HPC/Module naming scheme 2016: Difference between revisions

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# Move all your previous module commands from <code>.bashrc</code> to <code>~/.modules-carbon-1</code>, where they will apply only on CentOS-5.
# Move all your previous module commands from <code>.bashrc</code> to <code>~/.modules-carbon-1</code>, where they will apply only on CentOS-5.
# Place all your module selections for CentOS-6 in <code>~/.modules-carbon-2</code>. To begin, it will of course be simplest to copy the .*-1 file as *.2 and edit the latter.
# Place all your module selections for CentOS-6 in <code>~/.modules-carbon-2</code>. To begin, it will of course be simplest to copy the .*-1 file as *.2 and edit the latter.
== New and changed features ==
=== Module dependencies ===
New-style modules are less implicit (less automatic and less rigid) in loading modules that they depend on.
* Less automatic means that prior to loading a more advanced module you must load all its prerequisites, chosen from the same MPI and (usually) compiler flavor as the advanced module. A missing prerequisite will give errors of the form
… ERROR:151: '''Module''' 'troubled_name' '''depends on one of the module(s)''' 'other_name1 other_name2' …
To resolve this error, edit your <code>~/.bashrc</code> or <code>.modules-carbon-2</code> file and add <code>module load …</code> commands for the needed module(s) ''other_names'' before loading "troubled_name".
* Less rigid means that a module does not loads a ''specific'' version of a prerequisite, which gives you, the user, more flexibility in combining modules.
=== Name completion ===
When working interactively in a terminal, you can use a "completion" feature of the Bash shell to complete a partially typed module name and show all names available for the name typed so far. For example:
At a shell prompt (shown as "$"), type:
$ '''module load fft'''
Press the <code><TAB></code> key and the name will be expanded to <code>fftw3/</code> and you'll see two possible completing names, with the cursor waiting at the end of the longest common substring:
$ '''module load fftw3/'''_
fftw3/INTEL/3.3.2-1              fftw3/OPENMPI-1.4/INTEL/3.3.2-4 
Type the letter <code>O</code>, hit  the <code><TAB></code> key again, and the now single complete name will be completed, with the cursor waiting after an additional space character:
$ '''module load fftw3/O'''<TAB>
$ '''module module load fftw3/OPENMPI-1.4/INTEL/3.3.2-4''' _
=== Ignoring system defaults ===
By default, on Carbon the Intel compilers and the OpenMPI flavor of MPI continue to be pre-loaded for you. In other words, without any module customization, you'd see from the <code>module list</code> command:
<source lang="bash">
module list
</source>
Currently Loaded Modulefiles:
  1) intel/15/15.0.2                    2) openmpi/1.4/INTEL/1.4.5-intel12-2
You can now safely use the command
<source lang="bash">
module purge
</source>
and afterwards use <code>module load …</code> to only load your preferred compiler and MPI flavors, and applications depending on them.

Revision as of 17:11, August 12, 2015

Configuration files used

You have files:
.bashrc and … 		Remark CentOS-5 uses CentOS-6 uses
module names files module names files
– – current situation old .bashrc only new .bashrc only
– .modules-carbon-2 switch over, recommended new .modules-carbon-2 and .bashrc .modules-carbon-2 and .bashrc
.modules-carbon-1 – avoid old .modules-carbon-1 and .bashrc .bashrc only (.*-1 file is ignored)
.modules-carbon-1 .modules-carbon-2 for advanced users old .modules-carbon-1 and .bashrc .modules-carbon-2 and .bashrc

Configuration steps

CentOS-independent module selection (recommended)

To switch over to new hierarchical module names on both CentOS releases it's easiest to continue making all your module choices in ~/.bashrc, but you have to signal on the older platform to use the new module style:

  1. Create a customization file for new names, but leave it empty (you'll configure your choices in the next step). Use the command: 
    touch ~/.modules-carbon-2
  2. Edit your .bashrc file and update your module selections as follows:
    • Remove version numbers from module names of the old-style packagename/version, leaving only packagename. This is the recommended approach, as you will automatically benefit from future versions.
    • To insist on a specific version for a pacakge affected by the new-style names, use the form packagename/compilername/version or packagename/mpiname/compilername/version as appropriate. To see available flavors and versions, separately run the command module avail packagename.

CentOS-dependent module selection

If you encounter difficulties with making your module selection work in both CentOS-5 and CentOS-6, use separate configurations:

  1. Move all your previous module commands from .bashrc to ~/.modules-carbon-1, where they will apply only on CentOS-5.
  2. Place all your module selections for CentOS-6 in ~/.modules-carbon-2. To begin, it will of course be simplest to copy the .*-1 file as *.2 and edit the latter.
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