Questions tagged [environment-modules]

The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles.

Typically users initialize their environment when they log in by setting environment information for every application they will reference during the session. The Environment Modules package is a tool that simplify shell initialization and lets users easily modify their environment during the session with modulefiles.

Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the environment can be modified on a per-module basis using the module command which interprets modulefiles. Typically modulefiles instruct the module command to alter or set shell environment variables such as PATH, MANPATH, etc. modulefiles may be shared by many users on a system and users may have their own collection to supplement or replace the shared modulefiles.

Modules can be loaded and unloaded dynamically and atomically, in an clean fashion. All popular shells are supported, including bash, ksh, zsh, sh, csh, tcsh, fish, as well as some scripting languages such as perl, ruby, tcl and python.

Modules are useful in managing different versions of applications. Modules can also be bundled into metamodules that will load an entire suite of different applications.

80 questions
1
vote
1 answer

Modulefile - Module loading when module unload is called

So I am trying to have module files dynamically load/unload when you load one. I am trying to do this in a way so that I can unload conflicting modules (instead of just using the conflict variable as it just throws an error) However, when I call…
Matthew
  • 138
  • 2
  • 9
1
vote
1 answer

loading-environment-modules-within-a-python-script

Loading environment modules within a python script The above solution behaves differently in the python interactive shell and within an executable python file & I need some help in understanding how to get it to work in the exe.py setting, where…
bobox
  • 359
  • 3
  • 16
1
vote
3 answers

How to issue "module load" in a shell or Perl script (i.e., non-interactively)

I can use the "module load xyz" command interactively, but when run from a script, it says it can't find the "module" command. Is there any way of loading modules in a script?
catamount
0
votes
1 answer

Lmod / easybuild categories

I'm having my first tinker with modules. I've installed lmod and easybuild and have built a package (SAMtools) with its dependencies. Running module av shows the modules are available. It lists them twice, once in the 'all' category and also in…
Gaspode
  • 149
  • 1
  • 10
0
votes
0 answers

Setup open-mpi in environmental module

I have tried to set up open mpi in environmental module. First of all, when I use this command : module load mpi/openmpi-x86_64 , the error : ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'mpi/openmpi-x86_64' occurs. There is no…
M.K Kim
  • 1
  • 1
0
votes
1 answer

ERROR: Unable to locate a modulefile for 'gcc/9.4.0'

ERROR: Unable to locate a modulefile for 'gcc/9.4.0' Hi everyone. I don't have much experience on linux, and I have some problems on loading a module. I use a command like: module load gcc/9.4.0 but get a result like: ERROR: Unable to locate a…
0
votes
0 answers

Execute bash script that loads environment modules (Intel fortran compiler) from within Python

I have a Python script that calls three instances of a program written in Fortran to be run in parallel. I managed to get this set up running with the following code snippet, where f"{sim}.out" is the compiled program: from subprocess import Popen,…
MathiesW
  • 31
  • 4
0
votes
1 answer

Running remote Pycharm interpreter with tensorflow and cuda (with module load)

I am using a remote computer in order to run my program on its GPU. My program contains some code with tensorflow functions, and for easier debugging with Pycharm I would like to connect via ssh with remote interpreter to the computer with the GPU.…
0
votes
1 answer

How to solve "no module named" problem for Python when using Environment Modules package?

I am using a software environment loaded with the Environment Modules package (not to be confused with Python modules) using module load my_env. Within this environment, I am attempting to run a python script that imports a self-defined Python…
edwardliang2019
  • 302
  • 2
  • 9
0
votes
1 answer

Can't output lmod commands to text file using python in hpc environment

I am trying to run this script on an h.p.c environment with the goal of writing all modules available in the environment to a text file. The module system in use is lmod. This script works as expected for any regular bash command I have tried such…
0
votes
1 answer

Logic to test whether Linux environment modules are needed

I help maintain an R package that auto-generates shell scripts for using Slurm to run Rscript on a remote server. There is a template for a submit.sh script that is filled in with arguments supplied by the user in an R function. However some systems…
qdread
  • 3,389
  • 19
  • 36
0
votes
2 answers

Module load-PATH-env variables

I'm currently working on a remote server (through ssh) and I need to load some modules (module load [package1][package2] ecc). Specifically, it's required the numpy version 1.15.2, but in the directory containing all the numpy versions there are…
0
votes
1 answer

How to add module to environment module? So I can load it using module load

When I run module avail, I got: --------------------------------- /usr/share/modules/modulefiles --------------------------------- dot module-git module-info modules null use.own ---------------------------------…
Weiyu He
  • 93
  • 7
0
votes
2 answers

Including source shell script in lua modulefile

I am trying to create a module file for an application I have installed on the cluster. To run the program, I have to run a script named "phenix_env.sh" which contains the following: #!/bin/sh # export PHENIX="/src/phenix-1.19.2-4158" export…
Tanash
  • 461
  • 1
  • 5
  • 8
0
votes
1 answer

cannot find python's lib after module add

I'm trying to setup module for different python versions. After module installed, most reqiured python related files are copyied and modified from other server. But I got problem when I launch python: [root@rhelserver ld.so.conf.d]# module --debug…
Sam Zhong
  • 1
  • 2