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Frequently asked questions - Software

Could you please install software for me

Many packages that were installed in standard locations have been moved to the module system. Please search for the package using module spider before contacting the helpdesk.

I cannot find my software package in the module system

On LUNARC resources a hierarchical module naming scheme is deployed. This is explained in the Using installed software guide. Please contact LUNARC support if you cannot locate your package with the module spider command.

Loading a module unloads pre-requisites from a previously loaded module

Many software modules have complex pre-requisites. If you load multiple modules, they may try to load conflicting modules as pre-requisites. In this case the module loaded last purges conflicting pre-requisistes from previously loaded modules. If that happens, the modules loaded earlier can become dysfunctional and there is no guarantee that they will still work.

You have the following options to resolve the issues:

  • Have a look at whether there are different versions of the modules installed that have common pre-requisites. In many cases we have the same version of the software installed with different pre-requisites to help this issue.
  • Have a terminal dedicated to each of the modules. This should work if the modules do not really interact with each other, but e.g. one module creates files which the other module reads. Consider using the Lunarc HPC desktop which easily allows having multiple terminals within a single session
  • If this does not work or does not work satisfactory, contact the LUNARC helpdesk and discuss your situation.

My application fails because it can't find libgfortran.so.3

If your jobs fails with an error message like

error while loading shared libraries: libgfortran.so.3: cannot
open shared object file: No such file or directory
you are using software that has been compiled with a deprecated version of GCC. Please recompile you program on COSMOS using a newer version of GCC, preferably a GCC version we provided as a module.

I need LAPACK and BLAS - they used to be in /usr/lib64

Using an optimised BLAS library is important for achieving good performance. The libraries in /usr/lib64 are typically not highly optimised. We currently support OpenBLAS within the foss toolchain and MKL in the intel, iomkl, and gimkl toolchains. Both libraries show excellent performance when e.g. used to build HPL (high performance linpack).

When using OpenBLAS, please be aware that you might need to control the number of threads spawned.

The COSMOS modules providing MKL set the environment variable MKLROOT to assist the compiler in locating the library on the system. To link your application we suggest consulting the IntelĀ® Math Kernel Library Link Line Advisor for the arguments needed.

My MPI code using OpenBLAS runs slowly / does not perform as expected

OpenBLAS as installed in the foss toolchains is compiled with thread support. When OpenBLAS is used on COSMOS, it will typically figure how many cores you are allocated on that node and spawn as many threads. If this is not desirable (e.g. pure MPI code) you need to control the number of threads spawned by setting the OMP_NUM_THREADS variable. For example for an MPI code running as many tasks as cores requested this is typically be set to:

export OMP_NUM_THREADS=1

For more information, see also the LUNARC manual page on compiling MPI code with a toolchain.

I want to run VASP on COSMOS but it doesn't work

If you would like to use VASP on COSMOS, please ensure that you are registed on a license with the VASP developers in Vienna. To comply with the terms of our handling license, we have to confirm the validity of your license with the VASP developers before granting access. That will take normally take a few days but can take weeks under bad circumstances. Being named in a SUPR VASP group does not imply you are entitled to use VASP.

After registerering with the VASP team, contact the LUNARC helpdesk and provide the following information:

  • Your LUNARC userid
  • Name and Department of the license holder (typically your supervisor/research group leader)
  • The number of the license
  • Your name as stated on the license
  • Whether you require VASP 4 or VASP 5 access

In order to be able to continue the provision of VASP to our legitimate VASP users, we cannot make any exceptions.

The VASP5 executables on COSMOS are compiled using Intel MPI. They need to be started with srun. The VASP6 executable is build with OpenMPI. These executables need to be started with mpirun. Refer to the sample section of our batch system guide for a more comprehensive discussion.

I need access to Amber

Amber 22 is licensed software. To be able to use it please read through the license on the Amber website. Please review the "ASSIGNMENT RESTRICTIONS" in particular.

To gain access to the Amber installation on COSMOS, please submit a support request, confirming that you are accepting these rules. Your account will then be enabled to access to the amber package.

My MPI application doesn't launch

On COSMOS we support two MPI libraries: OpenMPI and Intel MPI. Depending on the toolchain utilised to compile your application different job launchers are required. Executables build with OpenMPI need to be launched with mpirun, while applications build with Intel MPI need to be started with srun.


Author: Joachim Hein (LUNARC)

Last Updated: 2022-10-06