Member Site › Forums › Rosetta 3 › Rosetta 3 – General › Submit job in parallel : MPI and jd2 ?
- This topic has 18 replies, 12 voices, and was last updated 10 years, 5 months ago by Anonymous.
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AuthorPosts
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March 31, 2010 at 7:18 am #590Anonymous
Hii everyone,
I am looking forward in generating 10,000 abinitio structures using rosetta abinitio package. I can complete the job running on one processor, but, am unable to do that using multiple processors and hence save time. I shall be thankful, if conveyed how to submit the job in parallel processors. I am stuck with the editing of the unknown file and its compilation to do that using MPI. Please let me know which file to edit in the jd2 folder of /src/prtocols to get the job done.
Please help!
thank u
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April 16, 2010 at 3:44 pm #4428Anonymous
This is an oversight by the people who maintain the abinitio code.
Someone in my lab had the same problem and ended up writing a patch. I’ll ask if they’re willing to share it with you.
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April 16, 2010 at 6:42 pm #4430Anonymous
He says you can have it. Post your email and we’ll send it along. It’s not officially supported but it works well enough.
Thank u for extending help. I am looking forward for yr reply. U can mail me at rv.rosetta@gmail.com
thanx again
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May 13, 2014 at 10:02 pm #10054Anonymous
Dear smlewis:
I also need the demo script to submit parallel Rosetta3.1 job under the MPI frame. Please email at ajrferrari@gmail.com
thanks,
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April 19, 2010 at 5:03 pm #4433Anonymous
> Hii everyone,
>
> I am looking forward in generating 10,000 abinitio structures using rosetta abinitio package. I can complete the job running on one processor, but, am unable to do that using multiple processors and hence save time. I shall be thankful, if conveyed how to submit the job in parallel processors. I am stuck with the editing of the unknown file and its compilation to do that using MPI. Please let me know which file to edit in the jd2 folder of /src/prtocols to get the job done.
>
> Please help!
>
> thank u -
April 19, 2010 at 5:05 pm #4434Anonymous
> Hii everyone,
>
> I am looking forward in generating 10,000 abinitio structures using rosetta abinitio package. I can complete the job running on one processor, but, am unable to do that using multiple processors and hence save time. I shall be thankful, if conveyed how to submit the job in parallel processors. I am stuck with the editing of the unknown file and its compilation to do that using MPI. Please let me know which file to edit in the jd2 folder of /src/prtocols to get the job done.
>
> Please help!
>
> thank uTo smlewis
Thank u for extending help. I am looking forward for yr reply. U can mail me at rv.rosetta@gmail.com
thanx again
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April 27, 2010 at 7:57 am #4437Anonymous
Dear smlewis:
I also need the demo script to submit parallel Rosetta3.1 job under the MPI frame. Please email at lennylv@hotmail.com
thanks,
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August 19, 2010 at 8:05 am #4574Anonymous
> Dear smlewis:
>
> I also need the demo script to submit parallel Rosetta3.1 job under the MPI frame. Please email at lennylv@hotmail.com
>
> thanks,
> -
August 19, 2010 at 8:07 am #4575Anonymous
Dear smlewis:
Can I also have the demo script to submit parallel Rosetta3.1 job under the MPI frame?
If yes , please mail me the script at mansy.pandit@gmail.com.Thanks and Best Regards,
mansi
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July 5, 2010 at 8:43 am #4476Anonymous
> Hii everyone,
>
> I am looking forward in generating 10,000 abinitio structures using rosetta abinitio package. I can complete the job running on one processor, but, am unable to do that using multiple processors and hence save time. I shall be thankful, if conveyed how to submit the job in parallel processors. I am stuck with the editing of the unknown file and its compilation to do that using MPI. Please let me know which file to edit in the jd2 folder of /src/prtocols to get the job done.
>
> Please help!
>
> thank uwould you please also send me one? thank you.
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July 16, 2010 at 3:09 am #4490Anonymous
/soft/openmpi-1.4.1-gnu/bin/mpirun -np 1024 -hostfile $HOSTFILE /soft/rosetta/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/mpi/AbinitioRelax.linuxgccrelease -database /soft/rosetta/rosetta_database -abinitio:relax 1 -in:file:fasta ${dir}/1reia.fa -in:file:frag3 ${dir}/aa1reia03_05.200_v1_3 -in:file:frag9 ${dir}/aa1reia09_05.200_v1_3 -out:nstruct 4096000 -out:pdb 1 -out:file:silent ${dir}/rtest.1024 -out:path ${dir} > ${dir}/rtest1024.out
works for me, better use fullpath command all.
first you should create aa1reia03_05.200_v1_3 aa1reia09_05.200_v1_3 by make_fragment.pl
> Hii everyone,
>
> I am looking forward in generating 10,000 abinitio structures using rosetta abinitio package. I can complete the job running on one processor, but, am unable to do that using multiple processors and hence save time. I shall be thankful, if conveyed how to submit the job in parallel processors. I am stuck with the editing of the unknown file and its compilation to do that using MPI. Please let me know which file to edit in the jd2 folder of /src/prtocols to get the job done.
>
> Please help!
>
> thank u -
September 29, 2010 at 12:24 pm #4637Anonymous
> Hii everyone,
>
> i want run rosetta on cluster.in the first i compale rosetta with mpi.my probleme is define hostfile?
>
> Please help!
>
> thank u -
September 29, 2010 at 1:42 pm #4638Anonymous
Defining the hostfile is a job of your MPI installation and not part of Rosetta. Look in the documentation for mpirun or your cluster job submisson system. Hostfile generation is automatic under LSF, and more-or-less automatic under mpirun on my system, so I don’t know why yours isn’t generating.
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January 3, 2011 at 12:42 pm #4789Anonymous
@smlewis please send me the MPI enabled version of Abinitiorelax executable at anirbanzz@gmail.com. Also please send a demo job submission script for the same.
Thanks.
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January 3, 2011 at 2:46 pm #4790Anonymous
The cc file is on the way. I don’t have a demo.
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August 1, 2011 at 9:50 pm #5921
Dear smlewis:
Would you also send the demo script to submit parallel Rosetta3.1 job under the MPI frame? My e-mail address is zgerek@asu.edu
Thanks. -
December 9, 2011 at 12:43 am #6383Anonymous
Hi lewis, I would also like to generate large number of structure in multiple processors. Please help me to know how to use mpi/jd2 for the similar purpose and gather the results for the same.
Please provide the flag for the multiple process job distribution/run also!!!!
Thanks in advance
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May 14, 2014 at 3:51 pm #10055Anonymous
Try a newer version of Rosetta. I believe abinitio fully supports MPI in the newer versions. Check out the new build page for how to build MPI Rosetta.
https://www.rosettacommons.org/docs/latest/Build-Documentation.html -
August 4, 2011 at 2:03 am #5939Anonymous
As I said above, I don’t have a demo. I’ll send the cc file along shortly. (Sorry it took me a few days to catch this – the forum didn’t do its email reminder to me for this thread.)
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