot;$(pwd)&quot;:\/mnt cp2k_prod_psmp mpirun -np 8 cp2k -i test.inp -o test.out\n<\/code><\/pre>\n<h2><a id=\"singularity%E9%83%A8%E5%88%86%E7%9A%84%E5%AE%89%E8%A3%85%E6%96%B9%E6%B3%95\" class=\"anchor\" aria-hidden=\"true\"><span class=\"octicon octicon-link\"><\/span><\/a>Singularity \u90e8\u5206\u7684\u5b89\u88c5\u65b9\u6cd5<\/h2>\n<p>\u9996\u5148\u5c06 docker \u6587\u4ef6\u6253\u5305, \u7136\u540e\u8f6c\u6362\u4e3a sif \u6587\u4ef6:<\/p>\n<pre><code class=\"language-bash\">docker save cp2k_prod_psmp -o cp2k2022.tar\nsingularity build cp2k2022.sif docker-archive:\/\/cp2k2022.tar\n<\/code><\/pre>\n<p>\u6211\u4eec\u57fa\u4e8e\u4ee5\u4e0a\u53ef\u4ee5\u6b63\u5e38\u8fd0\u884c\u7684\u7a0b\u5e8f, \u76f4\u63a5\u4f7f\u7528 singularity \u547d\u4ee4\u8fd0\u884c cp2k \u65f6\u4f1a\u53d1\u73b0\u627e\u4e0d\u5230 mpirun, \u4e5f\u627e\u4e0d\u5230 cp2k, \u8fd9\u8bf4\u660e\u8f6c\u6362\u8fc7\u7a0b\u4e22\u6389\u4e86 .bashrc \u4e2d\u4fdd\u5b58\u7684\u73af\u5883\u53d8\u91cf\u6587\u4ef6, \u56e0\u6b64\u6211\u4eec\u9700\u8981\u624b\u52a8\u6dfb\u52a0\u4e00\u6b21. singularity \u4e2d\u8be5\u73af\u5883\u53d8\u91cf\u4fdd\u5b58\u5728 \/.singularity.d\/env\/90-environment.sh \u4e2d. \u4e3a\u4e86\u4fee\u6539\u8be5\u6587\u4ef6, \u6211\u4eec\u9700\u8981\u5c06 sif \u6587\u4ef6\u89e3\u5305, \u4fee\u6539\u540e\u91cd\u65b0\u6253\u5305.<\/p>\n<pre><code class=\"language-bash\">singularity build --sandbox cp2k2022\/ cp2k2022.sif\n<\/code><\/pre>\n<p>\u4e3a\u4e86\u4e0d\u8ba9\u955c\u50cf\u6587\u4ef6\u53d8\u5927, \u76f4\u63a5\u4f7f\u7528\u7269\u7406\u673a\u5bf9\u73af\u5883\u53d8\u91cf\u8fdb\u884c\u4fee\u6539, \u5728 90-environment.sh \u4e2d\u6dfb\u52a0\u5982\u4e0b\u5185\u5bb9\u4ee5\u627e\u5230\u652f\u63f4\u7a0b\u5e8f\u5305\u4e0e cp2k \u672c\u4f53:<\/p>\n<pre><code class=\"language-bash\">source \/opt\/cp2k-toolchain\/install\/setup\nexport PATH=$PATH:\/opt\/cp2k\/exe\/local\nexport CP2K_DATA_DIR=\/opt\/cp2k\/data\nexport OMP_NUM_THREADS=1\n<\/code><\/pre>\n<p>\u6d4b\u8bd5\u4e00\u4e0b\u6548\u679c:<\/p>\n<pre><code class=\"language-bash\">singularity exec -B ${PWD}:\/mnt -H \/mnt cp2k2022\/ mpirun -np 8 cp2k H2O-hybrid-b3lyp.inp |tee H2O-hybrid-b3lyp.out\n<\/code><\/pre>\n<p>\u5176\u4e2d -B \u662f\u7c7b\u4f3c\u4e8e docker \u4e2d\u7684 -v \u6307\u4ee4, \u7528\u4e8e\u6307\u5b9a\u5171\u4eab\u76ee\u5f55\u4e0e\u6302\u5728\u4f4d\u7f6e; -H \u7528\u4e8e\u6307\u5b9a\u5de5\u4f5c\u76ee\u5f55, \u540e\u9762\u7684\u5219\u662f cp2k \u7684\u4e00\u822c\u8c03\u7528\u65b9\u6cd5, \u5355\u72ec\u6307\u5b9a cp2k \u65f6\u8c03\u7528\u7684\u662f cp2k.psmp (\u8f6f\u94fe\u63a5).<\/p>\n<p>\u4e00\u5207\u5b8c\u6210\u540e, \u91cd\u65b0\u6253\u5305:<\/p>\n<pre><code class=\"language-bash\">singularity build cp2k2022-new.sif cp2k2022\/\n<\/code><\/pre>\n<p>\u4e3a\u4e86\u8ba9\u4e4b\u540e\u63d0\u4ea4\u7684\u65f6\u5019\u66f4\u65b9\u4fbf, \u6211\u4eec\u5199\u4e00\u4e2a bash \u811a\u672c\u7528\u4e8e\u63d0\u4ea4\u6587\u4ef6:<\/p>\n<pre><code class=\"language-bash\">#!\/bin\/bash\nexport SIF=\/home\/tkaray\/cp2k2022.sif\nexport cpucores=8\nsingularity exec -B ${PWD}:\/mnt -H \/mnt ${SIF} mpirun -np ${cpucores} cp2k.psmp $1 |tee ${2:-cp2k.out}\n<\/code><\/pre>\n<p>\u4fdd\u5b58\u4e3a submit.sh, \u4e4b\u540e\u5c31\u53ef\u4ee5\u7528\u8fd9\u4e2a\u811a\u672c\u63d0\u4ea4\u6587\u4ef6\u4e86, \u9700\u8981\u6307\u5b9a inp \u548c out \u6587\u4ef6\u540d, \u5f53\u672a\u6307\u5b9a out \u65f6\u5c31\u4f1a\u4ee5\u9ed8\u8ba4\u6587\u4ef6\u540d\u8f93\u51fa.<\/p>\n<pre><code class=\"language-bash\">chmod a+x submit.sh\n.\/submit.sh test.inp test.out\n<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u8fd9\u662f\u4e00\u7bc7\u5173\u4e8ecp2k 2022 \u7248\u672c docker \u955c\u50cf, \u548c\u57fa\u4e8e d &hellip;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[30],"tags":[35],"class_list":["post-645","post","type-post","status-publish","format-standard","hentry","category-notes","tag-35"],"_links":{"self":[{"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/posts\/645","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/rayray.moe\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=645"}],"version-history":[{"count":1,"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/posts\/645\/revisions"}],"predecessor-version":[{"id":646,"href":"https:\/\/rayray.moe\/index.php?rest_route=\/wp\/v2\/posts\/645\/revisions\/646"}],"wp:attachment":[{"href":"https:\/\/rayray.moe\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=645"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/rayray.moe\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=645"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/rayray.moe\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=645"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}