Submit job in parallel : MPI and jd2 ?

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    • #590
      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

      • #4428
        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.

        • #4430
          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

            • #10054
              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,

            • #4433
              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

              • #4434
                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

                • #4437
                  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,

                    • #4574
                      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,
                        >

                      • #4575
                        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

                      • #4476
                        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

                        • #4490
                          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

                          • #4637
                            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

                            • #4638
                              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.

                              • #4789
                                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.

                                • #4790
                                  Anonymous

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

                                  • #5921
                                    htkratochvil
                                    Participant

                                      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.

                                    • #6383
                                      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

                                      • #10055
                                        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

                                        • #5939
                                          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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