[DFTB-Plus-User] DFTB+MPI-NEGF on SLURM

Thu Apr 9 11:49:30 CEST 2015

Yes, I did download the 4732 from the website.

I will apply this patch and recompile the code then.

Thank you for your support.

Kind regards,
Alessandro

*Alessandro Pirrotta*
PhD student

*Faculty of Science*
Department of Chemistry &
Nano-Science Center
University of Copenhagen
Universitetsparken 5, C321
2100 Copenhagen Ø
Denmark

DIR +45 21 18 11 90
MOB +45 52 81 23 41

alessandro.pirrotta at chem.ku.dk

alessandro.pirrotta at gmail.com

www.ki.ku.dk

On 9 April 2015 at 11:24, Gabriele Penazzi <penazzi at uni-bremen.de> wrote:

>  On 04/09/2015 11:07 AM, Alessandro Pirrotta wrote:
>
> Thank you both for your emails.
>
>  I run the job using the following commands and in both cases it seems
> like the same job is running in $NCPUS
> giving me $NCPUS outputs overlapping on the same file.
>
>  srun -n $NCPUS -cores-per-socket=$NCPUS dftb+mpi-negf.r4732_ifort_tested
> mpirun -np $NCPUS dftb+mpi-negf.r4732_ifort_tested
>
>  FYI I compiled it using the extlib from the website and the
> makefile make.x86_64-linux-ifort
>
>
> If you downloaded the code directly from the website you may give a look
> to this hotfix:
>
> https://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/2015/001784.html
>
> If colliding I/O persists, try to lower verbosity settings.
>
> Best,
> Gabriele
>
>
>
>
>   *Alessandro Pirrotta*
> PhD student
>
>
>
> *Faculty of Science*
> Department of Chemistry &
> Nano-Science Center
> University of Copenhagen
> Universitetsparken 5, C321
> 2100 Copenhagen Ø
> Denmark
>
> DIR +45 21 18 11 90
> MOB +45 52 81 23 41
>
>  alessandro.pirrotta at chem.ku.dk
>
> alessandro.pirrotta at gmail.com
>
> www.ki.ku.dk
>
> On 9 April 2015 at 10:56, Alessandro Pirrotta <tqn722 at alumni.ku.dk> wrote:
>
>> Thank you both for your emails.
>>
>>  I run the job using the following commands and in both cases it seems
>> like the same job is running in $NCPUS
>> giving me $NCPUS outputs overlapping on the same file.
>>
>>  srun -n $NCPUS -cores-per-socket=$NCPUS dftb+mpi-negf.r4732_ifort_tested
>> mpirun -np $NCPUS dftb+mpi-negf.r4732_ifort_tested
>>
>>  FYI I compiled it using the extlib from the website and the
>> makefile make.x86_64-linux-ifort
>>
>>
>>   *Alessandro Pirrotta*
>> PhD student
>>
>>
>>
>> *Faculty of Science*
>> Department of Chemistry &
>> Nano-Science Center
>> University of Copenhagen
>> Universitetsparken 5, C321
>> 2100 Copenhagen Ø
>> Denmark
>>
>> DIR +45 21 18 11 90 <%2B45%2021%2018%2011%2090>
>> MOB +45 52 81 23 41 <%2B45%2052%2081%2023%2041>
>>
>>  alessandro.pirrotta at chem.ku.dk
>>
>> alessandro.pirrotta at gmail.com
>>
>> www.ki.ku.dk
>>
>>   On 9 April 2015 at 10:05, Gabriele Penazzi <penazzi at uni-bremen.de>
>> wrote:
>>
>>>   On 04/09/2015 09:07 AM, Alessandro Pirrotta wrote:
>>>
>>> Dear DFTB+ users,
>>>
>>>  I am having a problem running the DFTB+ on SLURM.
>>> When I am connected to the front end of my account in my university
>>> computer cluster, the executable runs correctly: I have run the test and
>>> only 2 tests failed
>>> (
>>> ======= spinorbit/EuN =======
>>> electronic_stress    element              0.000101791078878
>>> Failed
>>> stress               element              0.000101791078878
>>> Failed
>>> )
>>>
>>>  When I submit a job with SLURM and I execute normally ./dftb+ I get a
>>> MPI error (see below).
>>> If I run "mpi -n 1 dftb+" the job runs correctly over a node and a
>>> single core.
>>> *How do I run dftb+ over a single node, using n cores?*
>>>
>>> *[cut]*
>>>
>>> Hi Alessandro,
>>>
>>> when running NEGF, the parallelization is very different with respect to
>>> solving the aigenvalue problem. dftb+negf is parallelized on two level: MPI
>>> by distribution of energy points and possibly OMP by linking with threaded
>>> blas/lapack libraries. The former is on us and it is mandatory to compile
>>> supporting MPI, the latter is on the BLAS/LAPACK vendor and it may be
>>> active or not depending on the way you compile it. See the README.NEGF and
>>> README.PARALLEL files in the src directory.
>>>
>>> If you link a threaded library, then you will have to specify how many
>>> OMP threads you assign per process in your job script. For example
>>>
>>> $ export OMP_NUM_THREADS=4
>>> $ mpirun -n 1 dftb+
>>>
>>> would use 4 cores on 1 process (the correct specification depends on
>>> your architecture, you may need or not additional flags but probably you
>>> have an howto related to your facility). Therefore the answer to you
>>> question is that you may want to use n threads on 1 process, or n processes
>>> on n cores, or (more likely) something in the middle depending on your
>>> system.
>>>
>>> A note on efficiency. As on "common" test systems (tens to thousands
>>> atoms) the lapack/scalack scale efficiently up to 2-4 threads, it is
>>> usually convenient to reserve some cores for threading. Also, as the
>>> parallelization on energy points implies solving N independent Green's
>>> functions, therefore it needs to allocate N times memory where N is the
>>> number of processes. For large systems it may be necessary to run a process
>>> per socket, to get the maximum available memory. With the current version
>>> also the Poisson is a bit more efficient if you have less processes on a
>>> socket, considering these points at the end of the day I usually run with 2
>>> or 4 omp threads (if I don't hit memory problems).
>>>
>>> Hope this helps,
>>> Gabriele
>>>
>>>
>>>
>>>
>>> --
>>> --
>>> Dr. Gabriele Penazzi
>>> BCCMS - University of Bremen
>>> http://www.bccms.uni-bremen.de/http://sites.google.com/site/gabrielepenazzi/
>>> phone: +49 (0) 421 218 62337
>>> mobile: +49 (0) 151 19650383
>>>
>>>
>>>  _______________________________________________
>>> DFTB-Plus-User mailing list
>>> DFTB-Plus-User at mailman.zfn.uni-bremen.de
>>> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>>>
>>>
>>
>
>
> _______________________________________________
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>
>
> --
> --
> Dr. Gabriele Penazzi
> BCCMS - University of Bremen
> http://www.bccms.uni-bremen.de/http://sites.google.com/site/gabrielepenazzi/
> phone: +49 (0) 421 218 62337
> mobile: +49 (0) 151 19650383
>
>
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