[ase-users] Dacapo/ Altix
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Wed Apr 27 10:17:28 CEST 2011
Hi,
does this job run on 8 cores?
Increasing the stack size may help:
https://wiki.fysik.dtu.dk/dacapo/Installation#id33
Best regards,
Marcin
Tadeu Leonardo Soares e Silva wrote:
> Dear Marcin
>
> I have installed Dacapo in Rocks/CentOS, but I do not get to install Dacapo
> in Opensuse/SGIAltix. What can cause this problem? Could you help me, please?
> Please find as attachment some files.
>
>
> * Ldd dacapo_intellinux_mpi.run
>
> linux-vdso.so.1 => (0x00007fffcbd8e000)
> libmkl_lapack.so
> => /sw/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_lapack.so
> (0x00007ff44378f000)
> libmkl_intel_lp64.so
> => /sw/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so
> (0x00007ff443395000)
> libmkl_core.so => /sw/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so
> (0x00007ff442fe2000)
> libguide.so => /sw/intel/Compiler/11.1/072/lib/intel64/libguide.so
> (0x00007ff44446a000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ff442dc5000)
> libmkl_intel_thread.so
> => /sw/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.so
> (0x00007ff441b81000)
> libmpi_f90.so.0 => /sw/mpi/intel/openmpi-1.4.2/lib64/libmpi_f90.so.0
> (0x00007ff44197d000)
> libmpi_f77.so.0 => /sw/mpi/intel/openmpi-1.4.2/lib64/libmpi_f77.so.0
> (0x00007ff441741000)
> libmpi.so.0 => /sw/mpi/intel/openmpi-1.4.2/lib64/libmpi.so.0
> (0x00007ff44146f000)
> libopen-rte.so.0 => /sw/mpi/intel/openmpi-1.4.2/lib64/libopen-rte.so.0
> (0x00007ff441207000)
> libopen-pal.so.0 => /sw/mpi/intel/openmpi-1.4.2/lib64/libopen-pal.so.0
> (0x00007ff440f8a000)
> libdl.so.2 => /lib64/libdl.so.2 (0x00007ff440d86000)
> libnsl.so.1 => /lib64/libnsl.so.1 (0x00007ff440b6e000)
> libutil.so.1 => /lib64/libutil.so.1 (0x00007ff44096b000)
> libm.so.6 => /lib64/libm.so.6 (0x00007ff440715000)
> libc.so.6 => /lib64/libc.so.6 (0x00007ff4403b7000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007ff4401a0000)
> /lib64/ld-linux-x86-64.so.2 (0x00007ff4443f6000)
> libifport.so.5 => /sw/intel/Compiler/11.1/072/lib/intel64/libifport.so.5
> (0x00007ff440067000)
> libifcoremt.so.5 => /sw/intel/Compiler/11.1/072/lib/intel64/libifcoremt.so.5
> (0x00007ff43fdc2000)
> libimf.so => /sw/intel/Compiler/11.1/072/lib/intel64/libimf.so
> (0x00007ff43fa2e000)
> libsvml.so => /sw/intel/Compiler/11.1/072/lib/intel64/libsvml.so
> (0x00007ff43f818000)
> libintlc.so.5 => /sw/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5
> (0x00007ff43f6da000)
>
>
> * Log openmpi.o19491
> =================================================================
> NACAD Supercomputer Center
> =================================================================
> --- Job Information ---
> Cores available per node = 8
> Cores allocated = 16
> Cores used = 16
> --- Nodes:cores Used ---
> r1i1n10:8 r1i1n9:8
> =================================================================
>
> Inicio : Seg Abr 25 18:59:17 BRT 2011
> Traceback (most recent call last):
> File "./teste.py", line 24, in <module>
> dyn.run(fmax=0.05)
> File "/home/users/tadeu33/local/ase-3.4.1/ase/optimize/optimize.py", line
> 114, in run
> f = self.atoms.get_forces()
> File "/home/users/tadeu33/local/ase-3.4.1/ase/atoms.py", line 571, in
> get_forces
> forces = self._calc.get_forces(self)
> File "/home/users/tadeu33/local/ase-
> 3.4.1/ase/calculators/jacapo/jacapo.py", line 2307, in get_forces
> self.calculate()
> File "/home/users/tadeu33/local/ase-
> 3.4.1/ase/calculators/jacapo/jacapo.py", line 2810, in calculate
> raise DacapoAbnormalTermination(s % txt)
> ase.calculators.jacapo.jacapo.DacapoAbnormalTermination: Dacapo output
> txtfile (teste332.txt) did not end normally.
> KPT: Chadi-Cohen asymptotic error estimate: 0.000118148205
> KPT: (see PRB 8, 5747 (1973); 13, 5188 (1976))
>
> KPT: nkpmem : 1
> Parallel : -- parallel configuration --
> Parallel : There are 16 processors divided into 8 groups
> Parallel : Processors per group : 2
> Parallel : k-points per processor group : 1
> Parallel : Each k-point is parallelized over 2 processors
>
> Fim : Seg Abr 25 18:59:19 BRT 2011
>
> * Command Line executed by dacapo.run script
>
> /sw/mpi/intel/openmpi-1.4.2/bin/mpirun -np 16 -
> machinefile /var/spool/torque/aux//19491.service0.ice.nacad.ufrj.br /home/use
> rs/tadeu33/bin/dacapo_intellinux_mpi.run teste332.nc -out teste332.txt -
> scratch /scratch/tadeu/
>
> * Netcdf Compilation
> cd netcdf-3.6.3
> export CC=icc
> export CXX=icpc
> export CFLAGS='-O3 -xssse3 -ip -no-prec-div -static'
> export CXXFLAGS='-O3 -xssse3 -ip -no-prec-div -
> static'
> export F77=ifort
> export FC=ifort
> export F90=ifort
> export FFLAGS='-O3 -xssse3'
> export CPP='icc -E'
> export CXXCPP='icpc -E'
> export CPPFLAGS='-DNDEBUG -DpgiFortran'
> ./configure --prefix=$HOME/local/netcdf-3.6.3_intel
> mkdir $HOME/local/netcdf-3.6.3_intel
> make check
> make install
>
>
>
> * Dacapo Compilation
> export BLASLAPACK='-
> L/sw/intel/Compiler/11.1/064/mkl/lib/em64t -lmkl_lapack -lmkl_intel_lp64 -
> lmkl_core -lguide -lpthread -lmkl_intel_thread'
> export NETCDF=$HOME/local/netcdf-3.6.3_intel/lib
> export FFTW=$HOME/local/fftw2-2.1.5-1.intel/lib
> export CC=icc
> export CXX=icpc
> export CFLAGS='-O3 -xssse3'
> export CXXFLAGS='-O3 -xssse3'
> export F77=ifort
> export FC=ifort
> export F90=ifort
> export FFLAGS='-O3 -xssse3'
> export CPP='icc -E'
> export CXXCPP='icpc -E'
> export MPIDIR=/sw/mpi/intel/openmpi-1.4.2
> export MPI_LIBDIR=${MPIDIR}/lib64
> export MPI_BINDIR=${MPIDIR}/bin
> export MPI_INCLUDEDIR=${MPIDIR}/include
> cp -a ../src/dacapo .
> cd dacapo/src
> make intellinux
> make intellinux MP=mpi
> cp intellinux_mpi/dacapo.run
> $HOME/bin/dacapo_intellinux_mpi.run
> cp intellinux_serial/dacapo.run
> $HOME/bin/dacapo_intellinux_serial.run
> cd $HOME/work/dacapo/Python
> python setup.py install --verbose --prefix='' --
> home=$HOME/local/dacapo
>
>
> Sincerely,
>
> Tadeu Leonardo
>
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> PEQ/COPPE renova o nivel de curso 7, maximo na CAPES:
> 45 anos de excelencia no ensino e pesquisa de pos-graduação em
> Engenharia Quimica.
>
> ************************************
>
> PEQ/COPPE : 45 years of commitment to excellence in teaching and
> research in Chemical Engineering.
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
--
***********************************
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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