[Pegasus-users] pegasus-monitord took 30G memory
polyactis at gmail.com
Thu May 3 13:58:53 PDT 2012
The error message looks like this:
Held 00:01 ??????PEAlignmentByBWA.sh_ID0009937
??????Error from slot1 at n6231.S1335855707.27@n6231: Failed to open
The folder above is a symbolic link to a local folder on central manager
n6223. slot1 at n6231 would just hit a dead link.
On Thu, May 3, 2012 at 1:54 PM, Yu Huang <polyactis at gmail.com> wrote:
> On Thu, May 3, 2012 at 1:46 PM, Karan Vahi <vahi at isi.edu> wrote:
>> Hi Yu
>> Hi Karan,
>> I stopped one workflow and moved the submit directory to a local
>> filesystem. However, after i restarted it, the jobs on the computing nodes
>> could not see the submit directory (cuz it's local on the central manager)
>> as they need to write to the *out.000 files. Is there anyway around it?
>> The jobs on the computing nodes don't need to see the submit directory
>> where Condor writes out the job.out.** files
>> Are you saying that you planned a workflow , started it, stopped it and
>> moved the submit directory to local filesystem ?
>> Pegasus in the submit files has an absolute path to the output and error
>> files. In case you moved the submit directory, then the condor submit files
>> have the wrong paths.
>> You might want to do perl replace on the paths in the submit files, or
>> plan a new workflow and launch it ( the --dir option should be a directory
>> on the local filesystem )
>> i did a symbolic link to the new path. not enough? i attached my
> pegasusrc file.
> is this entry causing some the problem?
>> Also, have you considered clustering your workflow ?
>> yes, in this case, i thought each job would take a long time. will
> enable it next time.
>> checking the options of pegasus-plan, doesn't seem to there is one for
>>> It is important to note that after sqlite there are 4 / if there are 3 /
>>> then sqlalchemy picks it up as a relative path.
>>> 2) For the next pegasus release 4.1.0 , we have put in a newer version
>>> of sqlalchemy 0.7.2 . Pegausus 4.0 has 0.6.4
>>> You can try installing pegasus 4.1.0cvs
> Yu Huang
> Postdoc in Nelson Freimer Lab,
> Center for Neurobehavioral Genetics, UCLA
> Office Phone:* +1.310-794-9598*
> Skype ID: crocea
Postdoc in Nelson Freimer Lab,
Center for Neurobehavioral Genetics, UCLA
Office Phone:* +1.310-794-9598*
Skype ID: crocea
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