BIRCH on HPC systems
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Rationale: HPC systems are generally pretty opaque about what is on the system and how to use tools. Nowhere is the user-oriented advantages of BIRCH needed more than on multiuser HPC systems.
While BIRCH has evolved from day 1 as a multiuser resource, there are certainly going to be challenges on major platforms that will need to be addressed. This page will be the place for making BIRCH the best solution for a user accessible HPC system.
The test platform will be the Digital Alliance of Canada.
Important DCA links
Contents |
About DCA
The nibi.alliancecan.ca runs AlmaLinux 9.6, which is a free distro of RedHat Linux.
Getting BIRCH to run on DAC
Unique aspects of the DAC system
- Many software programs and packages don't simply run with a default. Programs are often wrapped in modules, and you have to choose which version of the software to run. This is done using
module load module_name
module load only applies to the shell in which it was launched, so if you want a personal default, the user has to run module load in their .profile, .bashrc other file at login.
- GenBank files do not need to be backed up, but do require fast reads by BLAST and FASTA. Ideally, this would be found in the scratch space. However, scratch files expire monthly. It may be possible to copy files or otherwise change modification dates once per month to avoid deletion.
- [Scratch purging policy https://docs.alliancecan.ca/wiki/Scratch_purging_policy]
- DAC hosts don't have a mail server. Instead, you need to use the mail notification that is part of SLURM jobs. When a SLURM job is finished, (see [Running Jobs https://docs.alliancecan.ca/wiki/Running_jobs#Use_sbatch_to_submit_jobs]), you need to add lines to your SLURM script to send the output to an email address when completed.
Example of lines to add to a SLURM job:
#SBATCH --mail-user=your.email@example.com #SBATCH --mail-type=ALL
The Slurm documentation explains the possible values for the `--mail-type` option: https://slurm.schedmd.com/sbatch.html#OPT_mail-type
Java
in local.profile.source
module load java
To load the default java version each time a shell is launched. I tried putting this line in local.profile.login.source, but it appeared to have no effect.
