HPC/Module naming scheme 2016

Configuration files used

You have files: .bashrc and …		Remark	CentOS-5 uses:		CentOS-6 uses:
			files	module names	files	module names
–	–	Starting situation.	.bashrc only	v1	.bashrc only	v2
–	.modules-2	Switch over, recommended.	.modules-2 and .bashrc	v2	.modules-2 and .bashrc
.modules-1	–	Only recommended during transition.	.modules-1 and .bashrc	v1	.bashrc only
.modules-1	.modules-2	For advanced users.	.modules-1 and .bashrc	v1	.modules-2 and .bashrc

New-style module names

You may need to adapt the module names that you placed in your shell startup and job files to the new more hierarchical scheme. For most modules, with exceptions show below, the leading name component (the part before any "/") is the same in the old and new naming schemes. What always differs are the name parts after the first slash.

Name change rules

• To use the latest or automatically selected version of a package, remove version numbers from old-style module names of the formpackagename/version, leaving only packagename. This is the recommended approach, as you will automatically benefit from future updates and maintenance builds.
• To insist on a specific version for a package in new style names:
  • Inspect the available flavors and versions (some older modules were not migrated):

    module avail packagename.

  • Choose the new-style name up to the desired specificity. You may leave out trailing name or directory parts.

    For instance, instead of vasp5/5.3/openmpi-1.4/intel/5.3.3p3-mkl-3 you may write vasp5/5.3/openmpi-1.4 or vasp5/5.3, letting the system choose the versions for MPI and compiler that are chosen as defaults at a given time.

Renamed modules

For the following modules the newer naming convention allowed for and thus uses more consistent names:

OLD		NEW
-------------------------------------
asap3		asap/3

ase2		ase/2
ase3		ase/3

g09		gaussian/09
GaussView	gaussview  (lowercase)

The modules fftw3 and vasp5 did not change name due to more entrenched usage in the package itself, Unix group names, and compilation dependencies.

Determining default module versions

The module avail command under CentOS-6 no longer includes the marker "(default)" when one has been set in a .version file. I am not sure if this is a bug or by design, but the change certainly makes the output more consistent.

To determine which module will be loaded when an abbreviated name is used, I recommend to inspect the first relevant line in the output of one of these commands:

module show name
module help name

Customizing module selection by OS release

Configure in .bashrc

To switch over to new-style module names on both CentOS releases you could continue making all your module choices in ~/.bashrc.

• Tell CentOS-5 nodes to offer the new-style module catalog instead of the old one. To do so, simply create an empty customization file:

touch ~/.modules-2

• Then, apply the changes shown in the #Name change rules section above:

vi .bashrc
# or:
nano .bashrc

Use a text editor of your choice, such as nano or vi.

Configure in dedicated files

It is perhaps cleaner to perform the module selection in files dedicated for each CentOS release, so that you can better address possible incompatibilities. To migrate your existing configuration:

• Extract and copy your previous module selections into a conspicuously named but otherwise unused files:

cd      # Go to home directory
grep -C 1  module .bashrc > .modules-1.inactive

The grep -C option includes the given number of lines of context before and after lines matching the search expression.

• Clean up errant lines that the grep command above might have included, such as separators -- and conditionals (like if).

vi .modules-1.inactive
# or:
nano .modules-1.inactive

• Duplicate the file.
• Adapt contents to new module names, as shown for .bashrc in the previous section.

cp .modules-1.inactive .modules-2.inactive
vi .modules-2.inactive
# or:
nano .modules-2.inactive

Apply the changes shown in the #Rules section.

• Edit ~/.bashrc and remove all lines with module commands.

vi .bashrc

• Test.

bash -l     # open a sub-shell (option is lowercase L)
module list
exit        # leave the sub-shell

Differentiate module selection by OS release

If you encounter difficulties with making your module selection work simultaneously for CentOS-5 and CentOS-6, use separate configurations instead.

• Re-activate the older module selection.

cd      # Go to home directory
mv .modules-1.inactive .modules-1

• Clean up errant lines:

vi .modules-1
# or:
nano .modules-1

• Test – same as in previous section.