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HYPHY Package >> HyPhy bugs >> MPI environment detection fail when trying to use GARD http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1327514930 Message started by florent on Jan 25th, 2012 at 10:08am |
Title: MPI environment detection fail when trying to use GARD Post by florent on Jan 25th, 2012 at 10:08am
Hello,
i work on a iinux PC (under ubuntu 11.10) or on a computer cluster under debian ; both have openMPI environments, and mpi binaries (mpiexec, mpirun ..) available in the PATH. however, when I launch HYPHYMPI (with or without casting it with mpiexec like this : /path/to/mpiexec /path/to/HYPHYMPI), when i chose to use the GARD algorithm (choices 11 then 1), an error is issued: [ERROR] This analysis requires an MPI environment to run How can I get through this? with a custom batch file? thanks in advance Florent |
Title: Re: MPI environment detection fail when trying to use GARD Post by Sergei on Jan 25th, 2012 at 10:26am
Hi Florent,
I think your invocation of mpiexec is spawning a serial job. I would try [code] $/path/to/mpirun -np 10 /path/to/HYPHYMPI [/code] Sergei |
Title: Re: MPI environment detection fail when trying to use GARD Post by RMeister on Jun 12th, 2014 at 3:26pm
Hello Sergei,
I am having the same issue as Florent. I am attempting to run a GARD analysis on a ROCKS cluster. The cluster has both hyphy2.11 and openmpi and I have given the direct paths for both when trying to run the analysis. I end up getting the [ERROR] This analysis requires an MPI environment to run, whenever I attempt to run it. I have tried it by first just opening the program with the mpirun specified and navigating through 11 and 1, but when I hit 1 it throws the error. If I attempt to run it with the batchfile specified in the command, it throws the error again, but this time prints it out multiple times (the same number of processors I gave it to run with). Anyway I can fix this error? Thanks for your help. Russ. |
Title: Re: MPI environment detection fail when trying to use GARD Post by Steven on Jun 12th, 2014 at 4:21pm |
Title: Re: MPI environment detection fail when trying to use GARD Post by RMeister on Jun 13th, 2014 at 8:51am
Hello Steven,
Actually no, I do not usually use mpirun for jobs on our cluster. The other programs I run in an mpi environment are pre-scripted so that all is needed is to submit a script calling a different program name. For HYPHY, that is not the case. I looked at the link provided (I had seen it in the past but forgot about it). When I attempt to run the scripts in 2.1.2, it fails to execute. Must be an error on the cluster end then? -------------------------------------------------------------------------- mpirun was unable to launch the specified application as it could not access or execute an executable: Executable: /opt/hpl/openmpi-hpl/bin/xhpl Node: compute-1-1 while attempting to start process rank 0. -------------------------------------------------------------------------- 2 total processes failed to start |
Title: Re: MPI environment detection fail when trying to use GARD Post by Steven on Jun 13th, 2014 at 3:56pm
Hi Russ,
Can you make sure that you can run mpi jobs directly with help from your system administrator? Once I know that your configuration is correct, I can try troubleshooting. |
Title: Re: MPI environment detection fail when trying to use GARD Post by RMeister on Jun 14th, 2014 at 3:32am
Hi Steven,
I think you mean without the administrator? I can initiate mpiruns directly from a shell window or by submitting a script to the head node. I know it works for other programs, such as MrBayes. I use the same commands as I would to start Hyphy with multiple processors. Additionally I had asked the administrator a question about mpi jobs and he indicated that the "mpirun" command is how one calls for an mpi job. |
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