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12 June 2019, Charlottesville: Bioinformatics in a High-Performance Computing Environment #573

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Daniel-Mietchen opened this issue Jun 12, 2019 · 15 comments

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commented Jun 12, 2019

Good mix of people in the room, including some people from iGEM Virginia with whom I was trying to get in touch anyway, following the synthetic biology symposium last week (cf. #568 ).

In the afternoon, there will be room to discuss what software is/ should be running on the UVA HPC cluster Rivanna (see my separate notes on that). I'd like to use a MyBinder/ Docker/ Wikibase combo, and I'd like to learn more about the different file formats used in sequence analysis as well as about dark taxa.

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commented Jun 12, 2019

Another thing that's on my mind in this context is how things like http://wikigenomes.org/ can be integrated into sequence analysis workflows, or https://wikidp.org/ into software curation workflows.

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commented Jun 12, 2019

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commented Jun 12, 2019

I asked about how the environmental footprint of Rivanna is managed, and the VP for IT was mentioned as overseeing that. Will contact them.

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commented Jun 12, 2019

as allocation, users can use "rivanna-training" up to certain limits.

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commented Jun 12, 2019

For large file transfers, use Globus.

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commented Jun 12, 2019

For the hands-on, I am using the Terminal under rivanna-portal, along with instructions from
https://workshops.somrc.virginia.edu/lesson/ngs-seq-alignment/ .

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commented Jun 12, 2019

The hostname command gives udc-ba35-36 for me right now.
Gonna avoid that for running my jobs.

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commented Jun 12, 2019

after launching the ijob, hostname gives udc-ba26-28a.

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commented Jun 12, 2019

to get a list of all of a user's Rivanna jobs on that host machine, type
squeue -u UVACOMPUTEID, where UVACOMPUTEID is their compute id

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commented Jun 12, 2019

to get a list of most recently run jobs, type sacct, or sacct -S 2017-01-30 to get all the jobs run since a given start date. Output format can be specified using things like
sacct --format=jobid,jobname,start,elapsed,end -S 2017-01-30.
See sacct -h for details.

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commented Jun 12, 2019

echo $SLURM_CPUS_PER_TASK gives the number of cores requested by the ijob command

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commented Jun 12, 2019

If there is no scratch directory, then instead of
cd /scratch/dm7gn/ngs-aln-workshop/ref/,
one can do
cd /sfs/lustre/scratch/dm7gn/ngs-aln-workshop/ref/.

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commented Jun 12, 2019

met Sarah French. will send email to follow up.

under /project/genomes, there is a list of genomes for which indexes for alignment have already been built.

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commented Jun 12, 2019

Both the iGEM team and Sara are working on styrofoam.

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