- I cannot find the tool I want to use (or a specific version) among the available modules. What can I do?
A new ticket has to be sent in Helpdesk, to ask for installation. We recommend you have attached the URL of its official page.
- I execute my SLURM script and I get the error: init.c(379):ERROR:109: Unknown shell type ‘purge/load/unload’. How can I solve it?
The error occures due to the wrong initialization of module in the SLURM script. You can use:
- #!/bin/bash -l at the beginning to start a login shell, or
- to add the line:
before any call of the module command.
- Is there any way to ensure that the requested module is successfully loaded?
Yes. You can identify the correct version/path of the tool you are going to use by:
- checking its path by running: which [tool name] (e.g. which mafft). All modules are placed in /mnt/big/bioSW and /mnt/big/envSW directories. If the result is a path different from the latters, the load was not successful.
- checking its version by the use of the command arguments the developer has defined (usually –version, -v, –help, -h, etc.)
- How do I capture the module command output?
This ties in with the very first question. Since the module command is essentially an eval, the visible output to the screen must necessarily be sent to stderr. It becomes a matter on how to capture output from stderr for the various shells. The following examples just show how to spool the output from the avail command to a file. This also works for the various other module commands like list, display, etc. There are also various tricks for piping stderr to another program.
module avail 2> spoolfile
csh: (overwrite existing file)
module avail >&! spoolfile