[Wien] Segmentation fault in Supercell Calculation

[Laurence Marks]

Your options are probably wrong:

a) mpif90 is normally gfortran, the Intel version is mpiifort
b) It is easy to use the wrong linking with the Intel mkl libraries. Please
provide the information I requested.


On Tue, Jul 28, 2015 at 2:55 PM, Lan, Wangwei <wl13c at my.fsu.edu> wrote:

>  Dear Professor:
>
>
>  Yes, "x lapw0" works without mpi.
>
>
>  My mpi compile : mpif90
>
> I use Open MPI， version 1.4.5
>
> the parallel compilation options are
>
>  -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume
> buffered_io
>
> I use Intel MKL libraries, that part should be fine.
>
>
>  Thanks very much for your help.
>
>  Sincerely
> Wangwei Lan
>  ------------------------------
> *From:* wien-bounces at zeus.theochem.tuwien.ac.at <
> wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of Laurence Marks <
> L-marks at northwestern.edu>
> *Sent:* Tuesday, July 28, 2015 14:30
> *To:* A Mailing list for WIEN2k users
> *Subject:* Re: [Wien] Segmentation fault in Supercell Calculation
>
>  Does a simple "x lapw0" work, i.e. without mpi, for this specific case?
>
>  If it does then there is probably an error in how you have
> linked/compiled the mpi versions. Please provide:
>
>  a) The mpi compiler you used.
> b) Which type of mpi you are using (openmpi, mvapich, intel mpi etc)
> c) The parallel compilation options.
>
>  N.B., a useful resource is
> https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor
>
>  N.N.B., ulimit -s is not needed, this is (now) done in the software.
>
> On Tue, Jul 28, 2015 at 2:22 PM, Lan, Wangwei <wl13c at my.fsu.edu> wrote:
>
>>  Dear Professor Marks:
>>
>>
>>  I've check everything you have mentioned, they are all fine,
>> nevertheless it still don't work. I think the input files are ok since I
>> have no problem running in non-parallel mode.
>>
>> I tried to make the supercell smaller (2x1x1), then it works. However, I
>> don't know why that happens.
>>
>> By the way, I have "ulimit -s unlimited " in my .bashrc file. I'v also adjusted
>> the RKMAX and RMT before.
>>
>>
>>  Sincerely
>>
>> Wangwei Lan
>>
>>
>>
>>
>>  ------------------------------
>> *From:* wien-bounces at zeus.theochem.tuwien.ac.at <
>> wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of Laurence Marks <
>> L-marks at northwestern.edu>
>> *Sent:* Tuesday, July 28, 2015 13:09
>> *To:* A Mailing list for WIEN2k users
>> *Subject:* Re: [Wien] Segmentation fault in Supercell Calculation
>>
>>  You have what is called a "Segmentation Violation" which was detected
>> by 4 of the nodes and they called an error handler which stopped the mpi
>> job on all the CPU's.
>>
>>  This is normally because you have an error of some sort in your input
>> files, any of case.in0, case.clmsum (and clmup/dn if you are using spin
>> polarized).
>>
>>  1) Check that you do not have overlapping spheres and/or other mistakes.
>> 2) Check your error files, e.g. "cat *.error". Are any others (e.g.
>> dstart.error) not empty? Did you ignore an error during setup?
>> 3) Check the lapw0 output in case.output0* -- maybe shows what is wrong.
>>
>>  There are many possible sources, you have to find the specific one.
>>
>>
>> On Tue, Jul 28, 2015 at 12:57 PM, Lan, Wangwei <wl13c at my.fsu.edu> wrote:
>>
>>>  Dear WIEN2k user:
>>>
>>>
>>>  I am using wien2k_14.2 on CentOS release 5.8. ifort version 12.1.3
>>> with MKL.
>>>
>>>
>>>
>>>  After generating a 2x2x1 supercell with 30 atoms, I tried to do the
>>> scf calculation. However, I got some errors. I'v attached it at the end of
>>> this email. My wien2k was installed correctly. It works well for other
>>> calculations. It also worked if I run non-parallel calculation for
>>> supercell. I'v searched the mail-list, but can't find any solutions. Could
>>> you give me a hint on how to solve the problem? Thank you very much.
>>>
>>>
>>>
>>>  Sincerely
>>>
>>> Wangwei Lan
>>>
>>>
>>>
>>>  On lapw0.error shows:
>>>
>>>
>>>
>>> 'Unknown' - SIGSEGV
>>>
>>>
>>>
>>>  On super.dayfile shows:
>>>
>>>
>>>  Child id           0 SIGSEGV
>>>
>>>  Child id           8 SIGSEGV
>>>
>>>  Child id          18 SIGSEGV
>>>
>>>  Child id          23 SIGSEGV
>>>
>>>  Child id          17 SIGSEGV
>>>
>>>
>>>
>>>  On Screen shows:
>>>
>>> w2k_dispatch_signal(): received: Segmentation fault
>>>
>>> w2k_dispatch_signal(): received: Segmentation fault
>>>
>>> w2k_dispatch_signal(): received: Segmentation fault
>>>
>>> w2k_dispatch_signal(): received: Segmentation fault
>>>
>>> w2k_dispatch_signal(): received: Segmentation fault
>>>
>>> w2k_dispatch_signal(): received: Segmentation fault
>>>
>>> w2k_dispatch_signal(): received: Segmentation fault
>>>
>>>
>>> --------------------------------------------------------------------------
>>>
>>> MPI_ABORT was invoked on rank 18 in communicator MPI_COMM_WORLD
>>>
>>> with errorcode 451782144.
>>>
>>>
>>>  NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>>
>>> You may or may not see output from other processes, depending on
>>>
>>> exactly when Open MPI kills them.
>>>
>>>
>>> --------------------------------------------------------------------------
>>>
>>>
>>> --------------------------------------------------------------------------
>>>
>>> mpirun has exited due to process rank 18 with PID 26388 on
>>>
>>> node corfu.magnet.fsu.edu exiting without calling "finalize". This may
>>>
>>> have caused other processes in the application to be
>>>
>>> terminated by signals sent by mpirun (as reported here).
>>>
>>>
>>> --------------------------------------------------------------------------
>>>
>>> [corfu.magnet.fsu.edu:26369] 23 more processes have sent help message
>>> help-mpi-api.txt / mpi-abort
>>>
>>> [corfu.magnet.fsu.edu:26369] Set MCA parameter
>>> "orte_base_help_aggregate" to 0 to see all help / error messages
>>>
>>>
>>>  >   stop error
>>>
>>>
>>>
>>>
>>
>>
>>  --
>>  Professor Laurence Marks
>> Department of Materials Science and Engineering
>> Northwestern University
>> www.numis.northwestern.edu
>> Corrosion in 4D: MURI4D.numis.northwestern.edu
>> Co-Editor, Acta Cryst A
>> "Research is to see what everybody else has seen, and to think what
>> nobody else has thought"
>> Albert Szent-Gyorgi
>>
>
>
>
>  --
>  Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu
> Corrosion in 4D: MURI4D.numis.northwestern.edu
> Co-Editor, Acta Cryst A
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought"
> Albert Szent-Gyorgi
>



-- 
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
Corrosion in 4D: MURI4D.numis.northwestern.edu
Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
Albert Szent-Gyorgi
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