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HYPHY Package >> HyPhy bugs >> MPI environment detection fail when trying to use GARD
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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
Hello Russ,

Just as a sanity check, do you routinely use mpirun for other jobs on your ROCKS cluster?

Are you following the guidelines set out in 2.1.2 of the following link?

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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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