Pandora deadlock

[Alban Rousset]

Hi Pandora users.

I've some problems with executing Pandora on a cluster. I compile libpandora with OpenMP and when I submit my job I've a deadlock and all process waiting something... 

I try also to submit examples "segregation" or "randomWalkers" and I've the same problem...

Someone have a solution ? or just someone could send me a "ldd" copy of the link with de libpandora ?

I put a "ldd" of my libpandora :

        linux-vdso.so.1 =>  (0x00007fff221c6000)

libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fb1965a6000)

libgdal.so.1 => /Softs/lib/gdal/1.10.1/lib/libgdal.so.1 (0x00007fb195947000)

libhdf5.so.8 => /Softs/lib/hdf5-mpi/1.8.12//lib/libhdf5.so.8 (0x00007fb19545a000)

libz.so.1 => /lib64/libz.so.1 (0x00007fb195243000)

libgrass_gis.so => /Softs/lib/grass/6.4.3/grass-6.4.3/lib/libgrass_gis.so (0x00007fb194fee000)

libboost_filesystem.so.1.55.0 => /Softs/lib/boost/gcc/1.55.0/lib/libboost_filesystem.so.1.55.0 (0x00007fb194dd8000)

libboost_system.so.1.55.0 => /Softs/lib/boost/gcc/1.55.0/lib/libboost_system.so.1.55.0 (0x00007fb194bd4000)

libgomp.so.1 => /Softs/languages/gcc/4.8.1/lib64/libgomp.so.1 (0x00007fb1949c6000)

libdl.so.2 => /lib64/libdl.so.2 (0x00007fb1947c2000)

libmpi_cxx.so.1 => /Softs/openmpi/gcc/1.6.5/lib/libmpi_cxx.so.1 (0x00007fb1945a7000)

libmpi.so.1 => /Softs/openmpi/gcc/1.6.5/lib/libmpi.so.1 (0x00007fb194201000)

librt.so.1 => /lib64/librt.so.1 (0x00007fb193ff9000)

libnsl.so.1 => /lib64/libnsl.so.1 (0x00007fb193ddf000)

libutil.so.1 => /lib64/libutil.so.1 (0x00007fb193bdc000)

libm.so.6 => /lib64/libm.so.6 (0x00007fb193958000)

libstdc++.so.6 => /Softs/languages/gcc/4.8.1/lib64/libstdc++.so.6 (0x00007fb19364e000)

libgcc_s.so.1 => /Softs/languages/gcc/4.8.1/lib64/libgcc_s.so.1 (0x00007fb193438000)

libc.so.6 => /lib64/libc.so.6 (0x00007fb1930a5000)

/lib64/ld-linux-x86-64.so.2 (0x00000030f9600000)

libexpat.so.1 => /lib64/libexpat.so.1 (0x00007fb192e7c000)

libhdf5.so.6 => /Softs/lib/hdf5/1.9.63/lib/libhdf5.so.6 (0x00007fb19260d000)

libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x00007fb1922bb000)

libgrass_datetime.6.4.3.so => /Softs/lib/grass/6.4.3/grass-6.4.3/lib/libgrass_datetime.6.4.3.so (0x00007fb1920b2000)

libimf.so => /Softs/Intel/Compiler/11.0/069/lib/intel64/libimf.so (0x00007fb191d5c000)

libsvml.so => /Softs/Intel/Compiler/11.0/069/lib/intel64/libsvml.so (0x00007fb191b9e000)

libintlc.so.5 => /Softs/Intel/Compiler/11.0/069/lib/intel64/libintlc.so.5 (0x00007fb191a61000)

Regards, 

Rousset Alban

[Xavier Rubio]

Hi Alban, I attach my ldd (yours seem ok). I suspect that the problem
is related to some issue where you are using openmp in your code,
while another part is trying to use (or was compiled with) mpich.
Usually it is related to hdf5; did you use the same implementation and
version to compile it?

On the other hand, does it work if you execute it in a single computer
node (i.e. your own pc)?

All best,

Xavi

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[Alban Rousset]

Thank you for your LDD Xavier, it seems to be Ok... I don't remember if I use the same version and implementation for the compilation.. But I think yes

So I check this afternoon ^^

Yes examples and my own model works on single computer node (pc, laptop...)

Regards, 

Rousset Alban