[gpaw-users] Questions about Parallel Runs

[Duy Le]

which mpi are you using?
--------------------------------------------------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Mon, Apr 12, 2010 at 8:49 AM, Hongliang Xin <hxin at umich.edu> wrote:
> Here is the output. The gpaw has been built with mpi support. The output
> below does not seem right to me. We built gpaw with the system mpi, but it
> shows below that the library is linked to our user mpi (/home/morabim). Is
> this the problem? I will take a look and rebuild the gpaw.
>
> thanks,
>
> : ldd `which gpaw-python`
>     libgfortran.so.1 => /usr/lib64/libgfortran.so.1 (0x00002aeb72229000)
>     libpython2.4.so.1.0 => /usr/lib64/libpython2.4.so.1.0
> (0x00002aeb724c0000)
>     libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aeb727f1000)
>     libdl.so.2 => /lib64/libdl.so.2 (0x00002aeb72a0d000)
>     libutil.so.1 => /lib64/libutil.so.1 (0x00002aeb72c11000)
>     libm.so.6 => /lib64/libm.so.6 (0x00002aeb72e14000)
>     libmpi.so.0 => /home/morabitm/usr/lib/libmpi.so.0 (0x00002aeb73098000)
>     libopen-rte.so.0 => /home/morabitm/usr/lib/libopen-rte.so.0
> (0x00002aeb7322c000)
>     libopen-pal.so.0 => /home/morabitm/usr/lib/libopen-pal.so.0
> (0x00002aeb73385000)
>     libnsl.so.1 => /lib64/libnsl.so.1 (0x00002aeb734e5000)
>     libc.so.6 => /lib64/libc.so.6 (0x00002aeb736fd000)
>     /lib64/ld-linux-x86-64.so.2 (0x00002aeb7200c000)
>
> On Mon, Apr 12, 2010 at 4:58 AM, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
> wrote:
>>
>> Hi,
>>
>> is you gpaw built with mpi support?
>> What does:
>> ldd `which gpaw-python`
>> say?
>> To build the parallel version, mpicc must be in PATH at the build time,
>> or the customize.py must include the relevant mpi information.
>> Please look at the following example of  the
>> https://trac.fysik.dtu.dk/projects/gpaw/browser/trunk/doc/install/Linux/Niflheim/customize-thul-acml.py
>> (the scalapack settings and the platform_id variable at the end of the
>> customize.py are not relevant to your case - anyway
>> the example of using platform_id is described here
>> https://wiki.fysik.dtu.dk/gpaw/install/Linux/Niflheim/Niflheim.html#niflheim).
>>
>> Best regards,
>>
>> Marcin
>>
>> Hongliang Xin wrote:
>>>
>>> Dear gpaw-users,
>>>
>>> We have been trying to figure out what is the problem with the parallel
>>> gpaw calculations recently.
>>> I know there is definitely the problem due to the following several
>>> observations:
>>> 1. There is no benefit for calculations with multiple processors compared
>>> with one serial calculation.
>>> 2. It seems it only runs several serial versions of the program without
>>> any communication between nodes. 3. After calculation is done, there are
>>> always .gpaw and another .old.gpaw files with exactly the same size.
>>> 4. I did not see any indication that the job is paralleled.
>>>
>>> The gpaw is compiled without difficulty with the configuration as shown
>>> in the bottom. The job is submitted according to the gpaw documentation
>>> using:
>>> mpirun -np $NP -machinefile $PBS_NODEFILE gpaw-python Script.py
>>>
>>> Any suggestion will be very welcome.
>>>
>>> thanks,
>>>
>>> Hongliang
>>>
>>>
>>> * Using standard lapack
>>> * Architecture: linux-x86_64
>>> * Building a custom interpreter
>>> libraries ['acml', 'gfortran']
>>> library_dirs ['/home/software/rhel5/acml/4.0.1-gcc/gfortran64/lib']
>>> include_dirs
>>> ['/home/software/rhel5/python/lib64/python2.4/site-packages/numpy/core/include',
>>> 'c/libxc']
>>> define_macros []
>>> extra_link_args []
>>> extra_compile_args ['-Wall', '-std=c99']
>>> runtime_library_dirs []
>>> extra_objects []
>>>
>>> Parallel configuration
>>> mpicompiler mpicc
>>> mpi_libraries []
>>> mpi_library_dirs []
>>> mpi_include_dirs []
>>> mpi_define_macros []
>>> mpi_runtime_library_dirs []
>>>
>>>
>>>
>>> --
>>> Hongliang Xin
>>> Ph.D. Candidate
>>> Dept. of Chemical Engineering
>>> University of Michigan
>>> 3166 HH Dow
>>> 2300 Hayward
>>> Ann Arbor, MI 48109
>>> Phone: (734) 647-8051
>>> E-mail: hxin at umich.edu <mailto:hxin at umich.edu>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> 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
>>
>> ***********************************
>>
>
>
>
> --
> Hongliang Xin
> Ph.D. Candidate
> Dept. of Chemical Engineering
> University of Michigan
> 3166 HH Dow
> 2300 Hayward
> Ann Arbor, MI 48109
> Phone: (734) 647-8051
> E-mail: hxin at umich.edu
>
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