Changes between Version 33 and Version 34 of HPC_deploy


Ignore:
Timestamp:
2015-11-19T02:43:12+01:00 (8 years ago)
Author:
Pieter Neerincx
Comment:

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  • HPC_deploy

    v33 v34  
    55== Deploying (reference) data sets ==
    66
    7 ==== Where to put reference data ====
     7==== 1. Where to put reference data ====
    88
    99Reference data sets available to all (Hence not group specific data) can be deployed ''as-is'' in:
    … …  
    2828}}}
    2929
    30 ==== Syncing deployed reference data to nodes ==== #SyncRefData
     30==== 2. Syncing deployed reference data to nodes ==== #SyncRefData
    3131
    3232Before you can use reference data on cluster nodes it needs to be synced to various places.
    … …  
    137137For 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.
    138138
    139 === Find existing !EasyConfig or create a new one ===
     139==== 1. Find existing !EasyConfig or create a new one ====
    140140 * To search for existing !EasyConfigs in both the default robot search path as well as in our dir for custom !EasyConfigs:
    141141{{{
    … …  
    151151   Make sure to name the *.eb file exactly the same as the name of the eventually installed ''module'' and its ''version''.
    152152
    153 === Installing the software ===
     153==== 2. Installing the software ====
    154154Enable the ''robot'' option for automatic dependency resolution and **append** our dir for custom !EasyConfigs to the search path to make !EasyBuild search for deps in first the default and second our custom dir in that order of precedence.
    155155{{{
    … …  
    159159}}}
    160160
    161 === Specifying the default version of an app (optional) ===
     161==== 3. Specifying the default version of an app (optional) ====
    162162
    163163When you load an app into your environment with the {{{module load}}} command without specifying explicitly which version you want to use, Lmod will load the highest version number. This is usually fine, but if you installed a new version that is not yet well tested, you may want to explicitly configure an older version as the default. This can simply be accomplished by creating a **relative** symlink named default. Our module files are located at {{{/apps/modules/}}}. For example let's look at our NGS_DNA analysis pipeline. It is part of the ''bio'' collection of apps, so the the module files are in:
    … …  
    194194}}}
    195195
    196 === Deprecating a previously installed older version of an app (optional) ===
     196==== 4. Deprecating a previously installed older version of an app (optional) ====
    197197
    198198You can inform users that (a certain version of) an app is deprecated and will be removed in the near future by creating a custom message when an app is added to the environment with {{{module load}}}. Add your custom message to {{{/apps/modules/modules.admin}}}. For example with this modules.admin:
    … …  
    226226Note: You may have to [wiki:HPC_deploy#UpdateCacheAndSync update the Lmod caches] before a change in custom messages takes effect.
    227227
    228 === Updating the Lmod caches and syncing installed software to nodes === #UpdateCacheAndSync
     228==== 5. Updating the Lmod caches and syncing installed software to nodes ==== #UpdateCacheAndSync
    229229
    230230Before you can use the installed software it needs to be synced to various places and the Lmod caches needs to be updated.
    … …  
    243243
    244244== FAQ ==
    245 === Q: Why can I not re-deploy a module and receive an error that the module file is already present ===
     245==== Q: Why can I not re-deploy a module and receive an error that the module file is already present ====
    246246A: By default !EasyBuild will refuse to overwrite an existing installation. Modules that have been deployed and are used for production should never be modified: deploy a new version instead. During debugging/testing it may be necessary to overwrite a module though; I that case you can force install using ''-f'' like this:
    247247{{{
    248248$> eb -f --robot --robot-paths=:/apps/sources/EasyBuild/custom/ /path/to/MyEasyConfig-1.2.3.eb
    249249}}}
    250 === Q: I've updated the source code for an app, but when I try to re-deploy with !EasyBuild nothing changes; What is wrong? ===
     250==== Q: I've updated the source code for an app, but when I try to re-deploy with !EasyBuild nothing changes; What is wrong? ====
    251251A: !EasyBuild will first check whether the source code was previously already downloaded and cached. If yes, it will not re-download again. The cached sources are located in {{{/apps/sources/[a-z]/NameOfTheApp/}}}. Removing the existing download will force !EasyBuild to re-download the (updated) source code.
    252 === Q: !EasyBuild fails to download the source code. How can I continue the installation process? ===
     252==== Q: !EasyBuild fails to download the source code. How can I continue the installation process? ====
    253253A: First check if the location where !EasyBuild tries to download the source code is still up-to-date. If not update the !EasyConfig. If the location is correct, but !EasyBuild cannot access this location directly for example because it is blocked by our firewall or because it requires authentication, you can try to download the source manually and put it in the cache directory for the app in {{{/apps/sources/[a-z]/NameOfTheApp/}}}. When !EasyBuild finds the cached source code it will skip the download step and continue.