[gpaw-users] Segfaults when testing gpaw-python

[Marcin Dulak]

On 03/22/13 14:42, Hildur Guðmundsdóttir wrote:
> 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.
did numpy actually built with it's own blas?
Please check with something like:
find /usr/lib64/python2.7/site-packages/numpy/ -name _dotblas.so | xargs ldd
There should be no _dotblas.so is numpy uses it's own blas.
If yes: i would try to build gpaw with acml while keeping the default numpy.

Marcin
>
> 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
>>>>
>>>
>>>
>>>
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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
>>
>> ***********************************
>


-- 
***********************************
  
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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