[gpaw-users] installation of gpaw
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Fri May 21 09:39:19 CEST 2010
Hi,
let's continue on gpaw-users. The information is useful to the others.
Boris Averkiev wrote:
> Dear Marcin,
>
> Thank you very much for your reply.
> Of course I have forgotten to uncomment settings in customize.py, so now they worked and now I didn't change config.py (I started everything from the very beginning).
> Now I used gcc x86_64-suse-linux ver 4.1.2
> Open MPI 1.4.1 and the same mkl - mkl/10.2.5.035
>
> I didn't use any blas/lapack to build numpy - it compiled without them.
> So, should I reinstall NumPy with MKL?
>
i would say that is tricky to have both numpy and gpaw-python linked to
non-standard blas/lapack.
As a first try it's USUALLY better to have numpy built with it's
internal defaults.
You may consider downloading the file
https://svn.fysik.dtu.dk/projects/gpaw/trunk/gpaw/test/numpy_zdotc_graphite.py
and run it with gpaw-python.
If it crashes you have some problems with blas/lapack.
> I also set scalapack = False in customize.py, as you said.
> Now after command "python setup.py build_ext 2>&1 | tee build_ext.log" I've got
> * Scientific is not installed.
> You will not be able to write and read wave functions
> in the netCDF format.
> * Using standard lapack
> * Architecture: linux-x86_64
> * Building a custom interpreter
> So, it doesn't say anything about "Only a serial version of gpaw was built!"
> But gpaw-test still fails with the same output.
>
lines such:
MKL ERROR: Parameter 5 was incorrect on entry to ZHEEV
0.036 OK
suggest that you may have a mismatch in numpy's and gpaw-python
libraries, however:
*** libmkl_mc.so *** failed with error : /soft/intel/mkl/10.2.5.035/lib/em64t/libmkl_mc.so: undefined symbol: mkl_dft_commit_descriptor_s_c2c_md_omp
*** libmkl_def.so *** failed with error : /soft/intel/mkl/10.2.5.035/lib/em64t/libmkl_def.so: undefined symbol: mkl_dft_commit_descriptor_s_c2c_md_omp
MKL FATAL ERROR: Cannot load neither libmkl_mc.so nor libmkl_def.so
shows that linking is not correct. I think you should follow the intel
link advisor to find the correct linking.
Start with the minimum recommended, if you use gcc:
"-L$MKLPATH $MKLPATH/libmkl_solver_lp64_sequential.a -Wl,--start-group
-lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread"
which translates probably eventually to (strangely): ['mkl_intel_lp64',
'mkl_sequential', 'mkl_core', 'guide', 'mkl_lapack', 'mkl_def']
> May be I should also install SciPy?
>
you can do it later if you find that you need it (some new gpaw
functionality like vdw, response(? i think) needs it).
> Also during building it has messages like
> c/libxc/src/work_lda.c: In function âwork_ldaâ:
> c/libxc/src/lda_c_pw.c:125: warning: âvcpâ may be used uninitialized in this function
> c/libxc/src/lda_c_pw.c:125: warning: âdalphaâ may be used uninitialized in this function
> c/libxc/src/lda_c_pw.c:125: warning: âd2alphaâ may be used uninitialized in this function
>
>
> c/libxc/src/work_gga_x.c:46: warning: âldfdxâ may be used uninitialized in this function
>
> c/libxc/src/gga_xc_hcth.c:203: warning: initialization from incompatible pointer type
>
for the moment ignore this.
Marcin
>
> Thank you
>
> Boris
>
>
>
> --- On Tue, 5/18/10, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk> wrote:
>
>
>> From: Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
>> Subject: Re: [gpaw-users] installation of gpaw
>> To: "Boris Averkiev" <averkiev75 at yahoo.com>
>> Cc: gpaw-users at listserv.fysik.dtu.dk
>> Date: Tuesday, May 18, 2010, 11:25 PM
>> Hi,
>>
>> Boris Averkiev wrote:
>>
>>> I am trying to install gpaw on cluster in my home
>>>
>> directory (I am just user, not administrator). As it is
>> written in manual, I first did Custom installation
>>
>>> I installed NumPy - numpy-1.3.0 in my home
>>>
>> directory
>>
>>>
>>>
>> what blas/lapack did you use to build numpy?
>>
>>> Also I installed ASE - python-ase-3.3.1.1390
>>> We have blas and lapac libraries in MKL, so I
>>>
>> specified the path to these libraries in customize.py
>>
>>> #library_dirs =
>>>
>> ['/soft/intel/mkl/10.2.5.035/lib/em64t']
>>
>>> And libraries themselves
>>> #libraries = ['mkl_lapack', 'mkl_intel_thread',
>>>
>> 'mkl_def', 'mkl-mc', 'mkl_core', 'guide', 'mkl_intel_ilp64',
>> 'mkl_blas95_ilp64']
>>
>>> However, it didn’t work. When I run “python
>>>
>> setup.py build_ext 2>&1 | tee build_ext.log”
>> command, I got error “cannot find -lblas”, so I changed
>> all “blas” to “mkl_blas95_ilp64” and all
>> “lapack” to “mkl_lapack” in config.py. After that it
>> compiled, however it also gave the following message:
>>
>>>
>>>
>> there is no need to change config.py (it should not be
>> changed), are you sure that your settings in customize.py
>> are uncommented (I see # in front of the variables)?
>> Every time you compile please run `python setup.py clean`
>> (or just remove the build directory).
>> Linking with mkl is tricky: i would start with a guess at
>> http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/,
>> and then search for missing symbols using nm (for
>> undefined reference to symbol_ use: nm
>> /soft/intel/mkl/10.2.5.035/lib/em64t/lib*.so | grep "T
>> symbol_")
>> Please also set scalapack = False in customize.py first.
>>
>>> * Scientific is not installed.
>>> You will not be able to write and
>>>
>> read wave functions
>>
>>> in the netCDF format.
>>> * Using standard mkl_lapack
>>> * Compiling with ScaLapack
>>> * Architecture: linux-x86_64
>>> * Only a serial version of gpaw was built!
>>>
>>> We have MPI - intel mpi, but I don't know how should I
>>>
>> specify it.
>>
>>>
>>>
>> let's get the serial version working first.
>>
>> Best regards,
>>
>> Marcin
>>
>>> When I run test gpaw-test 2>&1 | tee test.log
>>> it fails. I have attached the test.log file
>>> Information about cluster - SGI Altix XE 1300 Linux
>>>
>> Cluster
>>
>>> Could you help me to resolve those problems?
>>> Thank you
>>> Boris
>>>
>>>
>>>
>>>
>> ------------------------------------------------------------------------
>>
>>> _______________________________________________
>>> gpaw-users mailing list
>>> gpaw-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>
>> -- ***********************************
>>
>> 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
>>
>> ***********************************
>>
>>
>>
>
>
>
>
>
--
***********************************
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
***********************************
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