aidenlab
Allow null queue and long_queue
Is your feature request related to a problem? Please describe.
SLURM/scripts/juicer.sh provides "#SBATCH -p $queue" or "#SBATCH -p $long_queue" with every job submission. At some supercomputing sites requesting an explicit partition is not recommended. To support such sites, juicer.sh should allow a null $queue and $long_queue.
Describe the solution you'd like
If the user provides no -q or -l arguments, and any site customization does not give values to $queue or $long_queue, then the "#SBATCH -p" directives should not be included in the job submission scripts.
Additional context
Compute Canada clusters (https://docs.computecanada.ca) have a complex partition structure. Jobs are sorted into appropriate partitions by a submission filter script and by Slurm itself based on run times, memory requests, etc., and recommended practice is that the user does not try to determine the correct partition.
A "queue" in PBS corresponds to a "partition" in Slurm.
I hope to provide a code patch presently.
Sorry, a code patch won't be forthcoming after all. I was able to patch this up in 'juicer.sh', but then discovered that 'split_rmdups.awk' would also have to be patched. I've got a fork that works on our systems, but it's a hack. Sending the changes back upstream would probably cause it to break on Slurm clusters where one should explicitly specify a partition.
Thanks for the update.
On Mon, Nov 16, 2020 at 2:00 PM Ross Dickson [email protected] wrote:
Sorry, a code patch won't be forthcoming after all. I was able to patch this up in 'juicer.sh', but then discovered that 'split_rmdups.awk' would also have to be patched. I've got a fork that works on our systems, but it's a hack. Sending the changes back upstream would probably cause it to break on Slurm clusters where one should explicitly specify a partition.
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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org
Dear Neva,
it seems I've ran into the same issue as Ross - certain research HPC at Canadian universities and the CCDB platforms do not allow selecting a partition for the standard user (except for researchers that have contributed hardware). Is there a way you would consider to provide a patch for this issue allowing not to specify partitions? I guess three files would have to be patched: 'juicer.sh', ‘split_rmdups.awk’ and 'mega.sh'.
Many thanks for your consideration. Martin
