[mcstas-users] openmpi compilation problem

Thu Jun 14 13:59:45 CEST 2012

Hi Jean-Francois,

Yup, you certainly have a conflict between your two MPI's now… :-)

What does your mpirun / mpicc lines in /usr/local/lib/mcstas/tools/perl/mcstas_config.perl say?

(I.e.
     MPIRUN => '/usr/local/bin/mpirun',
     MPICC => '/usr/local/bin/mpicc',
)

Also, check if you perhaps have a .mcstas/mcstas_config.perl in your homedir?

Best,

Peter

On Jun 14, 2012, at 13:49 , <Jean-Francois.Moulin at hzg.de<mailto:Jean-Francois.Moulin at hzg.de>> wrote:

Hi Emmanuel!

thanks for the answer. Yes the build works but, this is what I get when I try to use it:

(case A)
~/Lab/MCarlo/McStas$ mcgui refsans_simplified_0.instr
./refsans_simplified_0.out: error while loading shared libraries: libmpich.so.3: cannot open shared object file: No such file or directory

And this is correct, the file is not on my system... why did the configure look for mpich in the first place?

(caseB)
Well it wants MPICH? I tried and installed mpich2 from ubuntu repos (including dev), ./configure make make install...
mcgui now starts without problem and shows my instrument parameters (it did not in case A)
but the simulation returns errors...

mcrun: No MPI/grid machine list. Running locally.
 Define /home/jfmoulin/.mcstas/hosts
 or /usr/local/lib/mcstas/tools/perl/hosts
 or use option --machines=<file>
[jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357
[jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230
[jfm-lap:11887] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

 orte_ess_set_name failed
 --> Returned value A system-required executable either could not be found or was not executable by this user (-127) instead of ORTE_SUCCESS

Is there a reason to have conflicts between the two mpi (I have dependencies of other packages on openmpi) or do I forget a setup step?
I had the box running before and did not change my home dir so I guess it should still work
Anyway, thanks for your help!

Ciao
JF
-
Helmholtz Zentrum Geesthacht
Institut für Werkstoffforschung
Abteilung WPN, Instrument REFSANS
Lichtenbergstr. 1
85747 Garching FRM II
Tel.: +49 (0)89 289 10762
Internet: http://www.frm2.tum.de

-----Emmanuel FARHI <farhi at ill.eu<mailto:farhi at ill.eu>> schrieb: -----
An: Jean-Francois.Moulin at hzg.de<mailto:Jean-Francois.Moulin at hzg.de>, "McStas users list at mcstas.org<http://mcstas.org>" <mcstas-users at mcstas.org<mailto:mcstas-users at mcstas.org>>
Von: Emmanuel FARHI <farhi at ill.eu<mailto:farhi at ill.eu>>
Datum: 06/14/2012 10:22AM
Betreff: Re: [mcstas-users] openmpi compilation problem

Hi Jean-Francois,

to my knowledge, this is just a warning. The tar.gz configure; make;
make install should proceed OK still, and McStas should be able to find
MPI if 'mpicc' and 'mpirun' commands are available at the prompt.

OpenMPI seems OK on recent systems. It was less reliable than MPICH
until 2010-2011 (would stall for long simulations with e.g. ncount > 2e9).

Emmanuel.

On 06/13/2012 05:36 PM, Jean-Francois.Moulin at hzg.de<mailto:Jean-Francois.Moulin at hzg.de> wrote:
Hi to all!

new Linux distro, new problem! On Linux Mint 13 I do not manage to install due to mpi problems. As already suggested some months ago I installed openmpi (packages from Ubuntu repos: libopenmpi 1.4.3.2 and its dev).
The ./configure tells me that :
checking mpi.h presence... no
checking for mpi.h... no
WARNING: /usr/bin/mpicc may fail to compile without mpi.h

but I find this on my system:
./usr/lib/openmpi/include/mpi.h
After reading the output of configure -h, I tried
  ./configure -I/usr/lib/openmpi/include/:
configure: error: unrecognized option: `-I'
I tried putting this path in the cppflags envirt variable. To no avail.
seems I miss the point.
Since I get a Makefile I looked for an include section where I could manually put the path but that does not look so easy... (for me)

second question I am on a 64 bit machine, I should thus configure --with-pic right?

Thanks in advance for your help!

Best

Jean-Francois

-
Helmholtz Zentrum Geesthacht
Institut für Werkstoffforschung
Abteilung WPN, Instrument REFSANS
Lichtenbergstr. 1
85747 Garching FRM II
Tel.: +49 (0)89 289 10762
Internet: http://www.frm2.tum.deHelmholtz-Zentrum Geesthacht
Zentrum für Material- und Küstenforschung GmbH
Max-Planck-Straße 1 I 21502 Geesthacht I Deutschland/Germany

Geschäftsführer/Board of Management: Prof. Dr. Wolfgang Kaysser, Dipl.-Ing. Michael Ganß
Vorsitzender des Aufsichtsrates/Chairman of the Supervisory Board: MinDirig Wilfried Kraus
Amtsgericht Lübeck HRB 285 GE (Register Court)
Internet: http://www.hzg.de
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--
Emmanuel FARHI,www.ill.eu/computing/people/emmanuel-farhi<http://www.ill.eu/computing/people/emmanuel-farhi> \|/ ____ \|/
CS-Group ILL4/221, Institut Laue-Langevin (ILL) Grenoble  ~@-/ oO \-@~
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Helmholtz-Zentrum Geesthacht
Zentrum für Material- und Küstenforschung GmbH
Max-Planck-Straße 1 I 21502 Geesthacht I Deutschland/Germany

Geschäftsführer/Board of Management: Prof. Dr. Wolfgang Kaysser, Dipl.-Ing. Michael Ganß
Vorsitzender des Aufsichtsrates/Chairman of the Supervisory Board: MinDirig Wilfried Kraus
Amtsgericht Lübeck HRB 285 GE (Register Court)
Internet: http://www.hzg.de
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