User: andrespara
andrespara • 0
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Posts by andrespara
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Comment:
C: grid engine problem with OMA
... Thanks! I will try this ...
written 8 months ago by
andrespara • 0
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Comment:
C: grid engine problem with OMA
... Hi again, I wonder if I could send the jobs to **only** certain nodes so I can start multiple OMA runs with different datasets in the same grid. We have several nodes called "ubuntu-node2" "ubuntu-node3" and so on.
I am currently launching OMA with that line `qsub -v NR_PROCESSES=100 -b y -j y -t 1 ...
written 8 months ago by
andrespara • 0
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Comment:
C: grid engine problem with OMA
... When I try to execute "qsub start-oma.sh" it says
> qsub: Unknown option
bash start-oma.sh
works but starts only one process and with qstat I didn't notice any activity but maybe it is part of the intention of the script. ...
written 12 months ago by
andrespara • 0
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Comment:
C: grid engine problem with OMA
... A collaborator beat me and run Alex's solution first at the grid but I will check the script with your solution as soon as the current run ends. Thanks for your help Adrian. ...
written 12 months ago by
andrespara • 0
0
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Comment:
C: grid engine problem with OMA
... Thanks for the help Alex! It worked!! ...
written 12 months ago by
andrespara • 0
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Comment:
C: grid engine problem with OMA
... I also would like to know if OMA 2+ has been tested on open grid engine or if there is feedback other users on this set up or scenario.
Would it be better to change from open grid to Slurm for using OMA 2+? ...
written 12 months ago by
andrespara • 0
0
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Comment:
C: grid engine problem with OMA
... It didn't help, the variable is set up.
"`echo "NR_PROCESSES $NR_PROCESSES`" shows 100 ...
written 12 months ago by
andrespara • 0
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... wrong thread, sorry, ...
written 12 months ago by
andrespara • 0
3
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... Dear all,
Using the open grid engine and using this line
qsub -b y -j y -t 1-40 -cwd /usr/local/OMA/bin/OMA
I got this error
> Starting database conversion and checks...
> We require that job-arrays now explicitly specify the number of jobs
> in the array. You should add to your s ...
written 12 months ago by
andrespara • 0
• updated
12 months ago by
adrian.altenhoff • 440
0
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Comment:
C: How To Run Muscle In Batch?
... Hi, I would like to run this but with mafft alingment. I searched in the parallel manual and several variations, I guess this is not an issue with the dot in the replacement string, I removed and it didn't work. The simple strategy is `mafft seq.fa > align.fa` so I tried `ls *.fa | parallel linsi ...
written 2.7 years ago by
andrespara • 0
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12 months ago,
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For Which are free options for running OMA in a cluster?
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