singularityhub
ERROR: Resolution loop on 'bids/freesurfer/latest' detected, RHEL 9
The modules do not appear with Lmod via module available. Testing freesurfer, using TCL the module appears as:
bids/freesurfer/latest/module.tcl
ml bids/freesurfer/latest/module.tcl results in:
ERROR: Resolution loop on 'bids/freesurfer/latest' detected
I've switched between TCL and Lmod. We use the Bright Computing provisioning management system but I don't think that is related.
To Reproduce Steps to reproduce the behavior:
git clone https://github.com/singularityhub/singularity-hpc
cd singularity-hpc
pip install -e .[all]
/usr/local/bin/shpc install bids/freesurfer:latest
INFO: Using cached SIF image
Module bids/freesurfer:latest was created.
module use ./modules
This was installed within echo $MODULEPATH
Expected behavior The module should appear.
apptainer version 1.3.0-1.el9
/usr/local/bin/shpc --version
0.1.28
rpm -qa|grep -i lmod
Lmod-8.7.32-1.el9.x86_64
rpm -qa|grep -i tcl
tcl-8.6.10-7.el9.x86_64
tcl-devel-8.6.10-7.el9.x86_64
Anything else? If this is a question more than a bug, feel free to move it.
I'm not great with developing environment modules, but this seems relevant:
@marcodelapierre have you seen this before?
I am testing with Lmod version 8.7.47, and latest Singularity-HPC, and cannot reproduce.
Would you be able to provide the output of ml av bids, as well as the contents of the directory modules/bids/freesurfer/latest/ ?
Thank you
ml av bids
It does not return any values.
ls modules/bids/freesurfer/latest
99-shpc.sh bin module.lua
Since we have both TCL and Lmod installed which option should be used? Is it expected to not load modules when we use Lmod?
It should work for either or, but I've never tested shpc in an environment with both!
Is there any debugging or comments we can insert to see where the modules are failing to load?
shpc is just using standard environment modules or lmod, so you'd want to look in documentation for those projects. @marcodelapierre is much better at these modules than me so he might have some advice! I do most in the cloud these days, or user space kubernetes.
Hello @marcodelapierre is there anything I can do to work around this?
I am surprised that ml av bids does not return anything.
Is the root directory of that module tree in the $MODULEPATH? You should always make sure you have it, module use </modules/root/path>.
I would like to see the outcome of that command in the same shell environment that also generates the Error.
When you say you have both TCL + Lmod installed, I am assuming you mean TCL as the language and then Lmod modules, and that you do NOT also have installed Environment Modules (the TCL variation of Lmod). Is this correct?
In other words, I would expect module --version to reveal that you have an Lmod version installed.
With the assumption above, Lmod can handle both modules written in lua and in tcl. Lua is the native one for Lmod, hence preferable because it has more functionalities; Lmod can handle tcl modules too though.
For what regards SHPC, I cannot test at present, but for what I remember from past exploration, Lmod is capable of correctly using both Lua and Tcl modules generated by SHPC. (as said above, lua preferred because it is the native language of Lmod modules).
I am surprised that
ml av bidsdoes not return anything. Is the root directory of that module tree in the$MODULEPATH? You should always make sure you have it,module use </modules/root/path>.
Yes here's what echo $MODULEPATH returns after I load an existing (non SHPC) module:
/cluster/shared/modulefiles/scotch/7.0.5:/cluster/shared/modulefiles/bids/freesurfer/V30-a43f1f/module.lua:/cluster/shared/modulefiles/bids/freesurfer/V30-a43f1f:/cluster/shared/modulefiles/bids/freesurfer:/etc/scl/modulefiles:/etc/modulefiles:/usr/share/modulefiles:/cluster/shared/modulefiles
If I run ml on another non-SHPC module using the full path it shows up like this, with the full path:
ml /cluster/shared/modulefiles/metis/5.1.0
ml
Currently Loaded Modulefiles:
1) anaconda/2023.09 2) scotch/7.0.5 3) /cluster/shared/modulefiles/metis/5.1.0
These also show up as modules:
singularity-hpc/shpc/main/modules/templates/default_version
singularity-hpc/shpc/main/modules/templates/docker.tcl
singularity-hpc/shpc/main/modules/templates/singularity.tcl
singularity-hpc/shpc/main/modules/templates/view_module.tcl
I would like to see the outcome of that command in the same shell environment that also generates the Error.
Did the above help?
When you say you have both TCL + Lmod installed, I am assuming you mean TCL as the language and then Lmod modules, and that you do NOT also have installed Environment Modules (the TCL variation of Lmod). Is this correct? Both are installed at the same time:
$ rpm -qa|grep -i envi
environment-modules-5.3.0-1.el9.x86_64
rpm -qa|grep -i lmod
Lmod-8.7.32-1.el9.x86_64
In other words, I would expect
module --versionto reveal that you have an Lmod version installed.
module --version
Modules Release 5.3.0 (2023-05-14)
With the assumption above, Lmod can handle both modules written in lua and in tcl. Lua is the native one for Lmod, hence preferable because it has more functionalities; Lmod can handle tcl modules too though.
For what regards SHPC, I cannot test at present, but for what I remember from past exploration, Lmod is capable of correctly using both Lua and Tcl modules generated by SHPC. (as said above, lua preferred because it is the native language of Lmod modules).
This must be a clue as to why the 4 singularity-hpc modules appear. The ones ending in .tcl appear:
ls -l /cluster/shared/modulefiles/singularity-hpc/shpc/main/modules/templates
total 83
-rw-r--r-- 1 root root 112 Dec 17 09:26 default_version
-rw-r--r-- 1 root root 7094 Dec 17 09:26 docker.lua
-rw-r--r-- 1 root root 8490 Dec 17 09:26 docker.tcl
-rw-r--r-- 1 root root 5200 Dec 17 09:26 docs.md
drwxr-xr-x 2 root root 4096 Dec 17 09:26 includes
-rw-r--r-- 1 root root 0 Dec 17 09:26 __init__.py
-rw-r--r-- 1 root root 8062 Dec 17 09:26 singularity.lua
-rw-r--r-- 1 root root 9799 Dec 17 09:26 singularity.tcl
-rwxr-xr-x 1 root root 405 Dec 17 09:26 test.sh
-rw-r--r-- 1 root root 256 Dec 17 09:26 view_module.lua
-rw-r--r-- 1 root root 307 Dec 17 09:26 view_module.tcl
Attempting to load one of those gets this error:
ml singularity-hpc/shpc/main/modules/templates/singularity.tcl
Loading singularity-hpc/shpc/main/modules/templates/singularity.tcl
Module ERROR: invalid command name "% include "includes/load_view.tcl" %"
while executing
"{% include "includes/load_view.tcl" %}"
(file "/cluster/shared/modulefiles/singularity-hpc/shpc/main/modules/templates/singularity.tcl" line 45)
Please contact <root@localhost>
Using the full path to the module.lua file:
ml /cluster/shared/modulefiles/bids/freesurfer/V30-a43f1f/module.lua
Module ERROR: Magic cookie '#%Module' missing
In '/cluster/shared/modulefiles/bids/freesurfer/V30-a43f1f/module.lua'
Please contact <root@localhost>
Mmh OK. I would discourage having both Env Modules and Lmod active in the same shell environment, it adds unnecessary complexity and sources of issues.
Remember that ml is exclusive to Lmod, whereas module exists for both. So in your case you really have both active, as module --version mentions Env Modules.
You should not be seeing these:
singularity-hpc/shpc/main/modules/templates/default_version
singularity-hpc/shpc/main/modules/templates/docker.tcl
singularity-hpc/shpc/main/modules/templates/singularity.tcl
singularity-hpc/shpc/main/modules/templates/view_module.tcl
I think they come out of using module use on the wrong path.
From your first messages:
cd singularity-hpc
module use ./modules
To correctly use modules, you need to run module use with the modules subdirectory of the SHPC installation.
I would like to see the outcome of ml av bids after you run this.
What type of privileges do you have on that machine?
It would be good to be able to disable either Lmod or Env modules setup in the shell environment, to test in a more robust environment.
Sourcing of the corresponding scripts will typically be either in your .bashrc/.profile in your home, in which case you can comment out the corresponding line, or in the forms of scripts within /etc/profile.d/ directory. The latter case is trickier as it would require root privileges to move sourceable files out of it.
To correctly use modules, you need to run
module usewith the modules subdirectory of the SHPC installation.I would like to see the outcome of
ml av bidsafter you run this.
So within /cluster/shared/apps/singularity-hpc I ran
Tue Dec 17 root@node003 $ module use ./modules
Tue Dec 17 root@node003 $ ml av bids
Tue Dec 17 root@node003 $ ml
No Modulefiles Currently Loaded.
echo $MODULEPATH
/cluster/shared/apps/singularity-hpc/modules:/etc/scl/modulefiles:/etc/modulefiles:/usr/share/modulefiles:/cluster/shared/modulefiles
What type of privileges do you have on that machine?
root
It would be good to be able to disable either Lmod or Env modules setup in the shell environment, to test in a more robust environment.
Sure what would you like me to try?
EDIT I went to another node. This time I made some progress:
[root@prov singularity-hpc]# module use ./modules
[root@prov singularity-hpc]# ml av bids
---------------------- /cluster/shared/apps/singularity-hpc/modules -----------------------
bids/freesurfer/latest/module
------------------------------- /cluster/shared/modulefiles -------------------------------
bids/freesurfer/V30-a43f1f/module (D)
So if I do
ml bids/freesurfer/latest/module
[root@2402-prov-002 singularity-hpc]# ml
Currently Loaded Modules:
1) anaconda/2023.09 2) bids/freesurfer/latest/module
[root@prov singularity-hpc]# free
free freesurfer-inspect-deffile freesurfer-shell
freesurfer-container freesurfer-inspect-runscript freetype-config
freesurfer-exec freesurfer-run
Yep this is a node that has only Lmod-8.7.32-1.el9.x86_64 so having both definitely confuses the modules themselves.
Oh great! Looks like the EnvModules vs Lmod clash was indeed causing your issues.
Let us know if you need anything else, or if we can close this one.
It would be good to be able to disable either Lmod or Env modules setup in the shell environment, to test in a more robust environment.
Can you suggest a way to do this in the nodes that have both?
Oh great! Looks like the EnvModules vs Lmod clash was indeed causing your issues.
Let us know if you need anything else, or if we can close this one.
Looks like both Lmod and environment-modules are in use to get specific modules to load only on compute nodes, so when trying to uninstall environment-modules it wants to remove mpich, openmpi, etc.
It'd be great to know how to work around this.
Please start from this comment of mine above:
It would be good to be able to disable either Lmod or Env modules setup in the shell environment, to test in a more robust environment.
Sourcing of the corresponding scripts will typically be either in your .bashrc/.profile in your home, in which case you can comment out the corresponding line, or in the forms of scripts within /etc/profile.d/ directory. The latter case is trickier as it would require root privileges to move sourceable files out of it.
Please start from this comment of mine above:
It would be good to be able to disable either Lmod or Env modules setup in the shell environment, to test in a more robust environment.
Sourcing of the corresponding scripts will typically be either in your .bashrc/.profile in your home, in which case you can comment out the corresponding line, or in the forms of scripts within /etc/profile.d/ directory. The latter case is trickier as it would require root privileges to move sourceable files out of it.
That's where I'm not clear. Are you suggesting to run the source cmd on
/cluster/shared/apps/singularity-hpc/modules/bids/freesurfer/latest/module and put it in my .bashrc? That means all users that want this module need to do the same, unless I put it into a file in /etc/profile.d. Basically I'm asking for assistance in what to do next.
No worries, let me try and clarify.
Having the RPM packages for Lmod and Env modules is not enough to have them actually configured in the shell environment. Both applications rely on an initialisation script that needs to be sourced when the shell starts. We have proof that you have both running (ml -> lmod ; module --version --> suggest env modules), and this implies that at shell startup scripts for both are sourced.
Now, to have only one running, you need to locate where the scripts are sourced, and disable that.
Common setups:
LMOD:
-
.bashrc,.profileor.bash_profilesource the file<LMOD-ROOT>/lmod/init/profile -
/etc/profile.d/contains a copy or symlink of the lmod script file above; often, this is named in a meaningful way, e.g./etc/profile.d/z00_lmod.sh(otherwise need to grep the contents to find out)
ENV MODULES:
-
.bashrc,.profileor.bash_profilesource the file<MODULES-ROOT>/init/profile.sh -
/etc/profile.d/contains a copy or symlink of the env modules script file above; often, this is named in a meaningful way, e.g./etc/profile.d/modules.sh(otherwise need to grep the contents to find out)
So, what I suggest is to have a look at the following:
- contents of the files
.bashrc,.profileor.bash_profile - files within the directory
/etc/profile.d/There, you want to search for the info I mentioned just above. Select the software you want to disable, and then it will be a matter of either: - commenting the line that does the sourcing in the file
.bashrc,.profileor.bash_profile; or - moving out the script file from
/etc/profile.d/
I hope this can help.
OK I'm getting closer. I'm assuming I want to disable Environment Modules. I see we have:
/etc/alternatives/modules.sh
/etc/profile.d/modules.sh
There is also the .csh versions which I'll ignore for now.
file /etc/alternatives/modules.sh
/etc/alternatives/modules.sh: symbolic link to /usr/share/Modules/init/profile.sh
Which has:
cat /usr/share/Modules/init/profile.sh
# shellcheck shell=sh
# get current shell name by querying shell variables or looking at parent
# process name
if [ -n "${BASH:-}" ]; then
if [ "${BASH##*/}" = 'sh' ]; then
shell='sh'
else
shell='bash'
fi
elif [ -n "${ZSH_NAME:-}" ]; then
shell=$ZSH_NAME
else
shell=$(/usr/bin/basename "$(/usr/bin/ps -p $$ -ocomm=)")
fi
if [ -f "/usr/share/Modules/init/$shell" ]; then
. "/usr/share/Modules/init/$shell"
else
. '/usr/share/Modules/init/sh'
fi
And this file, which has the MODULEPATH in it and I believe this is for Lmod:
cat /etc/profile.d/00-modulepath.sh
[ -z "$MODULEPATH" ] &&
[ "$(readlink /etc/alternatives/modules.sh)" = "/usr/share/lmod/lmod/init/profile" -o -f /etc/profile.d/z00_lmod.sh ] &&
export MODULEPATH=/etc/modulefiles:/usr/share/modulefiles:/cluster/shared/modulefiles || :
So notice that it references /etc/alternatives/modules.sh which is a sym link to:
file /etc/alternatives/modules.sh
/etc/alternatives/modules.sh: symbolic link to /usr/share/Modules/init/profile.sh
So can I just use alternatives cmd to get around this?
FWIW:
ls /etc/profile.d/z00_lmod.sh
ls: cannot access '/etc/profile.d/z00_lmod.sh': No such file or directory
And this file is what appears to enable Lmod:
/usr/share/lmod/lmod/init/profile
########################################################################
. /etc/profile.d/00-modulepath.sh
# This is the system wide source file for setting up modules
########################################################################
if [ -z "${LMOD_ALLOW_ROOT_USE+x}" ]; then
LMOD_ALLOW_ROOT_USE=yes
fi
[...snip...]
Looks like /etc/profile.d/00-modulepath.sh is used by both EnvModules and Lmod, it has a conditional to check which one is active.
Yes, you want to disable the env modules sourceable files, so for instance having the alternatives file /etc/alternatives/modules.sh NOT pointing to Env Modules.
Also, for the same purpose /etc/profile.d/modules.sh should not be the Env Modules one.
What I don't understand in this setup is where the Lmod script is currently sourced, otherwise you would not be able to use ml.
What I would do:
- get rid of
/etc/alternatives/modules.shand/etc/profile.d/modules.sh - check whether Lmod
mlis still available - where is this setup? .bashrc/.bash_profile/.profile ? some other .sh file in /etc/profile.d/ ? - if still needed after 2., make sure that Lmod's
/usr/share/lmod/lmod/init/profileis sourced somewhere (eg by creating a symlink to/etc/profile.d/z00_lmod.sh) - make sure the conditional
/etc/profile.d/00-modulepath.shworks properly with your Lmod-only setup
I hope this helps.
Please be aware that I will be logging off at the end of today, and get back on my work computer on 6 Jan. I will not be responsive in the meanwhile.
All the best,
- get rid of
/etc/alternatives/modules.shand/etc/profile.d/modules.sh- check whether Lmod
mlis still available - where is this setup? .bashrc/.bash_profile/.profile ? some other .sh file in /etc/profile.d/ ?- if still needed after 2., make sure that Lmod's
/usr/share/lmod/lmod/init/profileis sourced somewhere (eg by creating a symlink to/etc/profile.d/z00_lmod.sh)- make sure the conditional
/etc/profile.d/00-modulepath.shworks properly with your Lmod-only setup
OK I removed the 2 suggested files, then created the sym link. However in order for bids/freesurfer/latest/module to appear I had to manually run the module use ./modules cmd after I cd /cluster/shared/apps/singularity-hpc
How do I get that module to be available without having to run module use? How can I customize the long module name bids/freesurfer/latest/module
Please be aware that I will be logging off at the end of today, and get back on my work computer on 6 Jan. I will not be responsive in the meanwhile.
Thanks perhaps @vsoch has an idea?
Hi,
To make the modules available from shell login, I suggest to add module use /cluster/shared/apps/singularity-hpc in your ~/.bash_profile or ~/.profile (depending on which one you have in your home).
To customise grouping of modules within the directory structure, please have a look at the Views functionality in the documentation, see if it can be helpful in your case.
To customise grouping of modules within the directory structure, please have a look at the Views functionality in the documentation, see if it can be helpful in your case.
What I mean is all of these show up:
ml avail
------------------ /cluster/shared/apps/singularity-hpc ------------------
modules/bids/freesurfer/latest/module
shpc/main/modules/templates/default_version
shpc/main/modules/templates/docker.tcl
shpc/main/modules/templates/docker
shpc/main/modules/templates/includes/default_version
shpc/main/modules/templates/includes/load_view (D)
shpc/main/modules/templates/singularity.tcl
shpc/main/modules/templates/singularity
shpc/main/modules/templates/view_module.tcl
shpc/main/modules/templates/view_module
So how would I hide those?
Also what causes this?
ml modules/bids/freesurfer/latest/module
Lmod Warning: MODULEPATH directory:
"/cluster/shared/apps/singularity-hpc" has too many non-modulefiles
(159). Please make sure that modulefiles are in their own directory and not
mixed in with non-modulefiles (e.g. source code)
Oh I see, thanks for clarifying.
Both issues come to the fact that the directory /cluster/shared/apps/singularity-hpc is in the MODULEPATH variable, which should NOT be the case. because that is a location of the SHPC installation, not a module directory tree.
Most likely this implies that somewhere the following command is executed, module use /cluster/shared/apps/singularity-hpc.
If you are not executing it yourself after shell start, then it is executed in some sourced script, such as the usual .bashrc, .bash_profile, .. or in one inside /etc/profile.d/. You should locate that command and get rid of it.
Both issues come to the fact that the directory
/cluster/shared/apps/singularity-hpcis in theMODULEPATHvariable, which should NOT be the case. because that is a location of the SHPC installation, not a module directory tree. Most likely this implies that somewhere the following command is executed,module use /cluster/shared/apps/singularity-hpc.
I only run module use /cluster/shared/apps/singularity-hpc then from ml avail all those extra shpc/main/modules/templates appear.
So I'm confused now, as previously you told me to:
To make the modules available from shell login, I suggest to add
module use /cluster/shared/apps/singularity-hpcin your~/.bash_profileor~/.profile(depending on which one you have in your home).
After I run the module use cmd the $MODULEPATH is:
echo $MODULEPATH
/etc/scl/modulefiles:/etc/modulefiles:/usr/share/modulefiles:/cluster/shared/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core
so indeed it does get added to/cluster/shared/apps/singularity-hpc in $MODULEPATH
Looking at my cmd history could one of these cause the $MODULEPATH to be updated?
shpc config set container_base /cluster/shared/apps/shpc-containers
shpc config set module_sys lmod
Instead of the one you have just mentioned, the correct module use command should be:
module use /cluster/shared/apps/singularity-hpc/modules
Using this one should fix the incorrect ml avail output, let me know :)
Using this one should fix the incorrect
ml availoutput, let me know :)
Ah now that looks much better:
module use /cluster/shared/apps/singularity-hpc/modules
ml av
------------------- /cluster/shared/apps/singularity-hpc/modules --------------------
bids/freesurfer/latest/module
Any ideas on how to fix having both Lmod and environment-modules without having to do the below on all nodes? I suppose this could be added to an Ansible play book just seems clumsy to scale it the way you suggested:
- get rid of
/etc/alternatives/modules.shand/etc/profile.d/modules.sh- check whether Lmod
mlis still available - where is this setup? .bashrc/.bash_profile/.profile ? some other .sh file in /etc/profile.d/ ?- if still needed after 2., make sure that Lmod's
/usr/share/lmod/lmod/init/profileis sourced somewhere (eg by creating a symlink to/etc/profile.d/z00_lmod.sh)- make sure the conditional
/etc/profile.d/00-modulepath.shworks properly with your Lmod-only setup
Perhaps this is a feature request, to allow usage/confguration with Lmod and environment-modules installed?
And thanks for you patience and responding to my issues, I bet this thread will help others in the future.
Hi, no worries, indeed these are enjoyable and useful conversation within the community :)
I don't have much experience on the cluster sys admin side nor on removing one of the modules installation. I would suggest to look around for a scriptable, effective way of removing it, that can be implemented within the cluster manager of your cluster - for this second part consulting with other team members of the cluster operations team may help I reckon.
Regarding allowing to use both modules systems at once, as far as I know this is not a limitation of SHPC per se. I may be wrong, but Lmod and EnvModules themselves were designed as alternative options. As such, their shell setups have inherently overlapping and conflicting aspects.
In my experience, I have only seen deployments with one of them being installed. However, this is just my experience. I encourage you to consider reaching out to their developer teams (https://github.com/tacc/lmod, https://github.com/envmodules/modules) and gauge their feedback on this one.
Well I uninstalled Lmod and module use /cluster/shared/apps/singularity-hpc/modules runs but does not make freesurfer available. And thus, creating a symbol link to /usr/share/lmod/lmod/init/profile won't work as Lmod is uninstalled. $MODULEPATH does however add the path to SHPC:
echo $MODULEPATH
/cluster/shared/apps/singularity-hpc/modules:/etc/scl/modulefiles:/usr/share/Modules/modulefiles:/etc/modulefiles:/usr/share/modulefiles:/cluster/shared/modulefiles
What else could be preventing the module from appearing?
I also ran: shpc config set module_sys tcl as Lmod is now gone. No difference.
Running the following results in the below error:
ml bids/freesurfer/latest/module
Module ERROR: Magic cookie '#%Module' missing
In '/cluster/shared/apps/singularity-hpc/modules/bids/freesurfer/latest/module.lua'
Please contact <root@localhost>
So is an additional step needed for Environment Modules?
EDIT: I see that for Environment Modules I need to use --module-sys tcl so I ran:
shpc install --module-sys tcl bids/freesurfer
However I get this error:
module load bids/freesurfer/V30-a43f1f/module.tcl
Loading bids/freesurfer/V30-a43f1f/module.tcl
Module ERROR: No extra specification allowed on this command
while executing
"conflict bids/freesurfer:V30-a43f1f"
(file "/cluster/shared/apps/singularity-hpc/modules/bids/freesurfer/V30-a43f1f/module.tcl" line 85)
Please contact <root@localhost>
What's interesting is the help cmd works:
module help bids/freesurfer/latest
-------------------------------------------------------------------
Module Specific Help for /cluster/shared/apps/singularity-hpc/modules/bids/freesurfer/V30-a43f1f/module.tcl:
This module is a singularity container wrapper for bids/freesurfer:V30-a43f1f vV30-a43f1f
so Line 85:
80 # If we have wrapper base set, honor it, otherwise we use the moduleDir
81 set wrapperDir "/cluster/shared/apps/singularity-hpc/modules/bids/freesurfer/V30-a43f1f"
82
83 # conflict with modules with the same alias name
84 conflict freesurfer
85 conflict bids/freesurfer:V30-a43f1f
Here's a module --debug output:
module --debug use /cluster/shared/apps/singularity-hpc/modules
DEBUG setState: cmdline set to '/usr/share/Modules/libexec/modulecmd.tcl bash --debug use /cluster/shared/apps/singularity-hpc/modules'
DEBUG setState: machine set to 'x86_64'
DEBUG setConf: tcl_ext_lib set to '/usr/lib64/libtclenvmodules.so'
DEBUG Load Tcl extension library (/usr/lib64/libtclenvmodules.so)
DEBUG setState: tcl_ext_lib_loaded set to '1'
DEBUG setConf: siteconfig set to '/etc/environment-modules/siteconfig.tcl'
DEBUG sourceSiteConfig: Source site configuration (/etc/environment-modules/siteconfig.tcl)
DEBUG setState: siteconfig_loaded set to '1'
DEBUG setConf: locked_configs set to ''
DEBUG setState: supported_shells set to 'sh bash ksh zsh csh tcsh fish cmd tcl perl python ruby lisp cmake r'
DEBUG setState: shell set to 'bash'
DEBUG setState: subcmd set to 'use'
DEBUG setState: subcmd_args set to '/cluster/shared/apps/singularity-hpc/modules'
DEBUG setState: init_error_report set to '1'
DEBUG setConf: verbosity set to 'debug'
DEBUG setState: is_stderr_tty set to '1'
DEBUG setConf: term_background set to 'dark'
DEBUG setConf: colors set to 'hi=1:db=2:tr=2:se=2:er=91:wa=93:me=95:in=94:mp=1;94:di=94:al=96:va=93:sy=95:de=4:cm=92:aL=100:L=90;47:H=2:F=41:nF=43:S=46:sS=44:kL=30;48;5;109'
DEBUG setConf: color set to '1'
DEBUG setConf: pager set to '/usr/bin/less -eFKRX'
DEBUG setState: paginate set to '1'
DEBUG setState: report_format set to 'regular'
DEBUG setState: reportfd set to 'file4'
DEBUG setState: timer set to '0'
DEBUG lappendState: modulefile appended with '{}'
DEBUG parseModuleCommandName: (command=use, cmdvalid=1, cmdempty=0)
DEBUG setConf: avail_indepth set to '1'
DEBUG setConf: search_match set to 'starts_with'
DEBUG parseModuleCommandArgs: (show_oneperline=0, show_mtime=0, show_filter=, search_filter=, search_match=starts_with, dump_state=0, addpath_pos=prepend, not_req=0, tag_list=, otherargs=/cluster/shared/apps/singularity-hpc/modules)
DEBUG setConf: advanced_version_spec set to '1'
DEBUG setConf: variant_shortcut set to ''
DEBUG lappendState: always_read_full_file appended with '1'
DEBUG lappendState: commandname appended with 'use'
DEBUG setState: rc_running set to '1'
DEBUG setConf: ignore_user_rc set to '0'
DEBUG unsetState: rc_running unset
DEBUG setState: cwd set to '/root'
DEBUG lappendState: mode appended with 'load'
DEBUG add-path: (--ignore-refcount MODULEPATH /cluster/shared/apps/singularity-hpc/modules) cmd=prepend-path, mode=load, dflbhv=prepend
DEBUG setState: is_win set to '0'
DEBUG setState: path_separator set to ':'
DEBUG parsePathCommandArgs: (delim=:, allow_dup=0, idx_val=0, ign_refcount=1, bhv=prepend, var=MODULEPATH, val=/cluster/shared/apps/singularity-hpc/modules, nbval=1)
DEBUG unset-env: __MODULES_PUSHENV_MODULEPATH (internal=1, val=)
DEBUG getReferenceCountArray: (var=MODULEPATH, delim=:) got '/cluster/shared/modulefiles 1 /etc/scl/modulefiles 1 /cluster/shared/apps/singularity-hpc/modules 1 /usr/share/modulefiles 1 /etc/modulefiles 1 /usr/share/Modules/modulefiles 1'
DEBUG set-env: MODULEPATH=/cluster/shared/apps/singularity-hpc/modules:/etc/scl/modulefiles:/usr/share/Modules/modulefiles:/etc/modulefiles:/usr/share/modulefiles:/cluster/shared/modulefiles
DEBUG setState: mode set to ''
DEBUG setState: commandname set to ''
DEBUG setState: always_read_full_file set to ''
DEBUG setState: autoinit set to '0'
DEBUG setState: shelltype set to 'sh'
DEBUG setState: error_count set to '0'
DEBUG setState: return_false set to '0'
Edit: someone at the environment-modules Git wrote this
The conflict statement
conflict bids/freesurfer:V30-a43f1fis not valid due to the use of the:character which is the extra match specifier.I believe there is an issue with the generation of this modulefile. If the goal is to say that only one
bids/freesurfermodule can be loaded, the conflict statement should beconflict bids/freesurfer.I would suggest to report this to the singularity-hpc team.
Edit: Indeed removing in line 85 the :V30-a43f1f allows the module to load.
So on another cluster I get this error:
ml tensorflow/tensorflow/2.18.0rc0/module.tcl
Lmod has detected the following error:
/share/apps/Miniforge/lib/python3.12/site-packages/modules/tensorflow/tensorflow/2.18.0rc0/module.tcl:
(tensorflow/tensorflow/2.18.0rc0/module.tcl): expected boolean value but got
"bash"
While processing the following module(s):
Module fullname Module Filename
--------------- ---------------
tensorflow/tensorflow/2.18.0rc0/module.tcl /share/apps/Miniforge/lib/python3.12/site-packages/modules/tensorflow/tensorflow/2.18.0rc0/module.tcl
bash is mentioned here:
/share/apps/Miniforge/lib/python3.12/site-packages/modules/tensorflow/tensorflow/2.18.0rc0/module.tcl
if { [ module-info shell bash ] } {
if { [ module-info mode load ] } {
}
if { [ module-info mode remove ] } {