[Pytom-mail] mpirun problem

[Haixin S. <su...@ho...>]

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