Make all Lmod-based shell initialisations more robust, add additional features to facilitate site integration #153

ocaisa · 2026-01-28T16:50:43Z

Right now, if I use init/lmod/bash somewhere where I already have Lmod available I get

# Run the module command in my shell
ocaisa@~$ module av

----------------------------------- /usr/share/lmod/lmod/modulefiles -----------------------------------
   Core/lmod    Core/settarg (D)

  Where:
   D:  Default Module

If the avail list is too long consider trying:

"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

# Source EESSI
ocaisa@~$ source /cvmfs/software.eessi.io/versions/2023.06/init/lmod/bash
Lmod has detected the following error:  The following module(s) are unknown: "EESSI/2023.06"

Please check the spelling or version number. Also try "module spider ..."
It is also possible your cache file is out-of-date; it may help to try:
  $ module --ignore_cache load "EESSI/2023.06"

Also make sure that all modulefiles written in TCL start with the string #%Module


# ...but the module is available
ocaisa@~$ module av

------------------------ /cvmfs/software.eessi.io/versions/2023.06/init/modules ------------------------
   EESSI/2023.06

If the avail list is too long consider trying:

"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

which is quite confusing (the module is visibile but it couldn't be loaded). An issue for this was opened in https://gitlab.com/eessi/support/-/issues/221

This PR fixes that problem by forcing Lmod to do a hard(er) reset when initialising.

The PR also introduces new capabilities, a site can append to MODULEPATH and can add additional default modules that can be loaded before or after the EESSI module.

An example of such possible configuration (at a site where the original problem was seen, and that requires specific modules to be loaded to be able to submit jobs to the queuing system):

Last login: Thu Jan 29 16:19:58 2026 from 10.141.10.61
[vsc50801@gligar10 ~]$ export EESSI_VERSION=2025.06
[vsc50801@gligar10 ~]$ module list

Currently Loaded Modules:
  1) env/vsc/doduo (S)   2) env/slurm/doduo (S)   3) env/software/doduo (S)   4) cluster/doduo (S)

  Where:
   S:  Module is Sticky, requires --force to unload or purge
[vsc50801@gligar10 ~]$ cat configure_eessi.env
export EESSI_DEFAULT_MODULES_APPEND="cluster/default"
export EESSI_EXTRA_MODULEPATH="$PWD/vsc:/etc/modulefiles/vsc"
export EESSI_MODULE_FAMILY_NAME="env_software"
export EESSI_MODULE_STICKY=1
[vsc50801@gligar10 ~]$ source configure_eessi.env
[vsc50801@gligar10 ~]$ cd software-layer-scripts/
[vsc50801@gligar10 software-layer-scripts]$ source init/lmod/bash
Module for EESSI/2025.06 loaded successfully (requires '--force' option to unload or purge)
[vsc50801@gligar10 software-layer-scripts]$ module list

Currently Loaded Modules:
  1) EESSI/2025.06 (S)   2) env/vsc/doduo (S)   3) env/slurm/doduo (S)   4) cluster/doduo (S)

  Where:
   S:  Module is Sticky, requires --force to unload or purge

ocaisa · 2026-01-28T16:51:32Z

init/lmod/bash

+    # and clear out any memory Lmod might have
+    unset _ModuleTable001_
+    # Path to top-level module tree
+    export MODULEPATH="${EESSI_CVMFS_REPO}/init/modules"


Note this now exposes all EESSI versions, but loads a specific one

We should also allow people to be able to add to this default MODULEPATH

…s into better_init

trz42

Left some example comments in for bash only. They also apply to the other shells. Partly the naming of the files is off, the files have no header and don't explain some basic information. All this makes it harder to understand/review what the scripts shall do and if they do that actually. The use and/or naming of $EESSI_VERSION and $EESSI_DEFAULT_VERSION is confusing.

One more comment regarding using non-pinned code (here it's only in an echo statement though).

General comment: The title of the PR seems misleading. The PR seems to add capabilities. How does this make shell initialisations more robust?

It would be great if the PR had included some description: What problem does it solve? Or what improvement or additional feature it provides? What's the main idea to do this?

init/lmod/bash

.github/workflows/scripts/test_init_scripts.sh

.github/workflows/tests_init_module.yml

… available

…s into better_init

ocaisa · 2026-01-30T16:05:55Z

@trz42 I've hopefully addressed almost everything in the initial review (including adding a description to the PR). I've left the renaming of files to templates as follow-up issue #155 as it makes this PR harder again to review (and I don't touch that naming within the PR, it was an existing problem)

ocaisa · 2026-01-30T16:27:18Z

bot: build repo:eessi.io-2023.06-software instance:eessi-bot-deucalion for:arch=aarch64/a64fx
bot: build repo:eessi.io-2025.06-software instance:eessi-bot-deucalion for:arch=aarch64/a64fx

eessi-bot-deucalion · 2026-01-30T16:27:27Z

New job on instance eessi-bot-deucalion for repository eessi.io-2023.06-software
Building on: a64fx
Building for: aarch64/a64fx
Job dir: /home/eessibot/new-bot/jobs/2026.01/pr_153/910482

date	job status	comment
Jan 30 16:27:26 UTC 2026	submitted	job id `910482` awaits release by job manager
Jan 30 16:28:15 UTC 2026	released	job awaits launch by Slurm scheduler
Jan 30 16:29:18 UTC 2026	running	job `910482` is running
Jan 30 16:38:44 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-910482.out` ✅ no message matching `FATAL:` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.* created!` Artefacts `eessi-2023.06-software-linux-aarch64-a64fx-17697906840.tar.zst` size: 0 MiB (3261 bytes) entries: 5 modules under 2023.06/software/linux/aarch64/a64fx/modules/all no module files in tarball software under 2023.06/software/linux/aarch64/a64fx/software no software packages in tarball reprod directories under 2023.06/software/linux/aarch64/a64fx/reprod no reprod directories in tarball other under 2023.06/software/linux/aarch64/a64fx `2023.06/init/lmod/bash` `2023.06/init/lmod/csh` `2023.06/init/lmod/fish` `2023.06/init/lmod/ksh` `2023.06/init/lmod/zsh`
Jan 30 16:38:44 UTC 2026	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ SKIP ] ( 1/10) Skipping test: nodes in this partition only have 30720 MiB memory available (per node) according to the current ReFrame configuration, but 49152 MiB is needed [ SKIP ] ( 2/10) Skipping test: nodes in this partition only have 30720 MiB memory available (per node) according to the current ReFrame configuration, but 49152 MiB is needed [ SKIP ] ( 3/10) Skipping test: nodes in this partition only have 30720 MiB memory available (per node) according to the current ReFrame configuration, but 49152 MiB is needed [ SKIP ] ( 4/10) Skipping test: nodes in this partition only have 30720 MiB memory available (per node) according to the current ReFrame configuration, but 49152 MiB is needed [ OK ] ( 5/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node /15cad6c4 @BotBuildTests:a64fx+default P: latency: 1.72 us (r:0, l:None, u:None) [ OK ] ( 6/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node /6672deda @BotBuildTests:a64fx+default P: latency: 1.72 us (r:0, l:None, u:None) [ OK ] ( 7/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.2-gompi-2023b %scale=1_node /2a9a47b1 @BotBuildTests:a64fx+default P: bandwidth: 8827.92 MB/s (r:0, l:None, u:None) [ OK ] ( 8/10) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.1-1-gompi-2023a %scale=1_node /1b24ab8e @BotBuildTests:a64fx+default P: bandwidth: 8743.78 MB/s (r:0, l:None, u:None) [ OK ] ( 9/10) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/29Aug2024-foss-2023b-kokkos %scale=1_node /aeb2d9df @BotBuildTests:a64fx+default P: perf: 581.588 timesteps/s (r:0, l:None, u:None) [ OK ] (10/10) EESSI_LAMMPS_lj %device_type=cpu %module_name=LAMMPS/2Aug2023_update2-foss-2023a-kokkos %scale=1_node /04ff9ece @BotBuildTests:a64fx+default P: perf: 580.5 timesteps/s (r:0, l:None, u:None) [ PASSED ] Ran 6/10 test case(s) from 10 check(s) (0 failure(s), 4 skipped, 0 aborted) Details ✅ job output file `slurm-910482.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

eessi-bot-deucalion · 2026-01-30T16:27:33Z

New job on instance eessi-bot-deucalion for repository eessi.io-2025.06-software
Building on: a64fx
Building for: aarch64/a64fx
Job dir: /home/eessibot/new-bot/jobs/2026.01/pr_153/910483

date	job status	comment
Jan 30 16:27:32 UTC 2026	submitted	job id `910483` awaits release by job manager
Jan 30 16:28:12 UTC 2026	released	job awaits launch by Slurm scheduler
Jan 30 16:29:21 UTC 2026	running	job `910483` is running
Jan 30 16:34:36 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-910483.out` ✅ no message matching `FATAL:` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.* created!` Artefacts `eessi-2025.06-software-linux-aarch64-a64fx-17697906250.tar.zst` size: 0 MiB (3270 bytes) entries: 5 modules under 2025.06/software/linux/aarch64/a64fx/modules/all no module files in tarball software under 2025.06/software/linux/aarch64/a64fx/software no software packages in tarball reprod directories under 2025.06/software/linux/aarch64/a64fx/reprod no reprod directories in tarball other under 2025.06/software/linux/aarch64/a64fx `2025.06/init/lmod/bash` `2025.06/init/lmod/csh` `2025.06/init/lmod/fish` `2025.06/init/lmod/ksh` `2025.06/init/lmod/zsh`
Jan 30 16:34:36 UTC 2026	test result	😁 SUCCESS (click triangle for details) ReFrame Summary [ SKIP ] (1/4) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_allreduce %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node %device_type=cpu /e4bf9965 @BotBuildTests:a64fx+default [Skipping test: nodes in this partition only have 30720 MiB memory available (per node) according to the current ReFrame configuration, but 49152 MiB is needed] [ SKIP ] (2/4) EESSI_OSU_coll %benchmark_info=mpi.collective.osu_alltoall %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node %device_type=cpu /3da4890b @BotBuildTests:a64fx+default [Skipping test: nodes in this partition only have 30720 MiB memory available (per node) according to the current ReFrame configuration, but 49152 MiB is needed] [ OK ] (3/4) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_latency %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node /3255009a @BotBuildTests:a64fx+default P: latency: 0.86 us (r:0, l:None, u:None) [ OK ] (4/4) EESSI_OSU_pt2pt_CPU %benchmark_info=mpi.pt2pt.osu_bw %module_name=OSU-Micro-Benchmarks/7.5-gompi-2025a %scale=1_node /59f4b331 @BotBuildTests:a64fx+default P: bandwidth: 8211.52 MB/s (r:0, l:None, u:None) [ PASSED ] Ran 2/4 test case(s) from 4 check(s) (0 failure(s), 2 skipped, 0 aborted) Details ✅ job output file `slurm-910483.out` ✅ no message matching `ERROR:` ✅ no message matching `[\sFAILED\s].Ran . test case`

Make all shell initialisations more robust

143341c

ocaisa commented Jan 28, 2026

View reviewed changes

ocaisa added 10 commits January 28, 2026 20:50

Fix typo and tests

a428f68

Merge branch 'main' into better_init

6b057e8

See where the error is

c3d3159

Merge branch 'better_init' of github.com:ocaisa/software-layer-script…

1466e39

…s into better_init

Add new capabilities and new tests

3692346

Try to fix csg

46c878f

csh has very short maximum length for envvar names, stick to <32 chars

3a6c117

Some fancy new runners available!

785ae13

Actually use the CPU override

61db941

Merge branch 'main' into better_init

ec6f4e9

ocaisa mentioned this pull request Jan 29, 2026

Preferring Lmod-based initialisation EESSI/eessi-cli#6

Open

trz42 requested changes Jan 30, 2026

View reviewed changes

ocaisa added 10 commits January 30, 2026 10:13

Use specific commit for assert.sh, also run tests on system with Lmod…

dcce340

… available

Merge branch 'better_init' of github.com:ocaisa/software-layer-script…

5e5ed24

…s into better_init

Don't clobber an existing .cshrc

a97140a

Add a sanity check to make sure module command works

d779b54

Set explicit MODULEPATH

d91ded8

No quotes on ~

fc13853

Make test init script listen to EESSI_SOFTWARE_SUBDIR_OVERRIDE

7d621f1

Remove copy/pasted comment

78e286b

Add licence and more extensive documentation

4d97256

Add some additional comments to the bash script

30a8f7c

ocaisa mentioned this pull request Jan 30, 2026

Scripts init/bash and init/lmod/* are actually templates #155

Open

ocaisa changed the title ~~Make all shell initialisations more robust~~ Make all Lmod-based shell initialisations more robust, add additional features to facilitate site integration Jan 30, 2026

ocaisa added the ready-to-review label Jan 30, 2026

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Make all Lmod-based shell initialisations more robust, add additional features to facilitate site integration #153

Make all Lmod-based shell initialisations more robust, add additional features to facilitate site integration #153

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