[gpaw-users] gpaw-setup error

Mon Aug 18 15:26:22 CEST 2014

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]
> *Sent:* 18 August 2014 13:59
> *To:* Robert Warmbier; 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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>
>
> This communication is intended for the addressee only. It is 
> confidential. If you have received this communication in error, please 
> notify us immediately and destroy the original message. You may not 
> copy or disseminate this communication without the permission of the 
> University. Only authorised signatories are competent to enter into 
> agreements on behalf of the University and recipients are thus advised 
> that the content of this message may not be legally binding on the 
> University and may contain the personal views and opinions of the 
> author, which are not necessarily the views and opinions of The 
> University of the Witwatersrand, Johannesburg. All agreements between 
> the University and outsiders are subject to South African Law unless 
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