Reply To: Submit job in parallel : MPI and jd2 ?

[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