[gpaw-users] Segfaults when testing gpaw-python

Marcin Dulak Marcin.Dulak at fysik.dtu.dk
Fri Mar 22 12:42:05 CET 2013


On 03/22/13 12:02, Hildur Guðmundsdóttir wrote:
> On 03/22/2013 10:11 AM, Jens Jørgen Mortensen wrote:
>> Den 21-03-2013 12:21, Hildur Guðmundsdóttir skrev:
>>> Good morning
>>>
>>> I am trying to install GPAW on the NHPC cluster
>>> (http://nhpc.hi.is/content/hardware) and when running the tests with
>>> gpaw-python they stop on the fourth test, due to segmentation faults.
>>> This happens for numpy_zdotc_graphite.py, eigh.py and blas.py and no
>>> doubt others too. I do not get any output, the tests just stop
>>> running.
>>>
>>> When doing for instance:
>>> mpirun -np 2 gpaw-python gpaw/test/blas.py
>>>
>>> I get
>>> --------------------------------------------------------------------------
>>> mpirun noticed that process rank 1 with PID 11048 on node
>>> gardar-1.local exited on signal 11 (Segmentation fault).
>>> --------------------------------------------------------------------------
>>>
>>> I have compiled numpy and GPAW with gcc using the same mkl libraries
>>> for blas and lapack ('mkl_blas95_lp64', 'mkl_lapack95_lp64'). I'm
>>> using python2.7, numpy1.7.0, openmpi-1.4.4 and gpaw 0.9.0-8965. First
>>> I installed with the system provided numpy and got the same problem.
>>> Attached is my customize.py
>>>
>>> I saw this has happened to others before but couldn't find a solution
>>> for the problem, I would appreciate any advice.
>>
>> Does all tests pass in serial? Also when you run them with "mpirun 
>> -np 1 gpaw-python"?
>>
>> You may want to try the latest development version which should get 
>> rid of warnings from numpy-1.7.
>
> I am running the serial tests but so far only two have failed (aeatom 
> and pw/interpol), no segfaults.
> When I use "mpirun -np 1 gpaw-python" I get a segmentation fault on 
> the before mentioned tests (numpy_zdotc_graphite.py, eigh.py, blas.py) 
> and many others, whereas some work fine, like spinpol.py and 
> fermisplit.py.
any numpy*py test suggest the old problem related to numpy/gpaw-python blas.
Can you try numpy built with it's own internal blas/lapack?
You need to manually patch it, as described for example here:
https://wiki.fysik.dtu.dk/gpaw/install/Linux/r410_psmn.ens-lyon.html
Also to make sure: do you export /OMP_NUM_THREADS=1?/

Marcin
>
>
>>
>> Jens Jørgen
>>
>>> Thanks in advance,
>>>
>>> Hildur
>>>
>>>
>>> _______________________________________________
>>> gpaw-users mailing list
>>> gpaw-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>
>
>
>
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-- 
***********************************
  
Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk

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