Question: Error ruining OMA "OneMachineParallelInfo"
gravatar for dtejadamartinez
10 months ago by
dtejadamartinez10 wrote:

Hi, Trying to run OMA on 2 different cluster. In one cluster, it ran up to 32%, in another one it is cut at the beginning and the conversions are not finished.

But I get the same following error in both cases:

1523613044.955060 - 1 - [pid 22699]: Computing Orcinus_orca vs Bos_taurus (Part 95 of 503) Mem: 1.236GB
/home/nis/daniela/OMA/bin/oma: line 236: 22663 Terminated              $OMA_PATH/bin/omadarwin ${darwin_flag}  <<EOF
/home/dtejada/OMAstandalone/OMA.2.2.0/bin/oma: line 236:  9919 Segmentation fault      (core dumped) $OMA_PATH/bin/omadarwin ${darwin_flag}  <<EOF

Can you help me to solve this problem?


oma omastandalone • 351 views
ADD COMMENTlink modified 9 months ago by adrian.altenhoff450 • written 10 months ago by dtejadamartinez10

edited to add

There is a moment where conversions seem ready but the file says: conversion.running before that I run again OMA and I get the next error and the run die all.

 line 18: ulimit: stack size: cannot modify limit: Operation not permitted
only_run_dbconv := true
Starting database conversion and checks...
Process 15942 on login2: job nr 1 of 1
Reading GO file...

Best regards,

ADD REPLYlink modified 10 months ago by genomax62k • written 10 months ago by dtejadamartinez10

Tagging: adrian.altenhoff

ADD REPLYlink written 10 months ago by genomax62k

edited to add

The cluster use Sun Grid Engine, I'm still trying to run the data, including the Toy example, but this error always comes up:

Reading GO file... Segmentation fault (core dumped)


ADD REPLYlink written 10 months ago by dtejadamartinez10
gravatar for adrian.altenhoff
9 months ago by
adrian.altenhoff450 wrote:

From the output you mention I think the problem is due to a restriction on your system you modify the stacksize. Some function in OMA require a significant amount of recursions, so we try to increase the stacksize as much as possible (linux: ulimit -s unlimited; mac: ulimit -s hard).

Your output indicates that this operation failed. could you try to run these commands in a shell yourself. on some (HPC) setups, this might only be permitted for a real user session, but cannot be modified in a batched job. In that case, you would need to execute the ulimit command prior to submitting the job or add it to the job submission script.

ADD COMMENTlink written 9 months ago by adrian.altenhoff450
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