Submit job in parallel : MPI and jd2 ?

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.

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

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,

> 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

/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

> 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

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.

@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.

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

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.

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

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

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.)