[gpaw-users] gpaw-setup error

Mon Aug 18 15:50:56 CEST 2014

Ah, thank you. Replacing 'icc.py' with icc/mpicc did the job. :-)

I never checked the scalapack version number of the intel compiler. But the icc+mkl is about a factor of 2 faster than any gcc+whatever(not mkl) I tried on machines with AVX. It's also faster on all other Xeons I use, but not as much. Haven't used a non-Xeon in years though, so can only speak for those cpus.
I usually don't have problems with that combination. But I don't use scalapack, so can't comment on that.

Best Robert

________________________________
From: Marcin Dulak [Marcin.Dulak at fysik.dtu.dk]
Sent: 18 August 2014 15:26
To: Robert Warmbier; gpaw-users at listserv.fysik.dtu.dk
Cc: gpaw-developers at listserv.fysik.dtu.dk
Subject: Re: [gpaw-users] gpaw-setup error

On 08/18/2014 02:37 PM, Robert Warmbier wrote:
Dear Marcin,

thanks for the information.
Hm, yes, I remember a discussion about the setups. I was considering linking the pbe setup to pbesol. Just found that this would be cheating ;-). I know vasp does it like that.

If I may ask: Why is it riskier to use a PBEsol setup generated with the same parameters used for the PBE setup than using the PBE setup for PBEsol?
In the PSL library  (or PSLibrary...) for quantum espresso they actually use the same set of parameters to generate UPF files for all kinds of xc-functionals.
i would start with PBE setups. The parameters found for PBE setups are generally not transferable to other functionals.
In the best case the generation of a setup for a different functional using PBE parameters will fail, but it may also generate a bad setup without an error
(bad means it gives incorrect results when used for some systems/properties).
Using PBE setups has the advantage that you can cite what you used - if you generate PBEsol yourself there is a risk
that if something in PBEsol generation goes wrong that make the results look right (there is always a chance for this to happen) it will be hard to reproduce.
Of course make some tests if your properties are OK to use PBE setups.

More directed to the developers mailing list:
The problem I had with gpaw-setup came from the weird circumstance, that the Intel compiler setup does not create a _gpaw.so file (or deletes it after creating). I couldn't find the part in the code, where the _gpaw.so is created. I would like to track that down. Does anyone know, how (where in the code) the _gpaw.so is created? The whole setup procedure seems to be trimmed towards gcc...
the problem may be in the icc.py wrapper -  no need to use this.
Please see an example of using intel here:
https://trac.fysik.dtu.dk/projects/gpaw/browser/trunk/doc/install/Linux/Niflheim/el6-dl160g6-tm-intel-2013.1.117-openmpi-1.6.3-mkl-2013.1.117-sl-hdf5-1.8.10.py
I must add that we dropped it in favor of gcc + acml due to stability problems and old scalapack distributed by intel.

Best regards,

Marcin

Best Robert

________________________________
From: Marcin Dulak [Marcin.Dulak at fysik.dtu.dk<mailto:Marcin.Dulak at fysik.dtu.dk>]
Sent: 18 August 2014 13:59
To: Robert Warmbier; gpaw-users at listserv.fysik.dtu.dk<mailto:gpaw-users at listserv.fysik.dtu.dk>
Subject: Re: [gpaw-users] gpaw-setup error

On 08/18/2014 11:58 AM, Robert Warmbier wrote:
Dear all,

I want to use the PBEsol functional. However, if I set xc='PBEsol', gpaw says

RuntimeError: Could not find paw.PBEsol-setup for "C".

So, I tried to generate a setup (any setup):

gpaw-setup C -f PBEsol
normally please do not generate setups.
Depending on the properties you investigate it may be OK to cheat
GPAW to use PBE setups in PBEsol calculations (just ln -s X.PBE.gz X.PBEsol.gz).
This is OK for total energy differences (and i think we have verified that also for bandgaps - both GGA and GW)
- one can exchange GGA setups and functionals more
or less freely, but this is not the case for GLLB and (i guess) maybe other properties.
See the attached plot.
The total energies become sometimes positive (people are usually worried about this) because the reference energy does
not correspond between the setup and used functional.

If you really want to generate setups
see http://listserv.fysik.dtu.dk/pipermail/gpaw-users/2014-August/002859.html

I get this error message:

rbw at rbw-desktop:~/gpawruns> gpaw-setup C
Traceback (most recent call last):
  File "/home/rbw/programs/gpaw/tools/gpaw-setup", line 5, in <module>
    from gpaw.atom.gpaw_setup import main
  File "/home/rbw/programs/gpaw/build/lib.linux-x86_64-2.7/gpaw/__init__.py", line 239, in <module>
    from gpaw.aseinterface import GPAW
  File "/home/rbw/programs/gpaw/build/lib.linux-x86_64-2.7/gpaw/aseinterface.py", line 11, in <module>
    from gpaw.xc import XC
  File "/home/rbw/programs/gpaw/build/lib.linux-x86_64-2.7/gpaw/xc/__init__.py", line 1, in <module>
    from gpaw.xc.libxc import LibXC
  File "/home/rbw/programs/gpaw/build/lib.linux-x86_64-2.7/gpaw/xc/libxc.py", line 1, in <module>
    import _gpaw
ImportError: No module named _gpaw
probably PYTHONPATH not set correctly - it must include the directory containing _gpaw.so.
i guess only gpaw-python works now.

That is using a current svn 11806 checkout.

Normal calculations run just fine. Nevertheless, it could be just a problem with my configuration:

I use this customize.py running 'python setup.py build':

Best regards,

Marcin
compiler = 'icc.py'
libraries  = ['fftw3']   # this should be removed - GPAW does not link to it

libraries += ['mkl_intel_lp64', 'mkl_core', 'mkl_sequential', 'pthread', 'm']
library_dirs += ['/home/rbw/programs/installs/openmpi-1.8.1-intel2013.1.3/lib64']
library_dirs += ['/opt/intel/mkl/lib/intel64']
library_dirs += ['/home/rbw/programs/installs/fftw-3.3.4-intel2013.1.3/lib64']  # also not necessary

include_dirs += ['/home/rbw/programs/installs/openmpi-1.8.1-intel2013.1.3/include']
include_dirs += ['-I/opt/intel/mkl/include']
include_dirs += ['/home/rbw/programs/installs/fftw-3.3.4-intel2013.1.3/include']
extra_link_args += ["-fPIC",'-lpthread','-lm']
extra_compile_args += ['-I/opt/intel/mkl/include','-static','-std=c99','-fPIC']
mpicompiler = 'icc.py'
mpilinker = 'icc.py'
hdf5 = False
scalapack = False
define_macros += [("GPAW_ASYNC",1)]
define_macros += [("GPAW_MPI2",1)]
include_dirs += ['/home/rbw/programs/installs/libxc-2.2.0-intel2013.1.3/include']
library_dirs += ['/home/rbw/programs/installs/libxc-2.2.0-intel2013.1.3/lib64']
if 'xc' not in libraries: libraries.append('xc')

Does anyone have any suggestions for me?

Best Robert

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