[gpaw-users] Gpaw on taito (CSC)

[Sakko Arto]

Dear Taito-users,

Below is shown how I have installed the trunk version of GPAW in Taito. It does not support ScaLAPACK, but otherwise it should work. I hope this helps!

With best regards,
 Arto



 1) Set modules:
    module purge
    module load gpaw-env
    module unload gpaw
    module unload gpaw-setups
    module unload ase

 2) Set environmental variables:
    export GPAW_SETUP_PATH=$USERAPPL/gpaw-setups-0.9.9672
    export PYTHONPATH=$USERAPPL/ase:$PYTHONPATH

 3) Install libxc-2.0.3 to $USERAPPL/libxc-2.0.3:
    configure --enable-static --prefix=$PWD CFLAGS=-fPIC
    make; make install

 4) Install atomic setups to $USERAPPL/gpaw-setups-0.9.9672

 5) Install ase to $USERAPPL/ase:
    python setup.py build
    python setup.py install --home=$PWD

 6) Install gpaw-trunk to $USERAPPL/trunk with the attached customize.py (modify it according to your own libxc path):
    python setup.py build
    python setup.py install --home=$PWD


________________________________________
From: gpaw-users-bounces at listserv.fysik.dtu.dk [gpaw-users-bounces at listserv.fysik.dtu.dk] on behalf of Marcin Dulak [Marcin.Dulak at fysik.dtu.dk]
Sent: 25 July 2014 16:35
To: leonardo espinosa
Cc: gpaw-users
Subject: Re: [gpaw-users] Gpaw on taito (CSC)

On 07/25/2014 03:26 PM, Marcin Dulak wrote:
On 07/25/2014 02:04 PM, leonardo espinosa wrote:
Hi,

I've have tested different combinations of optimization algorithms with the option that
Marcin suggested: export OMP_NUM_THREADS=1, and different combinations of versions of ase/gpaw.
The calculation still crashes with the same error message. I tried other options such us:

export NUMEXPR_NUM_THREADS=1
export MKL_NUM_THREADS=1
export MKL_DOMAIN_NUM_THREADS=1
export OMP_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export GOTO_NUM_THREADS=1

But nothing, the same error message.

Maybe I should start from the scratch, installing my own version.
However I though that somebody, gpaw user in TAITO can give
me a hand with a script o some hints.

when you run tests in parallel (e.g. on 8 cores), do any fail?
mpiexec gpaw-python `which gpaw-test`
please see also this comment (are you using scalapack?):
http://listserv.fysik.dtu.dk/pipermail/gpaw-users/2014-January/002523.html

Best regards,

Marcin

Best regards,

Marcin

Thanks again and any help with this annoying bug is always welcome.

Best,

leo




---
Leonardo A. Espinosa L.
Postdoctoral Researcher,
Aalto University,
Espoo, Finland.
http://goo.gl/WjBIXv<http://yonk.is/gI3>




On Thu, Jul 24, 2014 at 5:33 PM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk<mailto:Marcin.Dulak at fysik.dtu.dk>> wrote:
On 07/24/2014 08:39 AM, Jens Jørgen Mortensen wrote:
On 07/23/2014 04:41 PM, leonardo espinosa wrote:
Hi Ask,

Here I attached you the files,
thanks for your help.

It looks like the positions are out of sync on the different cores.  I think GPAW should return identical energies and forces from all cores.  Maybe the BFGS algorithm is causing this?  If that is the case then how do we deal with this?
is GPAW or numpy linked against a multithreaded blas?
>From https://wiki.fysik.dtu.dk/gpaw/install/installationguide.html - "Multithreading is not supported."
For some libraries like mkl,openblas you can disable multithreading with: export OMP_NUM_THREADS=1

Best regards,

Marcin



Maybe GPAW should accept a small divergence in the positions due to numerical noise and then just use the positions from rank 0?

Jens Jørgen

leo

---
Leonardo A. Espinosa L.
Postdoctoral Researcher,
Aalto University,
Espoo, Finland.
http://goo.gl/WjBIXv<http://yonk.is/gI3>




On Wed, Jul 23, 2014 at 5:26 PM, Ask Hjorth Larsen <asklarsen at gmail.com<mailto:asklarsen at gmail.com>> wrote:
Hi Leonardo

What is the error?  Also the logfile.

Best regards
Ask

2014-07-23 16:23 GMT+02:00 leonardo espinosa <espinosa.leal at gmail.com<mailto:espinosa.leal at gmail.com>>:
> Dear gpaw users,
>
> I'm trying to run a simple BFGS optimization of a benzene
> molecule on taito cluster (https://research.csc.fi/taito-user-guide),
> using different versions of gpaw: 0.9.0 and 0.10.0. I'm having
> some problems because after certain number of iterations the
> calculation crashes, anybody here that use gpaw-0.10.0 on taito
> without problem? Can you supply me with an example that runs?
>
> I attached you here the files that I'm using.
>
> Best regards,
>
> leo
>
>
>
>
> ---
> Leonardo A. Espinosa L.
> Postdoctoral Researcher,
> Aalto University,
> Espoo, Finland.
> http://goo.gl/WjBIXv
>
>
>





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

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<mailto:Marcin.Dulak at fysik.dtu.dk>

***********************************

-------------- next part --------------
A non-text attachment was scrubbed...
Name: customize.py
Type: text/x-python
Size: 277 bytes
Desc: customize.py
URL: <http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20140729/a48fb2a6/attachment.py>