User: andrespara

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andrespara0
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Posts by andrespara

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Comment: C: OMA core dumped error in a single node/machine
... Thanks, we abandoned that node for the moment and moved the work to another machine (a Desktop in fact). If/when I put more work on schedule with that grid an machines I will pay attention to that error and if it appears only for that node or somewhere else. Thanks! ...
written 21 days ago by andrespara0
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Comment: C: OMA core dumped error in a single node/machine
... Thanks Adrian, we will try to reproduce the error in other machines, by the way those machines have Ubuntu 14.04 running so that might interfere with the analysis (I am pushing or asking for an upgrade ATM). In the meantime another run in another Desktop machine outside the cluster was interrupted ...
written 26 days ago by andrespara0
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Comment: C: OMA core dumped error in a single node/machine
... Is there some way to diagnose or confirm this? I used a small dataset (3 individuals) in case some unexpected collisions occurred. Thanks ...
written 4 weeks ago by andrespara0
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Comment: C: OMA core dumped error in a single node/machine
... That particular node worked fine some months ago but along other more powerful nodes in a parallelization with open grid engine, I thought maybe something changed or maybe the parallelization is failing here [in the meantime I launched again a test with only 3 individuals and it also dropped to a si ...
written 4 weeks ago by andrespara0
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OMA core dumped error in a single node/machine
... Dear all, I am having problems running OMA, I am running it in a single machine/node to avoid errors or conflict with the open grid engine. Even when I use `OMA -c` first and then `OMA -n 9` the node drops to half that amount of processors in a few minutes and now a single processor is running. A ...
oma orthology written 4 weeks ago by andrespara0 • updated 23 days ago by Biostar ♦♦ 20
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Comment: C: grid engine problem with OMA
... Thanks! I will try this ...
written 11 months ago by andrespara0
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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 11 months ago by andrespara0
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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 14 months ago by andrespara0
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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 14 months ago by andrespara0
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Comment: C: grid engine problem with OMA
... Thanks for the help Alex! It worked!! ...
written 14 months ago by andrespara0

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Popular Question 14 months ago, created a question with more than 1,000 views. For Which are free options for running OMA in a cluster?

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