| T O P I C R E V I E W |
| mle25 |
Posted - Oct 05 2016 : 5:55:28 PM
Currently the afni version installed on Hugin is from 2011. A lot has changed since this version and I would like to update it for processing use in batch scripts and interactive nodes. What is the best way for doing this without the required sudo access needed?
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| 5 L A T E S T R E P L I E S (Newest First) |
| petty |
Posted - Oct 06 2016 : 4:43:18 PM
Also, there are two parallel environments set-up ( mpi and ompi ), so there's also the possibility that afni install, which is openmp, already knows how to utilize that. I've, personally, never done anything with the parallel environments |
| petty |
Posted - Oct 06 2016 : 4:33:38 PM
the "-l h_vmem" represents a specific request ... it works because virtual memory is set-up as a consumable. the only other configured consumable is "slots" .. .meaning how many slots your job occupies.
this is only going to be relevant for submitted jobs ( qsub ), not interactive jobs ( qrsh ).
If you had a job you could submit, that you knew would use 10 CPUs, you could submit that in a script with something like "qsub -v EXPERIMENT=This.01 -l h_vmem=10G,slots=10 script.sh"
Alternatively, if its something that you can parallelize yourself ( i.e.: iterations, loops, etc ) ... you could just submit 10 jobs, one for each iteration, which would only occupy 1 slot. You're much better off creating scripts, submitting those at batch jobs, than just interactively running commands.
here's a good overview:
http://bioinformatics.mdc-berlin.de/intro2UnixandSGE/sun_grid_engine_for_beginners/README.html |
| mle25 |
Posted - Oct 06 2016 : 4:19:02 PM
Thank you.
Another related question, Some of the afni commands and other packages allow for parallel computing to speed up a large job to run on multiple processors. I have tried to find an option like "qrsh -l h_vmem=10G bash -li" for requesting extra cpus so that I can run a parallel job without overloading a node. Is there a way to do this? |
| petty |
Posted - Oct 05 2016 : 9:25:32 PM
Also, i updated to the latest version.
the older versions are still in /usr/local/packages with the date/version included in the afni folder name |
| petty |
Posted - Oct 05 2016 : 9:01:54 PM
Generally, you'd just need to ask for it to be updated by sending an email to biac-help
Otherwise, if there are packages you just wanted to test, you could download your own version to an experiment folder and execute from there. If they were useful packages that others might want, we can install it to the OS |
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