Hi Joshua,
Thanks. I think it's already on the PATH and mpirun runs with no problem:
> > type mpirun
> mpirun is /usr/bin/mpirun
> > ls -l /usr/bin/mpirun
> lrwxrwxrwx 1 root root 24 Jun 6 16:33 /usr/bin/mpirun ->
> /etc/alternatives/mpirun*
> > ls -l /etc/alternatives/mpirun
> lrwxrwxrwx 1 root root 23 Jun 19 17:17 /etc/alternatives/mpirun ->
> /usr/bin/mpirun.openmpi*
I'm currently trying removing all the mpich and openmpi packages,
re-installing just the openmpi stuff, and doing a fresh build / install.
Regards,
-jh-
On 06/21/2017 11:39 AM, Joshua Lobo wrote:
> Hi John
>
> I think you need the path of your mpirun in the $PATH variable .
>
> Sincerely
> Joshua Lobo
>
> On Jun 21, 2017 12:15 PM, "John Heumann" <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi Schors,
>
> Thanks. I think both of those conditions are satisfied. The
> execution environment is identical to the build environment,
> except that I've sourced a simple bash file (attached) to put the
> freshly installed Relion bin and lib directories on that relevant
> paths.
>
> As for mpirun, I'm not currently running from the command line,
> only from the gui, which I assume will correctly select the _mpi
> version automatically. True?
>
> BTW, is it normal to need mpich installed in order to compile?
> Shouldn't the openmpi tools suffice?
>
> Regards,
> -jh-
>
>
> On 06/21/2017 10:15 AM, Sjors Scheres wrote:
>
> Hi John,
> It's important you run relion with the same MPI installation
> that you used to compile it with. Also, make sure you sue the
> _mpi version of the program when running with mpirun.
> HTH,
> Sjors
>
> On 06/21/2017 04:35 PM, John Heumann wrote:
>
> Hi,
>
> Please forgive a somewhat length post, since I'm not sure
> which of this information may be relevant. We recently
> updated several RHEL6 systems to 2.1, with no issues.
> However, I'm having all kinds of problems trying to get
> 2.1 and specifically mpi working properly on a new quad
> gpu system running Ubuntu 16.0.4.
>
> 1) Is this 2.1 supported on 16.04? I've assumed so, but I
> notice that on
> http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Download_%26_install
> <http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Download_%26_install>
> the "Installation using apt-get" still refers to an
> earlier release. Is this just because no 2.1 package has
> been created yet, or is there actually some known issue?
>
> If I ignore the apt-get package and build from source,
> everything seems to go fine. I don't see any obvious
> errors during configuration, compilation, or installation.
> But when I try to run using mpi, things behave badly.
> E.g. if try to run MotionCor2 with 5 mpi procs and all 4
> gpus, I'll get multiple errors like:
> ERROR in renaming:
> MotionCorr/job003/Micrographs/foo_1_Stk.mrc to
> MotionCorr/job003/Micrographs/foo_1_movie.mrcs
> (Okay, the name isn't really "foo". It's long, so I
> shortened it for clarity). There seem to be exactly 4 of
> these errors for each file. I.e. it seems like each of the
> 5 mpi procs are trying to process every file, rather than
> splitting up the work, and they're stepping on each other.
> If I just use 1 mpi rank but tell it to use all 4 gpus
> things run normally (although nvidia-smi never seems to
> show any gpu other than the last being used).
>
> Similarly, if I try to run ctffind (latest 4.1.5) with 8
> mpi ranks, I get fatal file errors, e.g.
> 00:26:05: Error: File
> 'CtfFind/job003/Micrographs/foo_004.txt' couldn't be
> removed (error 2: No such file or directory)
> and eventually a
> ERROR: Unexpected number of words on data line below
> Columns line in CtfFind/job003/Micrographs/foo_055.txt
> File: /home/heumannj/relion/src/ctffind_runner.cpp line: 803
>
> For what it's worth, both openmpi and mpich are installed
> on this system. Could this all reflect mpi version
> incompatabilities? I've tried removing mpich, but then
> cmake seems unable to find the required mpi comple tools.
>
> Sorry, if this is an obvious or known issue. I have very
> little experience with mpi builds, so I'm sort of
> stumbling around in the dark.
>
> Thanks in advance for any suggestions!
>
> Regards,
> -jh-
>
>
>
> --
> John M. Heumann
> Department of Molecular, Cellular, and Developmental Biology
> 347 UCB, University of Colorado
> Boulder, CO 80309-0347
>
--
John M. Heumann
Department of Molecular, Cellular, and Developmental Biology
347 UCB, University of Colorado
Boulder, CO 80309-0347
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