[gpaw-users] Questions about Parallel Runs

Mon Apr 12 16:03:29 CEST 2010

openmpi-1.3.2/gcc/bin/mpicc

This is the mpi available as I build the gpaw.

thanks,

Hongliang

On Mon, Apr 12, 2010 at 9:59 AM, Duy Le <ttduyle at gmail.com> wrote:

> 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
> >
> > _______________________________________________
> > gpaw-users mailing list
> > gpaw-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
> >
>

-- 
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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