[gpaw-users] Trouble converging simple molecule with BEEF-vdW

Wed Jan 16 23:53:11 CET 2019

Dear Ask,

I got it to work! The reason for the segmentation fault is an 
embarassing one.

I had compiled gpaw using mkl, but when I ran the test calculations I 
also set the paths to other BLAS libraries. It seems like, that having 
both mkl (and its blas) and blas in the library paths at the same time 
is where a conflict appeared.

Thank you very much for your help. I will use this version from now on.

Best wishes,
Georg

On 1/15/19 8:14 PM, Ask Hjorth Larsen wrote:
> Dear Georg, (re-added mailing list)
>
> Am Di., 15. Jan. 2019 um 23:32 Uhr schrieb Georg Kastlunger
> <georg_kastlunger at brown.edu>:
>> Dear Ask,
>>
>> thank you for your answer. I now updated to the current developers
>> version of gpaw and compiled including libvdwxc.
>>
>> I, however, get a segmentation fault if I want to run a calculation in
>> parallel. The script I used is the exact one you send in your last Mail.
> Right, combining fftw and MKL is tricky.  Hopefully we will solve that
> now though.
>
> What happens if you do "export GPAW_FFTWSO=<complete path to your
> fftw.so>" before running the calculation?  Make sure the compute node
> 'sees' the variable, e.g., by checking os.environ['GPAW_FFTWSO'] at
> runtime.
>
> I suspect there will be nothing to gain from putting 'vdwxc' *before*
> the other libraries in customize.py, but if the above line does not
> solve it, maybe try that anyway.
>
> Sorry for the 'maybe'-advice but things are sometimes quite tricky
> because MKL is both evil and nasty, and pollutes the C namespace with
> fftw-lookalike functions that don't implement the same functionality
> as the true fftw, and will easily cause segfaults when used together
> with the good and wholesome libraries such as the real fftw. :(
>
> Best regards
> Ask
>
>
>> I configured libvdwxc using:
>>
>> MPI_PATH="/gpfs/runtime/opt/mpi/openmpi_2.0.3_intel/"
>> PREFIX="/gpfs_home/gkastlun/data/gkastlun/opt/libvdwxc/install"
>> CFLAGS="-O3 "
>> FCFLAGS="-g "
>> ./configure CFLAGS=$CFLAGS FCFLAGS=$FCFLAGS --prefix=$PREFIX
>> --with-mpi=$MPI_PATH
>>
>> and it runs without warnings or errors. I guess the short summary is:
>>
>> configure: Final build parameters
>> configure: ----------------------
>> configure:
>> configure: TSTAMP   = 20190115T175432-0500
>> configure:
>> configure: DEBUG    = no (init: def)
>> configure: TIMING   = no (init: def)
>> configure:
>> configure: FFTW3    = yes (init: def)
>> configure: MPI      = yes (init: dir)
>> configure: PFFT     = no (init: def)
>> configure:
>> configure: CPP      =
>> /gpfs/runtime/opt/mpi/openmpi_2.0.3_intel//bin/mpicc -E
>> configure: CPPFLAGS =
>> configure: CC       = /gpfs/runtime/opt/mpi/openmpi_2.0.3_intel//bin/mpicc
>> configure: MPICC    =
>> configure: CFLAGS   = -O3
>> configure: FC       = /gpfs/runtime/opt/mpi/openmpi_2.0.3_intel//bin/mpif90
>> configure: MPIFC    =
>> configure: FCFLAGS  = -g
>> configure: LDFLAGS  =
>> configure: LIBS     = -lfftw3_mpi -lfftw3 -lm
>>
>> When I now run a calculation using "xc={'name': 'BEEF-vdW', 'backend':
>> 'libvdwxc'}" it works and converges fast in serial mode, giving the
>> following output in the preamble:
>>
>> XC parameters: vdW-BEEF with libvdwxc
>>     Mode: serial
>>     Semilocal: BEEVDW with 2 nearest neighbor stencil
>>     Corresponding non-local functional: vdW-DF2
>>     Local blocksize: 272 x 176 x 248
>>     PAW datasets: PBE
>>
>> In parallel mode it leads to a segmentation fault right after the
>> initialization with the preamble output:
>>
>> XC parameters: vdW-BEEF with libvdwxc
>>     Mode: mpi with 4 cores
>>     Semilocal: BEEVDW with 2 nearest neighbor stencil
>>     Corresponding non-local functional: vdW-DF2
>>     Local blocksize: 68 x 176 x 248
>>     PAW datasets: PBE
>>
>> I have compiled gpaw with the debug option and the error I get is
>> attached. Unfortunately, I can not really read it.
>>
>> I also attached my customize.py.
>>
>> Is this a known issue or did I do something wrong?
>>
>> Best wishes and thank you for your help,
>> Georg
>>
>>
>> On 1/15/19 8:47 AM, Ask Hjorth Larsen via gpaw-users wrote:
>>> Dear Georg,
>>>
>>> Am So., 13. Jan. 2019 um 17:57 Uhr schrieb Georg Kastlunger via
>>> gpaw-users <gpaw-users at listserv.fysik.dtu.dk>:
>>>> Dear Ask,
>>>>
>>>> thank you for your quick reply.
>>>>
>>>> I was able to converge the molecule now. The problem seemed to be the
>>>> grid spacing. If I use a grid spacing below 0.18 the calculation does
>>>> not converge.
>>> Strange.  I did a test with libvdwxc, vacuum 6.5, and spacing 0.13 on
>>> a desktop computer.  It converged in 19 iterations:
>>>
>>> http://dcwww.camd.dtu.dk/~askhl/files/vdw-molecule-kastlunger.py
>>> http://dcwww.camd.dtu.dk/~askhl/files/vdw-molecule-kastlunger.txt
>>>
>>> (I again recommend switching to libvdwxc if at all possible, since the
>>> old implementation is very inefficient)
>>>
>>> Best regards
>>> Ask
>>>
>>>> Best wishes,
>>>> Georg
>>>>
>>>>
>>>> On 1/11/19 9:11 PM, Ask Hjorth Larsen via gpaw-users wrote:
>>>>> Dear Georg,
>>>>>
>>>>> Am Sa., 12. Jan. 2019 um 02:00 Uhr schrieb Georg Kastlunger via
>>>>> gpaw-users <gpaw-users at listserv.fysik.dtu.dk>:
>>>>>> Dear GPAW community,
>>>>>>
>>>>>> I am currently having some trouble converging a calculation of a simple
>>>>>> molecule (4-mercaptobenzoic acid) applying the BEEF-vdW XC-functional.
>>>>>>
>>>>>> Relaxing the same structure with RPBE did not create any problems
>>>>>> before. Also, when adsorbing the molecule to a metal slab the
>>>>>> calculation converges like a charm.
>>>>>>
>>>>>> I have attached the structure and a minimal script. As you can see, I
>>>>>> have already played around with some parameters for improving
>>>>>> convergence. Unfortunately, nothing helped.
>>>>>>
>>>>>> Did anyone experience the same issue before and knows about some tricks
>>>>>> to converge this system?
>>>>> I ran it using the libvdwxc backend and it converged in 16 iterations,
>>>>> although I changed gpts/vacuum so it would run on an old laptop.
>>>>>
>>>>> calc = GPAW(h=0.2,
>>>>>                xc={'name': 'BEEF-vdW', 'backend': 'libvdwxc'},
>>>>>                txt='out.txt',
>>>>>                eigensolver = Davidson(3),
>>>>>                )
>>>>> atoms.set_calculator(calc)
>>>>> atoms.center(vacuum=4.0)
>>>>>
>>>>> The libvdwxc backend requires installing (drumroll) libvdwxc.  It is
>>>>> much faster, uses less memory, and is scalable (the old implementation
>>>>> scales to 20 cores max, and some things are not parallel).  However it
>>>>> uses a different parametrization of the kernel and does not include
>>>>> the 'soft correction', which means the values will differ slightly.
>>>>>
>>>>> As for the old (slow) implementation, I see now that it also converged
>>>>> after 16 iterations with the same parameters as above.  But I am using
>>>>> GPAW master (i.e. 1.5.0 basically).
>>>>>
>>>>> Best regards
>>>>> Ask
>>>>>
>>>>>> Thank you in advance,
>>>>>>
>>>>>> Georg
>>>>>>
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