[gpaw-users] Segfaults when testing gpaw-python

Hildur Guðmundsdóttir hildur.gud at gmail.com
Fri Mar 22 14:42:01 CET 2013


On 03/22/2013 11:42 AM, Marcin Dulak wrote:
> 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

I have tried the blas/lapack patch for numpy and /OMP_NUM_THREADS=1/. I 
still get the same problem.

Hildur

>>
>>
>>>
>>> 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
>>>
>>
>>
>>
>> _______________________________________________
>> gpaw-users mailing list
>> gpaw-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>
>
> -- 
> ***********************************
>   
> 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
>
> ***********************************

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20130322/22e21ffa/attachment-0001.html 


More information about the gpaw-users mailing list