Submit job in parallel : MPI and jd2 ?

[Anonymous]

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

[Anonymous]

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.

[Anonymous]

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

[Anonymous]

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,

[Anonymous]

> 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

[Anonymous]

> 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

To smlewis

Thank u for extending help. I am looking forward for yr reply. U can mail me at rv.rosetta@gmail.com

thanx again

[Anonymous]

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,

[Anonymous]

> 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,
>

[Anonymous]

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

[Anonymous]

> 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

would you please also send me one? thank you.

leuven@yeah.net

[Anonymous]

/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

[Anonymous]

> 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

[Anonymous]

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.

[Anonymous]

@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.

[Anonymous]

The cc file is on the way. I don’t have a demo.

[Anonymous]

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.

[Anonymous]

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

[Anonymous]

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

[Anonymous]

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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