Changes between Version 30 and Version 31 of HPC_deploy


Ignore:
Timestamp:
2015-11-19T02:00:44+01:00 (8 years ago)
Author:
Pieter Neerincx
Comment:

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Legend:

Unmodified
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  • HPC_deploy

    v30 v31  
    8585 * '''name''' and '''version''' are pretty clear [[BR]]
    8686 * '''homepage''' and '''description'''; are recommended when releasing a future release of the tool. [[BR]]
    87  * '''toolchain'''; can be left like it is in the example (only when multiple tools need to be installed before this, you should use toolchain (see manual online of Easybuild). [[BR]]
     87 * '''toolchain'''; can be left like it is in this example. Only when multiple tools need to be installed as dependencies for compiling or installing this one, a toolchain is required. See the [http://easybuild.readthedocs.org/en/latest/index.html !EasyBuild docs] for details. [[BR]]
    8888 * '''easyblock'''; this is the type of data, tar.gz = ‘Tarball’ , executable = ‘Binary’ . All the different easyblocks are described [https://github.com/hpcugent/easybuild-easyblocks/tree/master/easybuild/easyblocks/generic here]  [[BR]]
    89  * If there any '''dependencies''' (in this case Molgenis-Compute), you put it in the name of your eb file (name will look like this: NGS_DNA-3.1.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80)  [[BR]]
     89 * If there are any language/framework '''dependencies''' (in this case Molgenis-Compute), you put it in the name of your eb file; Name may look for example like this: NGS_DNA-3.1.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80  [[BR]]
    9090 * '''Using variables''' instead of typing the same string 5 times is done with %s and then between () the name of the variable. [[BR]]
    9191 * One necessary step is to set '''sanity_check_paths''', this is a check whether the file is unpacked/installed correctly.  [[BR]]
    92  * All the installed eb configs are put automatically in the /apps/modules/all folder, but with '''moduleclass''' you can specify an extra module path.  '''N.B.''''''' when typing the command module avail on the cluster will only display the non-all modules. So specifying an extra moduleclass is necessary to find your module back in module avail  [[BR]]
     92 * All the installed eb configs are put automatically in the /apps/modules/all folder, but with '''moduleclass''' you can specify an extra module path.  '''N.B.''' when typing the command module avail on the cluster will only display the non-all modules. So specifying an extra moduleclass is necessary to find your module back in module avail  [[BR]]
    9393
    9494For more complicated installations like for example for ''R'', please read the [https://hpcugent.github.io/easybuild/ documentation] online and have a look at existing !EasyConfigs.
    … …  
    122122$> ls -ahl /apps/modules/bio/NGS_DNA/
    123123total 20K
    124 drwxrwsr-x  2 umcg-gvdvries  umcg-depad 4.0K Nov 12 15:28 .
    125 drwxrwsr-x 64 umcg-pneerincx umcg-depad 4.0K Nov 18 17:43 ..
    126 lrwxrwxrwx  1 umcg-rkanninga umcg-depad   71 Aug 25 10:52 3.0.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80 -> /apps/modules/all/NGS_DNA/3.0.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80
    127 lrwxrwxrwx  1 umcg-rkanninga umcg-depad   71 Nov  4 09:04 3.1.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80 -> /apps/modules/all/NGS_DNA/3.1.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80
    128 lrwxrwxrwx  1 umcg-rkanninga umcg-depad   71 Nov 12 15:28 3.2.1-Molgenis-Compute-v15.11.1-Java-1.8.0_45 -> /apps/modules/all/NGS_DNA/3.2.1-Molgenis-Compute-v15.11.1-Java-1.8.0_45
    129 lrwxrwxrwx  1 umcg-pneerincx umcg-depad   45 Sep 24 16:22 default -> 3.1.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80
    130 }}}
    131 Note that all module files for all apps are in {{{/apps/modules/all/}}} and we only see symlinks in {{{/apps/modules/bio/}}}. Version 3.2.1 is the latest, but 3.1.2 has been designated as default using a symlink. The symlink must be a relative one pointing to file or another symlink in the same directory. You may have to [wiki:#UpdateCacheAndSync update the Lmod caches] before the change in default version takes effect. We can check with if the symlink was recognised using:
     124drwxrwsr-x  2 prefix-someuser  umcg-depad 4.0K Nov 12 15:28 .
     125drwxrwsr-x 64 prefix-someuser umcg-depad 4.0K Nov 18 17:43 ..
     126lrwxrwxrwx  1 prefix-someuser umcg-depad   71 Aug 25 10:52 3.0.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80 -> /apps/modules/all/NGS_DNA/3.0.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80
     127lrwxrwxrwx  1 prefix-someuser umcg-depad   71 Nov  4 09:04 3.1.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80 -> /apps/modules/all/NGS_DNA/3.1.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80
     128lrwxrwxrwx  1 prefix-someuser umcg-depad   71 Nov 12 15:28 3.2.1-Molgenis-Compute-v15.11.1-Java-1.8.0_45 -> /apps/modules/all/NGS_DNA/3.2.1-Molgenis-Compute-v15.11.1-Java-1.8.0_45
     129lrwxrwxrwx  1 prefix-someuser umcg-depad   45 Sep 24 16:22 default -> 3.1.2-Molgenis-Compute-v15.04.1-Java-1.7.0_80
     130}}}
     131Note that all module files for all apps are in {{{/apps/modules/all/}}} and we only see symlinks in {{{/apps/modules/bio/}}}. Version 3.2.1 is the latest, but 3.1.2 has been designated as default using a symlink. The symlink must be a relative one pointing to a file or another symlink in the same directory. You may have to [wiki:HPC_deploy#UpdateCacheAndSync update the Lmod caches] before the change in default version takes effect. We can check with if the symlink was recognised using:
    132132{{{
    133133$> module avail NGS_DNA
    … …  
    181181--------------------------------------------------------------------------
    182182}}}
    183 Note: You may have to [wiki:#UpdateCacheAndSync update the Lmod caches] before a change in custom messages takes effect.
     183Note: You may have to [wiki:HPC_deploy#UpdateCacheAndSync update the Lmod caches] before a change in custom messages takes effect.
    184184
    185185=== Updating the Lmod caches and syncing installed software to nodes === #UpdateCacheAndSync