Re: [Pytom-mail] mpirun problem

[Dustin M. <dus...@gm...>]

Hi Haixin,

This is a known problem with MPI and pytom dynamically linked libraries.

It is mentioned in the pytom FAQ: http://pytom.org/doc/pytom/faq.html

You need to have the LD_PRELOAD variable set in you shell:
BASH:
export LD_PRELOAD='/usr/local/openmpi/lib/libmpi.so'
CSH:
setenv LD_PRELOAD '/usr/local/openmpi/lib/libmpi.so'

--
Hope this helps,
Dustin Morado
John Briggs Group
MRC LMB

___

Cheers,
Dustin M.


On Tue, Oct 3, 2017 at 4:06 AM, Haixin Sui <su...@ho...> wrote:

> I followed Dustin's advice on the job xml file and I also modified two of
> the basic programs as he suggested. The "localization.py can now be
> successfully executed with the job.xml without using mpirun. If not working
> with parallel computing, the "localization.py" runs too slow to be
> practically useful.
>
> However, I failed to make the "localization.py" run with openmpi! I am
> not sure if this is a problem with the openmpi environment we have or not.
> I tested the openmpi on both my work station and my laptop using two
> simple testing programs provided by openmpi distribution package. The
> test programs worked well on both. However, when I did mpirun with
> localization.py, I got the same error message on both of the two
> computers.The error message has been included in this email. Any ideas
> about what went wrong?
>
> Thanks for your help in advance !
>
> Haixin Sui
>
> ----------------------------
> hsui@Thinkpad-HR16395:~/subtomo$ mpirun -n 2 localization.py
> job_test_1.xml 2 2 2
> PyTom v0.971
>
> This license affects the software package PyTom and all the herein
> distributed source / data files.
> Authors:
> Thomas Hrabe
> Yuxiang Chen
> Friedrich Foerster
>
> Copyright (c) 2008-2016
> Max-Planck-Institute for Biochemistry
> Dept. Molecular Structural Biology
> 82152 Martinsried, Germany
> http://www.pytom.org
>
> This program is free software: you can redistribute it and/or modify
> it under the terms of the GNU General Public License as published by
> the Free Software Foundation, either version 3 of the License, or
> (at your option) any later version.
>
> This program is distributed in the hope that it will be useful,
> but WITHOUT ANY WARRANTY; without even the implied warranty of
> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
> GNU General Public License for more details.
>
> The complete license can be obtained from
> http://www.gnu.org/licenses/gpl-3.0.html.
>
> PyTom v0.971
>
> This license affects the software package PyTom and all the herein
> distributed source / data files.
> Authors:
> Thomas Hrabe
> Yuxiang Chen
> Friedrich Foerster
>
> Copyright (c) 2008-2016
> Max-Planck-Institute for Biochemistry
> Dept. Molecular Structural Biology
> 82152 Martinsried, Germany
> http://www.pytom.org
>
> This program is free software: you can redistribute it and/or modify
> it under the terms of the GNU General Public License as published by
> the Free Software Foundation, either version 3 of the License, or
> (at your option) any later version.
>
> This program is distributed in the hope that it will be useful,
> but WITHOUT ANY WARRANTY; without even the implied warranty of
> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
> GNU General Public License for more details.
>
> The complete license can be obtained from
> http://www.gnu.org/licenses/gpl-3.0.html.
>
> *** An error occurred in MPI_Init
> *** on a NULL communicator
> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> ***    and potentially your MPI job)
> [Thinkpad-HR16395:24468] Local abort before MPI_INIT completed completed
> successfully, but am not able to aggregate error messages, and not able to
> guarantee that all other processes were killed!
> -------------------------------------------------------
> Primary job  terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> *** An error occurred in MPI_Init
> *** on a NULL communicator
> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> ***    and potentially your MPI job)
> [Thinkpad-HR16395:24469] Local abort before MPI_INIT completed completed
> successfully, but am not able to aggregate error messages, and not able to
> guarantee that all other processes were killed!
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
>
>   Process name: [[24716,1],1]
>   Exit code:    1
> --------------------------------------------------------------------------
>
>
> Preliminary test of our openmpi shows no problem with other testing
> programs.
> ===============================================
> hsui@Thinkpad-HR16395:~/subtomo$ mpirun -n 2 hello_c
> Hello, world, I am 0 of 2, (Open MPI v1.10.2, package: Open MPI
> buildd@lgw01-57 Distribution, ident: 1.10.2, repo rev:
> v1.10.1-145-g799148f, Jan 21, 2016, 126)
> Hello, world, I am 1 of 2, (Open MPI v1.10.2, package: Open MPI
> buildd@lgw01-57 Distribution, ident: 1.10.2, repo rev:
> v1.10.1-145-g799148f, Jan 21, 2016, 126)
>
> hsui@Thinkpad-HR16395:~/subtomo$ mpirun -n 2 ring_c
> Process 0 sending 10 to 1, tag 201 (2 processes in ring)
> Process 0 sent to 1
> Process 0 decremented value: 9
> Process 0 decremented value: 8
> Process 0 decremented value: 7
> Process 0 decremented value: 6
> Process 0 decremented value: 5
> Process 0 decremented value: 4
> Process 0 decremented value: 3
> Process 0 decremented value: 2
> Process 0 decremented value: 1
> Process 0 decremented value: 0
> Process 0 exiting
> Process 1 exiting
>
>
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