{"id":904,"date":"2023-10-10T11:04:22","date_gmt":"2023-10-10T03:04:22","guid":{"rendered":"https:\/\/www.homechemer.com\/?p=904"},"modified":"2025-09-18T14:30:51","modified_gmt":"2025-09-18T06:30:51","slug":"%e5%ae%9e%e7%94%a8%e4%b8%bb%e4%b9%89%e7%9a%84linux%e5%91%bd%e4%bb%a4%e5%92%8cbash%e8%84%9a%e6%9c%ac%e5%9f%ba%e7%a1%80%e5%85%a5%e9%97%a8","status":"publish","type":"post","link":"https:\/\/www.homechemer.com\/computchem\/11","title":{"rendered":"\u5b9e\u7528\u4e3b\u4e49\u7684Linux\u547d\u4ee4\u548cBash\u811a\u672c\u57fa\u7840\u5165\u95e8\uff08\u66f4\u65b0\u4e2d\uff09"},"content":{"rendered":"\n

\u5b9e\u7528\u4e3b\u4e49\u7684Linux\u547d\u4ee4\u548cBash\u811a\u672c\u57fa\u7840\u5165\u95e8\uff08\u66f4\u65b0\u4e2d\uff09
Pragmatical Tutorial for Basic Linux Commands and Bash Scripts (in Updating)<\/strong><\/p>\n\n\n\n

Jiawei Xu, Yingqi Li
Released: 2023-10-10 \/ Updated: 2023-10-10<\/p>\n\n\n\n

Linux\u7cfb\u7edf\u53ca\u5176\u81ea\u5e26\u7684Bash\u8bed\u8a00\u662f\u8ba1\u7b97\u5316\u5b66\u79d1\u7814\u5de5\u4f5c\u4e2d\u5fc5\u987b\u638c\u63e1\u7684\u57fa\u672c\u6280\u80fd\u3002\u672c\u6587\u65e8\u5728\u8ba9\u8ba1\u7b97\u5316\u5b66\u521d\u5b66\u8005\u5feb\u901f\u719f\u6089Linux\u7cfb\u7edf\u548cBash\u8bed\u8a00\uff0c\u4ece\u800c\u80fd\u591f\u5c3d\u5feb\u5f00\u5c55\u76f8\u5173\u5de5\u4f5c\uff0c\u8282\u7701\u65f6\u95f4\uff0c\u5c11\u8d70\u5f2f\u8def\u3002\u540c\u65f6\u672c\u6587\u4e5f\u4ecb\u7ecd\u4e86Linux\u7cfb\u7edf\u4e0b\u5b89\u88c5\u8f6f\u4ef6\u3001\u961f\u5217\u7cfb\u7edf\u4f7f\u7528\u3001\u76d1\u63a7\u4efb\u52a1\u7b49\u7684\u4e00\u822c\u505a\u6cd5\u3002<\/p>\n\n\n\n

\u672c\u6559\u7a0b\u4e2d\uff0c\u4ee5\u201c$\u201d\u5f00\u5934\u7684\u4ee3\u7801\u5757\u4ee3\u8868\u6b64\u4e3a\u5728Linux\u7ec8\u7aef\u4e2d\u6267\u884c\u7684\u6307\u4ee4\uff08\u4e0d\u5305\u62ec$\u5176\u672c\u8eab\uff0c\u53ea\u662f\u4e00\u4e2a\u6307\u793a\u7b26\u800c\u5df2\uff09\u3002<\/p>\n\n\n\n

1. Linux\u7cfb\u7edf\u7684\u57fa\u672c\u67b6\u6784<\/h2>\n\n\n\n

1.1 Linux\u7cfb\u7edf\u7684\u6587\u4ef6\u7ed3\u6784<\/h2>\n\n\n\n

\u4e0d\u540c\u4e8eWindows\u7cfb\u7edf\u5e38\u89c1\u7684\u5206\u76d8\u67b6\u6784\uff0cLinux\u7cfb\u7edf\u91c7\u7528\u6811\u72b6\u7ed3\u6784\u3002Linux\u91c7\u7528\u7684\u662f\u4e00\u4e2a\u5c42\u7ea7\u5f0f\u7684\u6587\u4ef6\u7cfb\u7edf\u7ed3\u6784\uff0c\u8fd9\u79cd\u7ed3\u6784\u4ee5\u6839\u76ee\u5f55\u201c\/\u201d\u4e3a\u57fa\u7840\uff08\u6240\u4ee5\u4e00\u5b9a\u4e0d\u80fd\u5c1d\u8bd5\u8fd0\u884crm -rf \/\uff0c\u8fd9\u4ee3\u8868\u5f3a\u5236\u9012\u5f52\u5220\u9664\u6839\u76ee\u5f55\uff0c\u4e5f\u5c31\u662f\u628a\u6574\u4e2a\u7cfb\u7edf\u90fd\u5220\u6389\uff0c\u91cc\u9762\u7684\u6570\u636e\u81ea\u7136\u4e5f\u5168\u6ca1\u4e86\uff01\uff09\uff0c\u6240\u6709\u5176\u4ed6\u6587\u4ef6\u548c\u76ee\u5f55\u90fd\u662f\u4ece\u8fd9\u91cc\u5f00\u59cb\u5ef6\u4f38\u3002\u8fd9\u79cd\u67b6\u6784\u76f8\u6bd4\u4e8eWindows\u66f4\u52a0\u6709\u6761\u7406\u3002<\/p>\n\n\n\n

1.2 \u6587\u4ef6\u8def\u5f84<\/strong><\/p>\n\n\n\n

\u53ef\u4ee5\u4ee5\u7edd\u5bf9\u8def\u5f84\u548c\u76f8\u5bf9\u8def\u5f84\u4e24\u79cd\u529e\u6cd5\u6765\u5b9a\u4f4d\u67d0\u4e00\u6587\u4ef6\u3002<\/p>\n\n\n\n

1.2.1 \u7edd\u5bf9\u8def\u5f84<\/strong><\/p>\n\n\n\n

\u7edd\u5bf9\u8def\u5f84\uff08absolute path\uff09\u6307\u4ece\u6839\u76ee\u5f55\u5f00\u59cb\u63cf\u8ff0\u8def\u5f84\uff0c\u4f8b\u5982\u201c\/hitachi\/mako\/is\/my\/waifu.py\u201d\u5c31\u662fwaifu.py\u8fd9\u4e2apython\u811a\u672c\u7684\u7edd\u5bf9\u8def\u5f84\u3002<\/p>\n\n\n\n

1.2.2 \u76f8\u5bf9\u8def\u5f84<\/strong><\/p>\n\n\n\n

\u76f8\u5bf9\u8def\u5f84\uff08relative path\uff09\u6307\u4ee5\u67d0\u4e00\u7279\u5b9a\u6587\u4ef6\u5939\u4e3a\u8d77\u70b9\u5f00\u59cb\u63cf\u8ff0\u8def\u5f84\u3002\u5e38\u89c1\u7684\u53c2\u7167\u7269\u6709\uff0c\u5f53\u524d\u76ee\u5f55\u201c.\u201d\uff0c\u4e0a\u4e00\u76ee\u5f55\u201c..\u201d\uff0c\u5f53\u524d\u7528\u6237\u7684\/usr\u76ee\u5f55\u201c~\/\u201d\u3002\u4f8b\u5982\u201c..\/play\/genshin.sh\u201d\u4ee3\u8868\u4e0a\u4e00\u76ee\u5f55\u4e2d\u7684\/play\u76ee\u5f55\u4e0b\u7684genshin.sh\u811a\u672c\u3002\u53c8\u4f8b\u5982\u201c.\/arknights.sh\u201d\u4ee3\u8868\u5f53\u524d\u76ee\u5f55\u4e0b\u7684arknights.sh\u811a\u672c\u3002<\/p>\n\n\n\n

2. Linux\u7cfb\u7edf\u5fc5\u4f1a\u6280\u80fd<\/strong><\/p>\n\n\n\n

2.2 grep<\/strong> (Globally search a Regular Expression and Print) \u6b63\u5219\u8868\u8fbe\u5f0f\u5168\u5c40\u641c\u7d22\u4e0e\u8f93\u51fa
\u57fa\u672c\u7528\u6cd5\uff1agrep\u547d\u4ee4\u7528\u4e8e\u5bf9\u6587\u672c\u8fdb\u884c\u641c\u7d22\uff0c\u5e76\u9ed8\u8ba4\u8f93\u51fa\u5339\u914d\u884c\u3002<\/p>\n\n\n\n

$ grep \"SCF Done:\" test.log # \u4eceGaussian16\u8f93\u51fa\u6587\u4ef6\u4e2d\u67e5\u627e\u5305\u542b\u201cSCF Done:\u201d\u7684\u6240\u6709\u884c\u5e76\u8f93\u51fa\u3002
$ grep \"FINAL SINGLE POINT ENERGY\" test.out # \u4eceORCA\u8f93\u51fa\u6587\u4ef6\u4e2d\u67e5\u627e\u5305\u542b\u201cFINAL SINGLE POINT ENERGY\u201d\u7684\u6240\u6709\u884c\u5e76\u8f93\u51fa\u3002
$ grep E(CASSCF) test.out # \u5982\u679c\u76ee\u6807\u5b57\u7b26\u4e32\u4e0d\u542b\u6709\u7a7a\u683c\uff0c\u4e5f\u53ef\u4ee5\u7701\u7565\u5f15\u53f7\u3002<\/code><\/pre>\n\n\n\n
\u4e00\u4e9b\u6269\u5c55\u6848\u4f8b\uff1a<\/p>\n\n\n\n
$ grep \"SCF Done:\" test.log | tail -1 # \u4eceGaussian16\u8f93\u51fa\u6587\u4ef6\u4e2d\u67e5\u627e\u5305\u542b\u201cSCF Done:\u201d\u7684\u6240\u6709\u884c\uff0ctail\u63a7\u5236\u53ea\u8f93\u51fa\u6700\u540e\u4e00\u6b21\u5339\u914d\u7684\u7ed3\u679c\u3002
$ grep \"Frequencies --\" freq.log | head -1 # head\u63a7\u5236\u53ea\u8f93\u51fa\u7b2c\u4e00\u6b21\u5339\u914d\u7684\u7ed3\u679c\u3002
$ grep \"SCF Done:\\|EUMP2\" test.log # \u67e5\u627e\u5305\u542b\u201cSCF Done:\u201d\u6216\u201cEUMP2\u201d\u7684\u6240\u6709\u884c\u3002\u5176\u4e2d\u201c|\u201d\u7528\u4e8e\u5e76\u5217\u591a\u4e2a\u5173\u952e\u8bcd\uff0c\u201c\\\u201d\u662f\u8f6c\u4e49\u7b26\u3002<\/code><\/pre>\n\n\n\n
\u4f7f\u7528set\u5c06grep\u547d\u4ee4\u7684\u8f93\u51fa\u6309\u7a7a\u683c\u5206\u5272\uff0c\u9010\u5355\u8bcd\u5b58\u50a8\u3002\u4ee5\u4e0b\u4e24\u884c\u547d\u4ee4\u5373\u53ef\u4eceGaussian16\u7684\u8f93\u51fa\u6587\u4ef6\uff08\u5982\u4f18\u5316\u4efb\u52a1\uff09\u4e2d\u83b7\u53d6\u6700\u540e\u4e00\u6b21SCF\u8fed\u4ee3\u7684\u80fd\u91cf\u7ed3\u679c\uff1a<\/p>\n\n\n\n
$ set `grep \"SCF Done:\" test.log | tail -1` # \u53cd\u5f15\u53f7\uff08``\uff09\u4e2d\u7684\u5185\u5bb9\u5c06\u4f1a\u4ee5\u547d\u4ee4\u5f62\u5f0f\u6267\u884c\uff0c\u5e76\u5c06\u8f93\u51fa\u7ed3\u679c\u4f20\u9012\u7ed9set\uff0c\u53d6\u6d88\u5c4f\u5e55\u8f93\u51fa\u3002
$ echo $5 # echo\u8868\u793a\u8f93\u51fa\uff0c\u9ed8\u8ba4\u8f93\u51fa\u5230\u5c4f\u5e55\u3002\u6b64\u5904\u8f93\u51fagrep\u7ed3\u679c\u7684\u7b2c\u4e94\u4e2a\u5355\u8bcd\uff0c\u5bf9\u5e94\u4e8eSCF\u80fd\u91cf\u3002<\/code><\/pre>\n\n\n\n
\u7c7b\u4f3c\u5730\uff0c\u4ee5\u4e0b\u547d\u4ee4\u53ef\u4ee5\u8bfb\u53d6\u6700\u5c0f\u7684\u4e00\u4e2a\u9891\u7387\uff0c\u53ef\u7528\u4e8e\u68c0\u67e5\u865a\u9891\uff1a<\/p>\n\n\n\n
$ set `grep \"Frequencies --\" freq.log | head -1`
$ echo $3
$ set `grep \"Frequencies --\" freq.log | head -1`; echo $3 # \u7528\u5206\u53f7\u5206\u9694\uff0c\u53ef\u5728\u540c\u4e00\u884c\u4e2d\u4e66\u5199\u591a\u884c\u547d\u4ee4\u3002<\/code><\/pre>\n\n\n\n
2.3 sed<\/strong>\uff08Stream EDitor\uff09\u6d41\u7f16\u8f91\u5668<\/p>\n\n\n\n
sed\u6700\u91cd\u8981\u7684\u529f\u80fd\u662f\u5bf9\u6587\u4ef6\u8fdb\u884c\u64cd\u4f5c\uff0c\u5982\u63d2\u5165\u3001\u5220\u9664\u548c\u67e5\u627e\u66ff\u6362\u3002<\/p>\n\n\n\n
# \u63d2\u5165
$ sed -i \"1i\\%nprocshared=32\" test.gjf # \u5728\u7b2c1\u884c\u524d\u63d2\u5165(i)\uff0c\u76f4\u63a5\u5bf9\u6587\u4ef6\u8fdb\u884c\u64cd\u4f5c(-i)\u3002\u201c\\\u201d\u4ec5\u4e3a\u4e86\u4fbf\u4e8e\u89c2\u770b\uff0c\u53ef\u7701\u7565\uff0c\u6b64\u5904\u4e0d\u8d77\u5b9e\u9645\u4f5c\u7528\u3002
$ sed -i \"1a\\%nprocshared=32\" test.gjf # \u5728\u7b2c1\u884c\u540e\u63d2\u5165(a)\u3002
$ sed -i \"\/%chk\/i %nprocshared=32\" test.gjf # \u67e5\u770b\u5305\u542b\u201c%chk\u201d\u7684\u884c\uff0c\u5728\u5176\u524d\u63d2\u5165\u201c%nprocshared=32\u201d\u3002
$ sed -i \"1i\\%nprocshared=32\\n%mem=96GB\" test.gjf # \u63d2\u5165\u8fde\u7eed\u591a\u884c\uff0c\u201c\\n\u201d\u8868\u793a\u6362\u884c\u7b26\u3002
# \u5220\u9664
$ sed -i \"\/nproc\/d\" test.gjf # \u5220\u9664(d)\u5305\u542b\u201cnproc\u201d\u7684\u6240\u6709\u884c\u3002
$ sed -i \"1d\" test.gjf # \u5220\u9664\u7b2c1\u884c\u3002
# \u67e5\u627e\u66ff\u6362
sed -i \"s\/nproc=2\/nproc=32\/g\" test.gjf # \u67e5\u627e\u6240\u6709\u7684\u201cnproc=2\u201d\u5b57\u6bb5\uff0c\u5e76\u5c06\u5176\u66ff\u6362\u4e3a\u201cnproc=32\u201d\u3002
sed -i \"\/nproc\/c\\%nprocshared=32\" test.gjf # \u5c06\u5305\u542b\u201cnproc\u201d\u7684\u6574\u884c\u66ff\u6362(c)\u4e3a\u201c%nprocshared=32\u201d<\/code><\/pre>\n\n\n\n
\n\n\n\n
\u5b9e\u4f8b\u7ec3\u4e60  <\/mark><\/strong>\u73b0\u6709\u4e00\u6279Multiwfn\u4ea7\u751f\u7684.gjf\u6587\u4ef6\uff0c\u9700\u5c06\u5176\u4fee\u6539\u4e3aMOKIT\u505aGKS-EDA\u8ba1\u7b97\uff08\u5b9e\u9645\u4e0a\u662f\u751f\u6210XEDA\u8f93\u5165\u6587\u4ef6\uff09\u7684\u8f93\u5165\u6587\u4ef6\u3002\u7ed3\u6784\u4e2d\u5305\u542b1\u4e2aFe\u539f\u5b50\u548cH\u3001C\u3001N\u3001O\u7ec4\u6210\u7684\u6709\u673a\u914d\u4f53\uff0c\u5c06Fe\u539f\u5b50\u5355\u72ec\u5212\u5206\u4e3a\u4e00\u4e2a\u7247\u6bb5\uff0c\u5176\u4f59\u914d\u4f53\u4f5c\u4e3a\u53e6\u4e00\u4e2a\u7247\u6bb5\u3002\u8bd5\u5b9e\u73b0\u4e4b\u3002<\/p>\n\n\n\n
\u5206\u6790<\/mark><\/strong>  \u9700\u8981\u5b9e\u73b0\u4ee5\u4e0b\u51e0\u4e2a\u529f\u80fd\uff1a1. \u6839\u636e\u5b9e\u9645\u9700\u6c42\u8bbe\u5b9a\u5e76\u884c\u6838\u6570\u548c\u5185\u5b58\uff1b2. \u5220\u9664\u201c%chk\u201d\u884c\uff1b3. \u4fee\u6539\u5173\u952e\u8bcd\u884c\uff1b4. \u5c06Multiwfn\u4ea7\u751f.gjf\u7684\u9ed8\u8ba4\u6807\u9898\u66ff\u6362\u4e3a\u201c{gks}\u201d\uff1b5. \u4fee\u6539\u7535\u8377\u548c\u81ea\u65cb\u591a\u91cd\u5ea6\uff1b6. \u6309\u7167\u7247\u6bb5\u5212\u5206\u89c4\u5219\u5bf9\u539f\u5b50\u6392\u5e8f\uff0c\u5e76\u9644\u4e0a\u6240\u5c5e\u7247\u6bb5\u5e8f\u53f7\u3002<\/p>\n\n\n\n
\u5b9e\u73b0<\/mark><\/strong>  \u9996\u5148\u8003\u8651\u5bf9\u5176\u4e2d\u4e00\u4e2a\u8f93\u5165\u6587\u4ef6\u5b8c\u6210\u4ee5\u4e0a\u5de5\u4f5c\u3002<\/p>\n\n\n\n
<\/code><\/pre>\n\n\n\n
\n\n\n\n
<\/p>\n\n\n\n
3. Bash\u811a\u672c\u57fa\u7840<\/strong><\/p>\n\n\n\n
3.1 \u5faa\u73af\u8bed\u53e5<\/strong><\/p>\n\n\n\n
3.1.1 for\u5faa\u73af<\/strong>
for\u5faa\u73af\u662f\u6700\u57fa\u672c\u7684\u5faa\u73af\u8bed\u53e5\uff0c\u5176\u57fa\u672c\u7ed3\u6784\u4e3a\uff1afor<\/mark> variable<\/em> in<\/mark> range<\/em>; do<\/mark> commands<\/em>; done<\/mark>\uff0c\u5176\u4f9d\u6b21\u5c06range<\/em>\u4e2d\u7684\u6bcf\u4e2a\u503c\u8d4b\u503c\u7ed9\u5faa\u73af\u53d8\u91cfvariable<\/em>\uff0c\u4e3a\u5176\u6267\u884c\u5faa\u73af\u4f53commands<\/em>\u6240\u5b9a\u4e49\u7684\u547d\u4ee4\u3002\u4f8b\u5982\u4ee5\u4e0b\u8bed\u53e5\u5c06\u4f1a\u8f93\u51fa10\u6b21\u201cHello World!\u201d\uff1a<\/p>\n\n\n\n
for i in {1..10} # \u4e0ePython\u4e0d\u540c\uff0cBash\u4e2d\u7684{1..10}\u662f\u4e00\u4e2a\u95ed\u533a\u95f4\ndo\n  echo \"Hello World!\"\ndone<\/code><\/pre>\n\n\n\n
Bash\u811a\u672c\u5bf9\u7f29\u8fdb\u4e0d\u654f\u611f\uff0c\u4f46\u4e3a\u4fdd\u8bc1\u4ee3\u7801\u7684\u53ef\u8bfb\u6027\uff0c\u4e5f\u5e94\u5408\u7406\u5b89\u6392\u7f29\u8fdb\u3002\u4ee5\u4e0a\u547d\u4ee4\u8f83\u4e3a\u7b80\u5355\uff0c\u4e5f\u53ef\u5199\u6210\u5355\u884c\u7684\u5f62\u5f0f\uff1a<\/p>\n\n\n\n
for i in {1..10}; do echo \"Hello World!\"; done<\/code><\/pre>\n\n\n\n
\u66f4\u591a\u7684\u65f6\u5019\uff0c\u5faa\u73af\u4f53\u5185\u90e8\u9700\u8981\u5bf9\u5faa\u73af\u53d8\u91cf\u7684\u503c\u8fdb\u884c\u5f15\u7528\uff1a<\/p>\n\n\n\n
for i in {1..10}; do echo $i; done # $i\u8868\u793a\u53d8\u91cfi\u7684\u503c\uff0c\u8be5\u547d\u4ee4\u5c06\u4f1a\u9010\u884c\u8f93\u51fa1\u523010\u517110\u4e2a\u6570\u5b57\u3002\nfor i in .\/*.gjf; do g16 $i; done # \u53d8\u91cf\u4e5f\u53ef\u4ee5\u662f\u6587\u4ef6\u540d\u7b49\uff0c\u8be5\u547d\u4ee4\u4e3a\u5f53\u524d\u76ee\u5f55\u4e0b\u6240\u6709.gjf\u540e\u7f00\u7684\u6587\u4ef6\u8fd0\u884cg16\u4efb\u52a1\u3002<\/code><\/pre>\n\n\n\n
\u7ed3\u5408\u5176\u4ed6Linux\u547d\u4ee4\uff0c\u6216\u8c03\u7528\u5916\u90e8\u7a0b\u5e8f\uff0c\u4ee5\u5b9e\u73b0\u66f4\u591a\u6837\u5316\u7684\u529f\u80fd\uff1a<\/p>\n\n\n\n
for i in .\/*.gjf\ndo\n  filename=`basename $i .gjf` # \u5c06i\u7684\u503c\u53bb\u6389\u540e\u7f00.gjf\uff0c\u5e76\u8d4b\u503c\u7ed9\u65b0\u7684\u53d8\u91cffilename\u3002\n  mkdir -p $filename; mv $i $filename; cd $filename # \u4e3a\u6bcf\u4e2a\u4efb\u52a1\u521b\u5efa\u5355\u72ec\u7684\u6587\u4ef6\u5939\u8fd0\u884c\u3002\n  g16 $filename.gjf\n  cd ..\ndone<\/code><\/pre>\n\n\n\n
\u4ee5\u4e0b\u547d\u4ee4\u5c06\u4f1a\u5b9e\u73b0\u6279\u91cf\u8f6c\u6362\u5f53\u524d\u76ee\u5f55\u4e0b\u7684\u6240\u6709.fchk\u6587\u4ef6\u4e3a.gjf\u6587\u4ef6\uff1a<\/p>\n\n\n\n
for i in .\/*.fchk\ndo\n  Multiwfn $i >> tmp << EOF # >>\u5c06Multiwfn\u7684\u5c4f\u5e55\u8f93\u51fa\u91cd\u5b9a\u5411\u81f3\u4e34\u65f6\u6587\u4ef6tmp\uff1b<<\u5c06\u540e\u7eed\u5185\u5bb9\u91cd\u5b9a\u5411\u81f3Multiwfn\u6267\u884c\u3002\n100\n2\n10\n\nn\n0\nq\nEOF # EOF: End Of File\uff1b\u4e24\u4e2aEOF\u4e4b\u95f4\u7684\u6240\u6709\u5185\u5bb9\u5c06\u88ab\u91cd\u5b9a\u5411\u81f3Multiwfn\u3002\n  rm tmp # \u5220\u9664\u4e34\u65f6\u6587\u4ef6\u3002\ndone<\/code><\/pre>\n\n\n\n
<\/p>\n\n\n\n
4. \u672c\u7ec4\u5e38\u7528\u8f6f\u4ef6\u5b89\u88c5<\/strong><\/p>\n\n\n\n
\u5728\u4e0d\u4f7f\u7528\u7ba1\u7406\u5458\u6743\u9650\u7684\u60c5\u51b5\u4e0b\uff08\u5f88\u663e\u7136\uff0c\u4e0d\u4f7f\u7528\u7ba1\u7406\u5458\u6743\u9650\u7684\u524d\u63d0\u662f\u5728home\u76ee\u5f55\u4e0b\u5b89\u88c5\u7a0b\u5e8f\uff09\uff0cLinux\u7cfb\u7edf\u4e0b\u8f6f\u4ef6\u6216\u7a0b\u5e8f\u7684\u5b89\u88c5\uff0c\u4e00\u822c\u6839\u636e\u5b89\u88c5\u5305\u7684\u4e0d\u540c\u5206\u4e3a\u9884\u7f16\u8bd1\u7248\u672c\u5b89\u88c5\u548c\u4ece\u6e90\u7801\u5b89\u88c5\u3002\u9884\u7f16\u8bd1\u7248\u672c\u7684\u7a0b\u5e8f\u5b89\u88c5\u4e00\u822c\u975e\u5e38\u7b80\u5355\uff0c\u89e3\u538b\u540e\u6839\u636e\u5b9e\u9645\u60c5\u51b5\u8bbe\u7f6e\u73af\u5883\u53d8\u91cf\u5373\u53ef\uff0c\u5982Gaussian16\u3001ORCA\u7b49\u90fd\u63d0\u4f9b\u9884\u7f16\u8bd1\u7248\u672c\u5b89\u88c5\u5305\u3002\u4ece\u6e90\u7801\u5b89\u88c5\u7684\u60c5\u51b5\u66f4\u4e3a\u590d\u6742\uff0c\u901a\u5e38\u5206\u4e3a\u4e09\u6b65\uff1a
1). \u914d\u7f6e (configure)<\/mark>
\u8bb8\u591a\u7a0b\u5e8f\u5bf9\u5e94\u4e8e\u4e00\u4e2a\u53ef\u6267\u884c\u6587\u4ef6configure\uff0c\u4e00\u822c\u662f\u5df2\u7ecf\u5177\u6709\u53ef\u6267\u884c\u6743\u9650\u7684Bash\u811a\u672c\u3002\u5176\u57fa\u672c\u547d\u4ee4\u662f\uff1a<\/p>\n\n\n\n
$ .\/configure --prefix=\/home\/jwxu\/programs\/install_dir<\/code><\/pre>\n\n\n\n
\u9009\u9879\u201c–prefix\u201d\u6307\u5b9a\u5b89\u88c5\u76ee\u5f55\u3002\u67d0\u4e9b\u7a0b\u5e8f\uff08\u5982Dalton\uff09\u5f3a\u5236\u8981\u6c42\u5b89\u88c5\u76ee\u5f55\u4e0d\u80fd\u4e0e\u7f16\u8bd1\u76ee\u5f55\u96f7\u540c\uff0c\u5373\u5b89\u88c5\u76ee\u5f55\u5fc5\u987b\u4e0e\u89e3\u538b\u7f29\u7684\u5f97\u5230\u76ee\u5f55\u4e0d\u540c\uff0c\u4f8b\u5982\u89e3\u538b\u7f29Dalton\u5230~\/programs\/dalton-src\uff0c\u5219\u5b89\u88c5\u76ee\u5f55\u5fc5\u987b\u662f\u4e0e\u4e4b\u4e0d\u540c\u7684~\/programs\/dalton\u7b49\u3002\u4e00\u822c\u603b\u662f\u5efa\u8bae\u4f7f\u7528\u4e0d\u540c\u7684\u5b89\u88c5\u76ee\u5f55\uff0c\u5b89\u88c5\u5b8c\u6210\u540e\u53ef\u4ee5\u5220\u53bb\u7f16\u8bd1\u76ee\u5f55\u8282\u7701\u7a7a\u95f4\uff0c\u4f46\u6709\u4e9b\u7a0b\u5e8f\u663e\u7136\u4e0d\u80fd\u8fd9\u4e48\u505a\uff0c\u5982Tcl-ChemShell\uff0c\u8fd9\u662f\u5f00\u53d1\u8005\u7684\u95ee\u9898\u3002
\u6709\u65f6\u8fd8\u9700\u8981\u63d0\u4f9b\u989d\u5916\u7684\u9009\u9879\uff0c\u6839\u636e\u5b9e\u9645\u60c5\u51b5\u8fdb\u884c\u5904\u7406\u3002
2). \u7f16\u8bd1 (compile)<\/mark>
\u4e00\u822c\u4f7f\u7528make\u547d\u4ee4\u8fdb\u884c\u7f16\u8bd1\u3002\u914d\u7f6e\u5b8c\u6210\u540e\u4f1a\u5728\u5f53\u524d\u76ee\u5f55\u4ea7\u751f\u4e00\u4e2aMakefile\u6587\u4ef6\uff0cmake\u547d\u4ee4\u6839\u636eMakefile\u7684\u5185\u5bb9\u8fdb\u884c\u7f16\u8bd1\uff0c\u53ef\u901a\u8fc7\u4ee5\u4e0b\u65b9\u5f0f\u5e76\u884c\u7f16\u8bd1\u52a0\u5feb\u901f\u5ea6\uff1a<\/p>\n\n\n\n
$ make -j # \u4f7f\u7528\u5168\u90e8\u53ef\u7528\u7ebf\u7a0b\u6570\u3002
$ make -j16 # \u4f7f\u752816\u7ebf\u7a0b\u7f16\u8bd1\u3002<\/code><\/pre>\n\n\n\n
\u67d0\u4e9b\u60c5\u51b5\u4e0b\u5e76\u884c\u7f16\u8bd1\u53ef\u80fd\u4f1a\u51fa\u9519\uff0c\u6b64\u65f6\u5e94\u5148\u53bb\u6389-j\u9009\u9879\u5c1d\u8bd5\u8fdb\u884c\u4e32\u884c\u7f16\u8bd1\u3002\u7f16\u8bd1\u5b8c\u6210\u540e\uff0c\u76f8\u5173\u53ef\u6267\u884c\u7a0b\u5e8f\u548c\u5e93\u6587\u4ef6\u5df2\u7ecf\u5b58\u5728\u4e8e\u7f16\u8bd1\u76ee\u5f55\u5185\u7684\u5404\u4e2a\u5b50\u6587\u4ef6\u5939\u4e2d\u3002
3). \u5b89\u88c5 (install)<\/mark>
\u5982\u7a0b\u5e8f\u662f\u901a\u8fc7make\u7f16\u8bd1\u7684\uff0c\u5219\u8fd0\u884c\u4ee5\u4e0b\u547d\u4ee4\u5b89\u88c5\uff1a<\/p>\n\n\n\n
$ make install [-j]<\/code><\/pre>\n\n\n\n
\u4e4b\u540e\u76f8\u5173\u6587\u4ef6\u88ab\u5b89\u88c5\u81f3\u914d\u7f6e\u65f6\u6307\u5b9a\u7684\u5b89\u88c5\u76ee\u5f55\u3002\u6b64\u65f6\u53ef\u5220\u53bb\u7f16\u8bd1\u76ee\u5f55\u4ee5\u8282\u7701\u7a7a\u95f4\u3002\u5728.bashrc\u6216\u961f\u5217\u7cfb\u7edf\u811a\u672c\u4e2d\u6dfb\u52a0\u76f8\u5173\u73af\u5883\u53d8\u91cf\uff0c\u5c31\u53ef\u4ee5\u6b63\u5e38\u4f7f\u7528\u7a0b\u5e8f\u4e86\u3002
\u5927\u591a\u6570\u7a0b\u5e8f\u90fd\u662f\u901a\u8fc7\u4ee5\u4e0a\u4e09\u6b65\u8fdb\u884c\u5b89\u88c5\uff0c\u4f46\u5e76\u4e0d\u90fd\u662f\u4f7f\u7528\u4ee5\u4e0a\u547d\u4ee4\uff0c\u5982Dalton\u901a\u8fc7cmake\u7f16\u8bd1\uff0c\u67d0\u4e9bPython\u7a0b\u5e8f\u4f1a\u63d0\u4f9bsetup.py\u7528\u4e8e\u5b89\u88c5\uff0c\u8fd9\u5728\u540e\u9762\u9047\u5230\u65f6\u518d\u8fdb\u884c\u8be6\u7ec6\u89e3\u91ca\u3002<\/p>\n\n\n\n
4.1 Intel\u5168\u5bb6\u6876<\/strong><\/p>\n\n\n\n
Intel\u5168\u5bb6\u6876\uff0c\u4e00\u822c\u6307\u7684\u662f\u5305\u542bIntel\u7f16\u8bd1\u5668\u3001MKL\u6570\u5b66\u5e93\u3001Intel MPI\u5e76\u884c\u5e93\u7b49\u5e38\u7528\u5de5\u5177\u5728\u5185\u7684\u4e00\u7cfb\u5217Intel\u4ea7\u54c1\u7684\u4ee3\u79f0\uff0c\u8bb8\u591a\u5e38\u7528\u8f6f\u4ef6\u5728\u7f16\u8bd1\u6216\u8fd0\u884c\u65f6\u90fd\u4f1a\u7528\u5230\u3002\u4ee5\u5728\u7ebf\u7248\u4e3a\u4f8b\uff08\u5982\u673a\u5b50\u65e0\u6cd5\u8054\u7f51\uff0c\u5219\u4e0b\u8f7d\u79bb\u7ebf\u7248<\/a>\uff09\uff0c\u9996\u5148\u5230Intel\u5b98\u7f51(https:\/\/www.intel.cn\/content\/www\/cn\/zh\/homepage.html<\/a>)\u4e0b\u8f7d\u6240\u9700\u7248\u672c\u7684Intel oneAPI Base Toolkit\u548cIntel oneAPI HPC Toolkit\uff0c\u7136\u540e\u8fd0\u884c\u5b89\u88c5\u7a0b\u5e8f\uff1a<\/p>\n\n\n\n
$ chmod +x l_BaseKit_p_2022.2.0.262.sh l_HPCKit_p_2022.2.0.191.sh
$ .\/l_BaseKit_p_2022.2.0.262.sh # \u6309\u7167\u63d0\u793a\u8fdb\u884c\u5b89\u88c5\u3002\u9ed8\u8ba4\u5b89\u88c5\u5728~\/intel\u76ee\u5f55\u4e0b\u3002
$ .\/l_HPCKit_p_2022.2.0.191.sh
$ cd ~\/intel\/oneapi
$ .\/modulefiles-setup.sh # \u6b64\u65f6\u5728~\/intel\/oneapi\/modulefiles\u76ee\u5f55\u4e0b\u4ea7\u751f\u4e86\u76f8\u5e94\u73af\u5883\u6587\u4ef6\u3002<\/code><\/pre>\n\n\n\n
\u5b89\u88c5tcl\u548cmodules\u73af\u5883\u7ba1\u7406\u5668\uff08\u5982\u5df2\u5b89\u88c5\uff0c\u53ef\u8df3\u8fc7\u6b64\u6b65\u9aa4\uff09\u3002\u6709\u4e9b\u60c5\u51b5\u4e0b\uff0c\u5728\u767b\u9646\u8282\u70b9\u5df2\u7ecf\u5b89\u88c5\u4e86tcl\uff0c\u7136\u800c\u8ba1\u7b97\u8282\u70b9\u4e0a\u5e76\u672a\u5b89\u88c5\uff0c\u5bfc\u81f4modules\u8fd0\u884c\u65f6\u62a5\u9519\u627e\u4e0d\u5230\u89e3\u91ca\u5668\u201c\/usr\/bin\/tclsh\u201d\uff0c\u5bf9\u4e8e\u975eroot\u7528\u6237\u53ef\u81ea\u884c\u5b89\u88c5tcl\u6765\u4fdd\u8bc1modules\u6b63\u5e38\u8fd0\u884c\u3002\u6ce8\u610f\uff0c\u5982\u679c\u4f7f\u7528\u96c6\u7fa4\u6216\u8d85\u7b97\uff0c\u5e94\u5411\u7ba1\u7406\u5458\u54a8\u8be2\u662f\u5426\u5df2\u7ecf\u5b89\u88c5\u4e86\u76f8\u5173\u73af\u5883\uff0c\u4ee5\u514d\u91cd\u590d\u5b89\u88c5\u3002<\/mark><\/p>\n\n\n\n
$ wget https:\/\/cfhcable.dl.sourceforge.net\/project\/tcl\/Tcl\/8.6.9\/tcl8.6.9-src.tar.gz
$ tar -xf tcl8.6.9-src.tar.gz
$ cd tcl8.6.9\/unix
$ .\/configure --prefix=\/home\/jwxu\/programs\/tcl-8.6.9
$ make -j && make install -j # \u5c06tcl\u5b89\u88c5\u5230\/home\/jwxu\/programs\/tcl-8.6.9

$ wget https:\/\/newcontinuum.dl.sourceforge.net\/project\/modules\/Modules\/modules-4.2.4\/modules-4.2.4.tar.gz
$ tar -xf modules-4.2.4.tar.gz
$ cd modules-4.2.4
$ .\/configure --prefix=\/home\/jwxu\/programs\/modules \\
            --with-tcl-lib=\/home\/jwxu\/programs\/tcl-8.6.9\/lib \\
            --with-tcl-inc=\/home\/jwxu\/programs\/tcl-8.6.9\/include \\
            --with-tclsh=\/home\/jwxu\/programs\/tcl-8.6.9\/bin\/tclsh # \u4e5f\u53ef\u80fd\u662ftclsh8.6
$ make -j # \u6b64\u6b65\u9aa4\u53ef\u80fd\u4f1a\u62a5\u9519\u201c\u672a\u5b9a\u4e49\u7684...\u201d\uff0c\u6ce8\u91ca\u6389\u76f8\u5173\u4ee3\u7801\u5373\u53ef\u3002
$ make install -j # \u5c06modules\u5b89\u88c5\u5230\/home\/jwxu\/programs\/modules

$ cp -r \/home\/jwxu\/intel\/oneapi\/modulefiles\/* \/home\/jwxu\/programs\/modules\/modulefiles
# \u4ee5\u4e0a\u5c06Intel\u76f8\u5173\u7684modules\u73af\u5883\u6587\u4ef6\u590d\u5236\u5230\u9ed8\u8ba4\u8def\u5f84\u3002\u4e5f\u53ef\u7528\u4ee5\u4e0b\u547d\u4ee4\u66ff\u4ee3\uff1a
$ export MODULEPATH=$MODULEPATH:\/home\/jwxu\/intel\/oneapi\/modulefiles # \u5982\u7528\u6b64\u6cd5\uff0c\u53ef\u5c06\u6b64\u884c\u547d\u4ee4\u6dfb\u52a0\u81f3~\/.bashrc\u6587\u4ef6\u3002

$ source \/home\/jwxu\/programs\/modules\/init\/profile.sh # \u53ef\u5c06\u6b64\u884c\u547d\u4ee4\u6dfb\u52a0\u81f3~\/.bashrc\u6587\u4ef6\u3002
$ module load compiler mkl mpi # \u5373\u8f7d\u5165Intel\u7f16\u8bd1\u5668\u3001MKL\u6570\u5b66\u5e93\u548cIntel MPI\u5e76\u884c\u5e93\u3002<\/code><\/pre>\n\n\n\n
4.2 Tcl-ChemShell 3.7.1<\/strong><\/p>\n\n\n\n
\u9996\u5148\u5b89\u88c5Tcl\uff0c\u53c2\u89c13.1\u4e2d\u76f8\u5173\u5185\u5bb9\u3002\u4f7f\u7528Intel\u7f16\u8bd1\u5668\u5b89\u88c5\u4e32\u884c\u7248\u672c\u7684Tcl-ChemShell\uff1a<\/p>\n\n\n\n
$ export CC=icc
$ export F77=ifort
$ export F90=ifort
$ export TCLROOT=\/home\/jwxu\/programs\/tcl-8.6.9
$ export LIBTCL=$TCLROOT\/lib\/libtcl8.6.so
$ export PATH=\/home\/jwxu\/programs\/chemsh-3.7.1\/bin:\/home\/jwxu\/programs\/chemsh-3.7.1\/scripts:$PATH
$ cd chemsh-3.7.1\/src\/config
$ .\/configure<\/code><\/pre>\n\n\n\n
\u6dfb\u52a0\u73af\u5883\u53d8\u91cf\uff0c\u6216\u5c06\u73af\u5883\u53d8\u91cf\u5199\u5165\u6295\u4efb\u52a1\u7684\u811a\u672c\u4e2d\uff1a<\/p>\n\n\n\n
$ export TCLROOT=\/home\/jwxu\/programs\/tcl-8.6.9
$ export LIBTCL=$TCLROOT\/lib\/libtcl8.6.so
$ export PATH=$TCLROOT\/bin:\/home\/jwxu\/programs\/chemsh-3.7.1\/bin:\/home\/jwxu\/programs\/chemsh-3.7.1\/scripts:$PATH<\/code><\/pre>\n\n\n\n
4.3 GAMESS-US<\/strong><\/p>\n\n\n\n
4.4<\/strong> GROMACS<\/p>\n\n\n\n
\u8fd9\u91cc\u4ee5\u672c\u7ec4\u5e38\u7528\u7684GROMACS-2022.5\u7248\u672c\u4e3a\u4f8b\uff0c\u9996\u5148\u6765\u51c6\u5907\/\u68c0\u67e5GROMACS\u5b89\u88c5\u7684\u524d\u7f6e\u6761\u4ef6<\/p>\n\n\n\n
1. fftw
fftw (i.e.\u5feb\u901f\u5085\u7acb\u53f6\u53d8\u6362\u5e93)
$ wget http:\/\/www.fftw.org\/fftw-3.3.8.tar.gz  # \u83b7\u5f97fftw\u7684\u6e90\u4ee3\u7801
$ .\/configure --prefix=\/home\/fftw338 --enable-sse2 --enable-avx --enable-float --enable-shared # --enable-avx2 \u53ef\u9009\uff0c\u524d\u63d0\u662f\u4f60\u7684cpu\u652f\u6301avx2,\u4f7f\u7528lscpu\u6307\u4ee4\u67e5\u770b\u8f93\u51fa\u7684\u201c\u6807\u8bb0\u201d\u4e00\u680f\u4e2d\uff0c\u662f\u5426\u6709avx2\u5b57\u6bb5.
$ make -j install

2. cmake
\u5728\u524d\u9762\uff0c\u6211\u4eec\u5df2\u7ecf\u4ecb\u7ecd\u4e86cmake\u7684\u7f16\u8bd1
$ cmake --version # \u67e5\u770bcmake\u7248\u672c

3. cuda # \u4ec5gpu\u52a0\u901f\u7248\u672c\uff08\u7528\u4e8eNvidia\u663e\u5361\uff09\uff0c\u6ce8\u610f\uff0c\u6781\u5ea6\u4e0d\u63a8\u8350\u5728\u4e0d\u91c7\u7528GPU\u52a0\u901f\u7684\u60c5\u51b5\u4e0b\u4ee5\u751f\u4ea7\u7528\u9014\u8dd1\u5206\u5b50\u52a8\u529b\u5b66\u7a0b\u5e8f\uff01
# \u8fd9\u91cc\u4ecb\u7ecd\u8054\u7f51\u548c\u4e0d\u8054\u7f51\u4e24\u79cd\u5b89\u88c5\u65b9\u5f0f\uff0c\u5747\u9ed8\u8ba4\u5df2\u7ecf\u5b89\u88c5Nvidia\u9a71\u52a8\uff08\u4e24\u8005\u53d6\u5176\u4e00\u5373\u53ef\uff09
# a.\u8054\u7f51\u5b89\u88c5\uff08\u9700\u8981root\u548c\u516c\u7f51\u8bbf\u95ee\u6743\u9650\uff09
$ nvidia-smi # \u5982\u679c\u6709\u6b63\u5e38\u8f93\u51fa\u663e\u5361\u4fe1\u606f\uff0c\u5219\u4ee3\u8868Nvidia\u9a71\u52a8\u5b89\u88c5\u597d\u4e86\uff0c\u53ef\u4ee5\u7ee7\u7eed\u5f80\u540e\u5b89\u88c5
$ sudo dnf config-manager --add-repo http:\/\/developer.download.nvidia.com\/compute\/cuda\/repos\/rhel8\/x86_64\/cuda-rhel8.repo # \u6dfb\u52a0Nvidia\u4e13\u5c5e\u4ed3\u5e93
$ sudo dnf clean all # \u6dfb\u52a0\u4ed3\u5e93\u540e\u6e05\u7f13\u5b58\u662f\u4e00\u4e2a\u597d\u4e60\u60ef
$ sudo sudo dnf -y install cuda-toolkit-12-2 # \u8fd9\u91cc\u662f\u4e0d\u5305\u62ecnvidia\u9a71\u52a8\u7684,\u4ee5cuda-12.2\u4e3a\u4f8b
# \u7136\u540e\u9700\u8981\u5199cuda\u7684\u73af\u5883\u53d8\u91cf\uff0c\u8fd9\u91cc\u6781\u5ea6\u63a8\u8350\u4f7f\u7528module\u7ba1\u7406\uff0cmodule\u6587\u4ef6\u9644\u5728\u4e86\u672c\u6587\u7684\u6700\u540e
$ module load cuda # \u5982\u679c\u4f7f\u7528module\u7ba1\u7406\u73af\u5883\u53d8\u91cf\uff0c\u9700\u8981\u5148load
$ nvcc --version # \u6b63\u5e38\u8f93\u51fa\u5219\u4ee3\u8868\u5b89\u88c5\u5b8c\u6bd5

4. gcc
# CentOS\u8f6f\u4ef6\u4ed3\u5e93\u81ea\u5e26\u7684gcc\u5f80\u5f80\u7248\u672c\u8ddf\u4e0d\u4e0agromacs\u7684\u9700\u6c42\uff0c\u8fd9\u91cc\u4ecb\u7ecd\u4e0b\u5982\u4f55\u7f16\u8bd1\u4f60\u60f3\u8981\u7684\u7248\u672c
$ wget http:\/\/ftp.gnu.org\/gnu\/gcc\/gcc-9.5.0\/gcc-9.5.0.tar.gz # \u83b7\u53d6gcc9.5\u7684\u6e90\u7801
$ tar xvf gcc-9.5.0.tar.gz
$ cd gcc-9.5.0
$ .\/contrib\/download_prerequisites # \u8fd0\u884cgcc\u81ea\u5e26\u7684\u8865\u5168\u4f9d\u8d56\u811a\u672c
$ mkdir build # \u7ed9\u7f16\u8bd1\u4ea7\u751f\u7684\u6587\u4ef6\u5355\u5f00\u4e00\u4e2a\u76ee\u5f55\u5b89\u653e\u662f\u4e00\u4e2a\u597d\u4e60\u60ef\uff0c\u53ef\u4ee5\u907f\u514d\u6c61\u67d3\u4ee3\u7801\u6811
$ cd build
$ ..\/configure --prefix=\/home\/gcc-9.5.0 --enable-language=c,c++,fortran --disable-multilib 
# \u4e00\u822c\u6559\u7a0b\u91cc\u9762\u4e0d\u4f1aenable fortran\uff0c\u7279\u522b\u6ce8\u610f\uff0c\u8fd9\u8fb9\u4e00\u5b9a\u8981enable fortran\uff0c\u5426\u5219\u6ca1\u6709gfortran\u7528
$ make -j # \u5982\u679c\u7f16\u8bd1\u62a5\u9519\uff0c\u5c1d\u8bd5-j12\u6216\u66f4\u5c0f\u5e76\u884c\u6838\u6570\uff0cgcc\u7f16\u8bd1\u5f88\u6162\uff0c\u8bf7\u8010\u5fc3\u7b49\u5f85
$ make install<\/code><\/pre>\n\n\n\n
\u968f\u540e\u5b89\u88c5gromacs\u672c\u4f53\uff0c\u5148\u524d\u5f80gromacs\u5b98\u7f51\u4e0b\u8f7d\u7a0b\u5e8f\u6e90\u7801\uff08\u6216\u8bb8\u7531\u4e8e\u67d0\u4e9b\u9b54\u6cd5\u56e0\u7d20\uff0c\u7b14\u8005\u53ea\u80fd\u4f7f\u7528\u5c40\u57df\u7f51\u7684wget\u83b7\u53d6\u6e90\u7801\u662f\u4e0d\u53ef\u884c\u7684\uff09\uff0c\u4f20\u5230\u5f85\u5b89\u88c5\u7684\u673a\u5668\u4e0a\uff0c\u89e3\u538b\uff0c\u8fdb\u5165\u76ee\u5f55\uff0c\u4e4b\u540e\uff1a<\/p>\n\n\n\n
$ mkdir build # \u4f9d\u65e7\u4fdd\u6301\u597d\u4e60\u60ef
$ cd build
$ export CMAKE_PREFIX_PATH=\/home\/fftw338 # \u6b64\u5904\u4e3a\u4e0a\u4e00\u6b65\u5b89\u88c5fftw\u7684\u8def\u5f84
$ cmake .. -DCMAKE_INSTALL_PREFIX=\/home\/gromacs-2022.5 -DCUDA_TOOLKIT_ROOT_DIR=\/usr\/local\/cuda-12.2 -DGMX_GPU=CUDA
# \u89e3\u91ca\u4e00\u4e0b\u4e0a\u9762\u7684configure\uff0cprefix\u662f\u5b89\u88c5\u8def\u5f84\uff1b-DCUDA_TOOLKIT_ROOT_DIR\u662f\u672c\u673aCUDA-toolkit\u6240\u5728\u7684\u8def\u5f84\uff1b-DGMX_GPU=CUDA\u4ee3\u8868\u7f16\u8bd1\u57fa\u4e8eCUDA       \u7684GPU\u52a0\u901f\u7248\u672c
$ make install -j
# \u6700\u540e\uff0c\u9700\u8981\u8bbe\u7f6egromacs\u7684\u73af\u5883\u53d8\u91cf\uff0c\u7b80\u5355\u5730\u8fdb\u884c\u7684\u8bdd\u53ea\u9700\u8981\uff1a
$ source \/home\/gromacs-2022.5\/bin\/GMXRC
# \u4f46\u662f\u4f9d\u65e7\u63a8\u8350\u4f7f\u7528modules\u8fdb\u884c\u7ba1\u7406\uff0c\u8fd9\u6837\u5728\u673a\u5668\u4e2d\u5b58\u5728\u591a\u4e2a\u7248\u672c\u7684\u65f6\u5019\uff0c\u4f9d\u65e7\u80fd\u4f18\u96c5\u4ece\u5bb9\u5730\u7ba1\u7406\u73af\u5883\u53d8\u91cf\u3002<\/code><\/pre>\n\n\n\n
\u81f3\u6b64\uff0cgromacs-2022.5\u7248\u672c\u5c31\u5b89\u88c5\u5b8c\u6bd5\u4e86\u3002\u5982\u679c\u60f3\u5b89\u88c5\u66f4\u9ad8\u7248\u672c\uff0c\u53ef\u80fd\u9700\u8981\u66f4\u9ad8\u7248\u672c\u7684gcc\u548ccmake\uff0c\u90a3\u4e48\u53ea\u9700\u8981\u53c2\u7167\u672c\u6587\u8fdb\u884c\u7f16\u8bd1\u5e76\u7528modules\u7ba1\u7406\u5373\u53ef\u3002<\/p>\n\n\n\n
4.5 AMBER<\/p>\n\n\n\n
AMBER\u7684\u5b89\u88c5\u57fa\u672c\u53c2\u7167http:\/\/bbs.keinsci.com\/thread-39265-1-1.html<\/a>\u4e00\u6587\uff0c\u6b64\u5904\u4f5c\u7b80\u5355\u7684\u6307\u4ee4\u5907\u5fd8\u5f55\uff0c\u8be6\u7ec6\u8fc7\u7a0b\u8bf7\u9605\u8bfb\u539f\u8d34\uff0c\u7b14\u8005\u611f\u8c22\u539f\u8d34\u4f5c\u8005\u7684\u65e0\u79c1\u5206\u4eab\u3002<\/p>\n\n\n\n
\u51c6\u5907\u90e8\u5206\uff1a<\/p>\n\n\n\n
1. \u4e00\u4e9b\u5305\u7ba1\u7406\u5668\u53ef\u4ee5\u89e3\u51b3\u7684\u4f9d\u8d56
$ sudo dnf install -y bzip2-devel cmake3 gcc-gfortran gcc-c++ lzip tcl-devel zlib libzip-devel epel-release cmake3

2. gcc
$ gcc --version # \u68c0\u67e5gcc\u662f\u5426\u88c5\u597d\u5e76\u52a0\u8f7d\uff0c\u7248\u672c\u662f\u5426\u8fc7\u65f6\uff0c\u5982\u5426\uff0c\u53c2\u8003\u4e0a\u4e00\u8282\u4e2dgcc\u7684\u88c5\u6cd5

3. openmpi
$ wget https:\/\/download.open-mpi.org\/release\/open-mpi\/v4.1\/openmpi-4.1.6.tar.bz2 # \u5982\u679c\u4e0b\u8f7d\u4e0d\u4e86\uff0c\u7528\u80fd\u7528\u9b54\u6cd5\u7684\u673a\u5b50\u624b\u52a8\u4e0b\u8f7d
$ tar xvf openmpi-4.1.6.tar.bz2
$ cd openmpi-4.1.6
$ .\/configure --prefix=\/home\/openmpi-4.1.6 --disable-builtin-atomics
$ make all install -j
# \u6700\u540e\u5199module file\u5373\u53ef\uff08\u89c1\u9644\u5f55\uff09

4.fftw
# \u4e0a\u4e00\u8282\u5df2\u7ecf\u8bb2\u8fc7fftw\u7684\u7b80\u5355\u5b89\u88c5\uff0c\u8fd9\u91cc\u7ed9\u4e00\u4e2a\u628afftw\u6240\u6709\u7cbe\u5ea6\u3001\u6240\u6709\u5e76\u884c\u6a21\u5f0f\u7684\u5e93\u4e00\u6b21\u88c5\u4e0a\u7684\u811a\u672c\uff0c\u89e3\u538b\u6e90\u7801\u540e\u8fdb\u5165\u76ee\u5f55\u6267\u884c\u5373\u53ef\u3002\u5177\u4f53\u5185\u5bb9\u89c1\u9644\u5f55\u7684.\/compile_fftw_all.sh
# \u5f53\u7136\uff0c\u4e5f\u8981\u7eb3\u5165module\u7ba1\u7406

5. intel mkl & Anaconda3
# Amber\u9700\u8981\u8fd9\u4e24\u4e2a\u524d\u7f6e\uff0c\u524d\u6587\u5df2\u7ecf\u8bb2\u8fc7\u5982\u4f55\u5b89\u88c5\uff08\u89c1intel\u5168\u5bb6\u6876\u7684\u5b89\u88c5\u90a3\u4e00\u5c0f\u8282\uff09\uff0c\u4e0d\u8d58\u8ff0\u3002
# \u7279\u522b\u6ce8\u610f\uff0cAnaconda3\u7684python\u7248\u672c\u52a1\u5fc5\u5c0f\u4e8e3.11\uff01

6. \u57fa\u4e8eOpen MPI\u7684MPI4Py
# \u4e0b\u8f7d\u6e90\u4ee3\u7801\uff1ahttps:\/\/pypi.python.org\/pypi\/mpi4py
$ tar xvf mpi4py-3.0.0.tar.gz
$ cd mpi4py-3.0.0
# \u4e0b\u9762\u9700\u8981\u7528vim\u6253\u5f00mpi.cfg\uff0c\u7136\u540e\u628a[openmpi]\u5904\u7684mpi_dir\u4fee\u6539\u6210\u672c\u673a\u5668\u4e0a\u7684\u8def\u5f84\u3002
python setup.py build --mpi=openmpi
python setup.py install --prefix=\/home\/mpi4py
# \u7136\u540e\u5199\u4e2amodule file\u7ba1\u7406\u73af\u5883\u53d8\u91cf\u5373\u53ef

7. Boost
$ .\/bootstrap.sh --prefix=\/home\/boost --with-libraries=all --with-toolset=gcc
# \u7136\u540e\u5728project-config.jam\u6dfb\u52a0\u4e00\u884c\uff1a 
using mpi : \/opt\/openmpi\/4.11.1\/bin\/mpicxx ;
$ .\/b2 -j8 --layout=tagged link=static,shared threading=multi install
# \u7136\u540e\u5199\u4e2amodule file\u7ba1\u7406\u73af\u5883\u53d8\u91cf\u5373\u53ef

8. CUDA
$ nvidia-smi
$ nvcc --version
# \u4e0a\u9762\u4e24\u4e2a\u547d\u4ee4\u90fd\u6b63\u5e38\u8f93\u51fa\uff0c\u5206\u522b\u8bf4\u660eNvidia\u9a71\u52a8\u548cCUDA\u6ca1\u6709\u95ee\u9898\uff0c\u53ef\u4ee5\u7ee7\u7eed\u5b89\u88c5\uff0c\u6709\u95ee\u9898\u8bf7\u53c2\u8003Nvidia\u5b98\u65b9\u6587\u6863\uff0c\u6216\u4e0a\u9762\u63d0\u5230\u7684\u535a\u6587\u8fdb\u884c\u5b89\u88c5\u3002
<\/code><\/pre>\n\n\n\n
\u672c\u4f53\u90e8\u5206\uff1a<\/p>\n\n\n\n
# \u5148\u52a0\u8f7d\u4e0b\u4e0a\u9762\u7684\u6240\u6709modules
# CMakeLists.txt\u524d\u9762\u52a0\u5165add_compile_definitions(THRUST_IGNORE_CUB_VERSION_CHECK)
$ cd build
# \u4e0b\u9762\u662fopenmpi\u7248\u672c\u7684\u7f16\u8bd1,\u7f16\u8f91run_cmake:
# \u5728Linux\u90a3\u6bb5\u628a-DCMAKE_INSTALL_PREFIX\u4fee\u6539\u4e3a\u60f3\u5b89\u88c5\u7684\u76ee\u5f55
# -DDOWNLOAD_MINICONDA\u9009\u4e3aFALSE\uff0c
# \u5220\u9664\u540e\u9762\u7684-DMINICONDA_USE_PY3\uff08\u5982\u6709\uff09\uff0c
# \u52a0\u5165-DTRUST_SYSTEM_LIBS=TRUE\uff0c
# \u52a0\u5165-DOPENMP=TRUE\uff0c
# \u5c06-DMPI\u6539\u6210TRUE
$ .\/run_cmake
$ make -j 8 # \u53ef\u80fd\u4f1a\u7206\u5185\u5b58\uff0c\u90a3\u5c31\u628a8\u6539\u62104\uff0c\u6216\u8005\u5e72\u8106\u53bb\u6389-j\uff0c\u7136\u540e\u53bb\u4ee5\u6b64\u4e3a\u6b63\u5f53\u7406\u7531\u6478\u9c7c\uff0c\u6478\u9c7c\u56de\u6765\u5c31\u7f16\u8bd1\u597d\u4e86
$ make install

# \u4e0b\u9762\u662fCUDA\u7248\u672c\u7684\u7f16\u8bd1\uff0c\u7f16\u8f91run_cmake:
# \u628a-DOPENMP\u540e\u9762\u6539\u6210FALSE\uff0c
# \u5982\u679c\u6709\u8d85\u8fc7\u4e00\u5f20\u8ba1\u7b97\u663e\u5361\u800c\u4e14\u60f3\u8981\u8de8\u5361\u8fd0\u884c-DMPI\u540e\u9762\u5199TRUE\uff0c\u5426\u5219\u5199FALSE\uff0c
# \u52a0\u5165-DCUDA=TRUE 
# \u52a0\u5165-DCUDA_TOOLKIT_ROOT_DIR=xxx\uff0c\uff08\u7528which nvcc\u786e\u8ba4\u6b64\u8def\u5f84\uff09
# \u4f7f\u7528NVLink\u7684\u8bdd\u8981\u52a0-DNCCL=TRUE\u3002
$ .\/run_cmake
$ make -j 8 
# \u53ef\u80fd\u4f1a\u7206\u5185\u5b58\uff0c\u90a3\u5c31\u628a8\u6539\u62104\uff0c\u6216\u8005\u5e72\u8106\u53bb\u6389-j\uff0c\u7136\u540e\u53bb\u4ee5\u6b64\u4e3a\u6b63\u5f53\u7406\u7531\u6478\u9c7c\uff08CUDA\u7248\u672c\u7f16\u8bd1\u65f6\u95f4\u66f4\u4e45\uff0c\u4f60\u53ef\u4ee5\u6478\u66f4\u4e45\u7684\u9c7c\uff09\uff0c\u6478\u9c7c\u56de\u6765\u5c31\u7f16\u8bd1\u597d\u4e86
$ make install

# \u6700\u540e\uff0c\u8bbe\u7f6e\u73af\u5883\u53d8\u91cf\uff0c\u4f9d\u65e7\u5efa\u8bae\u7528modules<\/code><\/pre>\n\n\n\n
\u9644\u5f55\uff1a\u672c\u8282\u63d0\u5230\u7684\u6240\u6709module files<\/p>\n\n\n\n
GCC<\/code><\/pre>\n\n\n\n
5. \u961f\u5217\u548c\u8fdb\u7a0b<\/strong><\/p>\n\n\n\n
5.1 \u961f\u5217\u7cfb\u7edf<\/strong><\/p>\n\n\n\n
5.1.1 \u961f\u5217\u7cfb\u7edf\u7b80\u4ecb<\/mark>
<\/p>\n\n\n\n
5.2 \u8fdb\u7a0b\u76d1\u63a7<\/strong><\/p>\n\n\n\n
\u5e38\u7528\u7684\u8fdb\u7a0b\u76d1\u63a7\u547d\u4ee4\u662ftop\u548cps u\uff0c\u4e8c\u8005\u5747\u4f1a\u6253\u5370\u5f53\u524d\u7cfb\u7edf\u8fd0\u884c\u7684\u5404\u4e2a\u8fdb\u7a0b\u4ee5\u53ca\u552f\u4e00\u5bf9\u5e94\u7684PID\u53f7\u3002\u5bf9\u4e8ePC\u673a\u6216\u672a\u5b89\u88c5\u961f\u5217\u7cfb\u7edf\u7684\u5c0f\u578b\u670d\u52a1\u5668\uff0c\u53ef\u4f7f\u7528\u8fd9\u4e24\u4e2a\u547d\u4ee4\u5b9e\u73b0\u8fdb\u7a0b\u76d1\u63a7\uff0c\u5f53\u67d0\u4e00\u8fdb\u7a0b\u7ed3\u675f\u540e\uff0c\u6267\u884c\u540e\u7eed\u8fdb\u7a0b\u3002\u4f8b\u5982\uff1a<\/p>\n\n\n\n
#!\/bin\/bash\nflag=1\nwhile [ \"$flag\" -eq 1 ]\ndo\n  sleep 1m # \u7b49\u5f851\u5206\u949f\u3002\n  PID=$1\n  PID_EXIST=$(ps u | awk '{print $2}' | grep -w $PID) # \u5224\u65ad\u5f53\u524d\u662f\u5426\u5b58\u5728\u8be5\u8fdb\u7a0b\u3002\n  if [ ! $PID_EXIST ]\n  then\n    mpirun -np 24 vasp\n    flag=0\n  else\n    echo \"Previous job unfinished. Continue waiting for 1 min...\"\n  fi\ndone<\/code><\/pre>\n\n\n\n
\u5047\u8bbe\u8be5\u811a\u672c\u4e3a.\/monitor.sh\u3002\u9996\u5148\u901a\u8fc7ps u\u547d\u4ee4\u67e5\u770b\u9700\u8981\u88ab\u76d1\u63a7\u7684\u8fdb\u7a0b\u6240\u5bf9\u5e94\u7684PID\u53f7\uff0c\u8fd0\u884c.\/monitor.sh PID\uff0c\u8be5\u811a\u672c\u4f1a\u5728\u540e\u53f0\u6bcf\u96941\u5206\u949f\u68c0\u67e5\u524d\u5e8f\u4efb\u52a1\u662f\u5426\u7ed3\u675f\uff0c\u5f53\u88ab\u76d1\u63a7\u7684\u8fdb\u7a0b\u7ed3\u675f\u540e\uff0c\u8be5\u811a\u672c\u4fbf\u4f1a\u6267\u884c\u201cmpirun -np 24 vasp\u201d\u3002\u540c\u65f6\uff0c\u8be5\u811a\u672c\u672c\u8eab\u5bf9\u5e94\u4e8e\u4e00\u4e2a\u201c\/bin\/bash monitor.sh\u201d\u7684\u8fdb\u7a0b\uff0c\u81ea\u7136\u4e5f\u662f\u53ef\u4ee5\u88ab\u76d1\u63a7\u7684\uff0c\u7531\u4e8e\u201cmpirun -np 24 vasp\u201d\u662f\u8be5\u8fdb\u7a0b\u7684\u5b50\u8fdb\u7a0b\uff0c.\/monitor.sh\u8fdb\u7a0b\u4f1a\u5728VASP\u8fd0\u884c\u7ed3\u675f\u540e\u7ed3\u675f\u3002\u867d\u7136\u4e0d\u77e5\u9053\u540e\u7eedVASP\u4efb\u52a1\u7684\u8fdb\u7a0b\u53f7\uff0c\u4f46\u901a\u8fc7\u76d1\u63a7.\/monitor.sh\u7684\u8fdb\u7a0b\u53f7\uff0c\u4e5f\u5c31\u5b9e\u73b0\u4e86\u5bf9\u540e\u7eedVASP\u4efb\u52a1\u7684\u76d1\u63a7\u3002<\/p>\n\n\n\n
<\/p>\n\n\n\n
<\/p>\n\n\n\n
<\/p>\n\n\n\n
<\/p>\n\n\n\n
<\/p>\n","protected":false},"excerpt":{"rendered":"
\u5b9e\u7528\u4e3b\u4e49\u7684Linux\u547d\u4ee4\u548cBash\u811a\u672c\u57fa\u7840\u5165\u95e8\uff08\u66f4 …<\/p>\n","protected":false},"author":9,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"spay_email":"","footnotes":""},"categories":[6,5],"tags":[],"class_list":["post-904","post","type-post","status-publish","format-standard","hentry","category-workshop","category-computchem"],"jetpack_featured_media_url":"","_links":{"self":[{"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts\/904","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/users\/9"}],"replies":[{"embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=904"}],"version-history":[{"count":43,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts\/904\/revisions"}],"predecessor-version":[{"id":2300,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=\/wp\/v2\/posts\/904\/revisions\/2300"}],"wp:attachment":[{"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=904"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=904"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.homechemer.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=904"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}