Using a pre-installed GPAW at Niflheim¶
This is the guide for using the pre-installed GPAW modules on Niflheim.
Modules on Niflheim¶
You can see which modules are available with the
module avail [package] command, for example:
$ module avail GPAW -------------------------- /home/modules/modules/all -------------------------- GPAW-setups/0.8.7929 GPAW-setups/0.9.9672 GPAW-setups/0.9.11271 GPAW-setups/0.9.20000 (D) GPAW/1.4.0-foss-2018a-Python-3.6.4 GPAW/1.4.0-foss-2018b-Python-3.6.6 GPAW/1.4.0-intel-2018b-Python-3.6.6 GPAW/1.5.1-foss-2018b-Python-3.6.6 GPAW/1.5.1-intel-2018b-Python-3.6.6 GPAW/1.5.2-foss-2018b-Python-3.6.6 GPAW/1.5.2-intel-2018b-Python-3.6.6 GPAW/19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6 GPAW/19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6 GPAW/20.1.0-foss-2019b-Python-3.7.4 GPAW/20.1.0-intel-2019b-Python-3.7.4 GPAW/20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4 GPAW/20.10.0-foss-2020b GPAW/20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4 GPAW/20.10.0-intel-2020b GPAW/21.1.0-foss-2020b-ASE-3.21.1 GPAW/21.1.0-intel-2020b-ASE-3.21.1 (D) Where: D: Default Module
You can see which modules you have loaded with
module list. You
can unload all modules to start from scratch with
Choose the right version of GPAW¶
This is a brief guide to which version of GPAW you should use. It reflects the situation in December 2020 and will be updated as the situation changes.
- I have an ongoing project
You should probably continue to use the version you are using in that project, unless you want to change. See the section below on using different versions for different project.
- I am a normal user
You should load
This will give the newest version of GPAW, as recommended by the developers. It has new features and is significantly faster, in particular on the new Xeon40 nodes. For ongoing projects that have been using an older version, you may find that some values have changed slightly - check for consistency, or be sure to always use the same version for ongoing projects. See below for a description on how to do that.
- I am sligtly conservative or need
The version of GPAW compiled with the FOSS toolchain is somewhat slower in many situations, but is better tested and may use less memory. You may also have to use this version if you want the functionality from
libvwdxclibrary, but be aware that many vad der Waals potentials do not use
IMPORTANT: You do not need to load Python, ASE, matplotlib etc. Loading GPAW pulls all that stuff in, in versions consistent with the chosen GPAW version.
If you want to generate Wannier functions with the Wannier90 module,
you need to explicitly load
Intel or foss versions?¶
The versions built with the Intel compilers and the Intel Math Kernel Library (MKL) are in average faster than the ones build with the Open Source (GNU) compilers (FOSS = Free and Open Source Software). On newer hardware this difference can be very significant, and we recommend using the Intel versions unless you have a good reason not to.
libvdwcx library of van der Waals exchange-correlation
potentials in incompatible with the MKL, so if you need these methods
you have to use the foss versions. However, most van der Waals
calculations use the native van der Waals support in GPAW, and works
fine with the Intel versions.
Module consistency is important: check it.¶
For a reliable computational experience, you need to make sure that all modules come from the same toolchain (i.e. that the software is compiled with a consistent set of tools). All modules you load should belong to the same toolchain.
module list to list your modules. Check for consistency:
(*) For use on the GPU nodes, so only available on the sm3090 and xeon40 partitions. Newer toolchains do not use a special toolchain for this.
module load XXX commands give warnings about reloaded
modules, you are almost certainly mixing incompatible toolchains.
Using different versions for different projects.¶
You do not have to use the same modules for all your projects. If you
want all jobs submitted from the folder
~/ProjectAlpha to run with
an one version of GPAW, but everything else with a another version,
you can put this in your .bashrc:
if [[ $SLURM_SUBMIT_DIR/ = $HOME/ProjectAlpha* ]]; then # Extreme consistency is important for this old project module purge module load GPAW/1.4.0-foss-2018a-Python-3.6.4 else # Performance is important for everything else. module load GPAW/20.10.0-intel-2020b module load scikit-learn/0.23.2-intel-2020b fi
module purge command in the special branch is because SLURM
will remember which modules you have loaded when you submit the job,
and that will typically be the default version, which must then be