The ABINIT Users Mailing List ( CLOSED )

[mmgarcia@if.usp.br]

Quoting Xavier Gonze <gonze@pcpm.ucl.ac.be>:

> Dear Marcelo Garcia,
> 
> Could you send also your input file ?
> Did you succeed to run one of the parallel test cases,
> found in Test_paral ?
> 
> Xavier
> 
> On 28 Jun 2006, at 00:14, mmgarcia@if.usp.br wrote:
> 
> > Hi.
> >
> >   I am having problems with abinip (Abinit-4.6.5) file made with  
> > Intel Cluster Tools 2.0. (ICT) I always get the following error:
> > ---------------------------------------------------------------------- 
> > ------
> > ,Min el dens=  3.8631E-05 el/bohr^3 at reduced coord.  0.8906   
> > 0.0500  0.8594
> > ,Max el dens=  3.9231E-01 el/bohr^3 at reduced coord.  0.5906   
> > 0.5500  0.2188
> > -P-0000  leave_test : synchronization done...
> >   suscep_stat : loop on k-points and spins done in parallel
> > rank 3 in job 1  nanomol07.lcca.usp.br_51942   caused collective  
> > abort of all ranks
> >   exit status of rank 3: killed by signal 9
> > ---------------------------------------------------------------------- 
> > ------
> > I use Scientific Linux 4.1 (Red Hat EL 4 update 1 clone)
> >
> >   My makefile_macros and the schell script used are listed bellow.
> >
> >   Does anyone else using ICT 2.0
> >
> >   Thanks
> >
> > Marcelo M. Garcia
> >
> > ---------------------------- Shell script -------------------------
> > #!/bin/sh
> > #PBS -N ppvSlab
> > #PBS -l nodes=3:ppn=2
> > #PBS -q workq
> > #PBS -e SLAB.e
> > #PBS -o SLAB.o
> > # Definicao das variaveis de ambiente.
> > ABINIP=/home/mmgarcia/abinit-4.6.5/abinip
> > MPIRUN=/opt/intel/ict/2.0/mpi/2.0/bin/mpiexec
> > MPDBOOT=/opt/intel/ict/2.0/mpi/2.0/bin/mpdboot
> > MPDEXIT=/opt/intel/ict/2.0/mpi/2.0/bin/mpdallexit
> > MPDTRACE=/opt/intel/ict/2.0/mpi/2.0/bin/mpdtrace
> > JOB=ppvSlab
> > SCR=/scratch/mmgarcia/${JOB}
> > if [ ! -d ${SCR} ] ; then
> >         echo "Criando diretorio de scratch"
> >         mkdir ${SCR}
> > fi
> > HOME=/home/mmgarcia/Systems/${JOB}
> > # Prepara o diretorio de scratch.
> > cd ${SCR}
> > cp -f ${HOME}/${JOB}.in .
> > cp -f ${HOME}/${JOB}.files .
> > rm -f ${JOB}.out
> > echo `pwd`
> > # Prepara linha de comando.
> > # PBS_NODEFILE diz quais nos foram alocados.
> > echo PBS_NODEFILE
> > cat $PBS_NODEFILE
> > # num. de processadores.
> > NPROCS=`wc -l < $PBS_NODEFILE`
> > # num de nos (no nosso caso, metade do numero de processadores).
> > echo NP
> > NP=`expr $NPROCS / 2`
> > echo $NP
> > # Cria o arquivo com os nos que iriamo receber o job.
> > cat $PBS_NODEFILE &> ${SCR}/pbsnodes.txt
> > # Dispara o daemon nos nos.
> > echo MPDBOOT
> > ${MPDBOOT} -r ssh -n ${NP} -f ${SCR}/pbsnodes.txt
> > echo MPDTRACE
> > ${MPDTRACE} &> maquinas.txt
> > # Executa o job paralelo.
> > ${MPIRUN} -np ${NPROCS} ${ABINIP}  < ${HOME}/${JOB}.files >  $ 
> > {JOB}.log
> > # Mata os daemons.
> > ${MPDEXIT}
> > # Fim da parte MPI.
> > # Copia o arquivo de saida do job para o diretorio correto.
> > cp -f ${HOME}/${JOB}.out ${HOME}
> > ---------------------------------------------------------------------- 
> > ---------
> >
> > ------------------- makefile_macros  
> > -------------------------------------------
> > # Machine type
> > MACHINE=P6
> > # Fortran optimized compilation
> > #FC=/opt/intel/compiler70/ia32/bin/ifc
> > F90DIR=/opt/intel/fc/9.1.032
> > #F90=${F90DIR}/bin/ifort
> > #FC=${F90DIR}/bin/ifort
> > F90=/opt/intel/ict/2.0/mpi/2.0/bin/mpiifort
> > FC=/opt/intel/ict/2.0/mpi/2.0/bin/mpiifort
> > FFLAGS=-FR -O3 -w -tpp7 -axW -static
> > FFLAGS_Src_2psp =-FR -O0 -w -tpp7 -axW
> > FFLAGS_Src_3iovars =-FR -O0 -w -tpp7 -axW
> > FFLAGS_Src_9drive =-FR -O0 -w -tpp7 -axW
> > FFLAGS_LIBS= -O3 -w
> > MKLDIR=/opt/intel/ict/2.0/cmkl/8.0.1/lib/32
> > #LIBS = ${MKLDIR}/libmkl_lapack.a ${MKLDIR}/libmkl_ia32.a ${MKLDIR}/ 
> > libguide.a ${F90DIR}/lib/libsvml.a -lpthread
> > LIBS = -L ${MKLDIR} -lmkl_lapack -lmkl_ia32 -lguide -lpthread -lmkl  
> > -lvml -lsvml
> > # C preprocessor, used to preprocess the fortran source.
> > CPP=/lib/cpp
> > CPP_FLAGS=-P -traditional -D__IFC
> > # The cpp directive CHGSTDIO changes the standard I/O definition
> > # Uncomment the next line for this to happen.
> > #CPP_FLAGS=-P -DCHGSTDIO
> >
> > # C optimized compilation.
> > #CC=/opt/intel/cc/9.1.038/bin/icc
> > CC=/opt/intel/ict/2.0/mpi/2.0/bin/mpiicc
> > CFLAGS=-O
> >
> > # Location of perl . Used to generate the script fldiff, in ~ABINIT/ 
> > Utilities .
> > PERL=/usr/bin/perl
> >
> > # List of machine-dependent routines
> > MACHINE_DEP_C_SEQ_SUBS_LIST=etime.o
> >
> > ####################################################################
> > # For the parallel version : MPICH / MYRINET
> >
> > # Compiler flags and definitions
> > FFLAGS_PAR= $(FFLAGS) -I /opt/intel/ict/2.0/mpi/2.0/include
> >
> > # List of machine-dependent routines
> > MACHINE_DEP_C_PAR_SUBS_LIST=etime.par
> >
> > # Location of the MPI library
> > #MPI_A=/usr/local/mpi-intel/lib/libmpich.a /usr/local/mpi-intel/lib/ 
> > libfmpich.a
> > #-Vaxlib
> > #MPI_A=/opt/intel/ict/2.0/mpi/2.0/lib/libmpigi.a #/opt/intel/ict/ 
> > 2.0/mpi/2.0/lib/libmpiic.a #/opt/intel/ict/2.0/mpi/2.0/lib/ 
> > libmpiif.a #/opt/intel/ict/2.0/mpi/2.0/lib/libmpigf.a #/opt/intel/ 
> > ict/2.0/mpi/2.0/lib/libmpigc.a #/opt/intel/ict/2.0/mpi/2.0/lib/ 
> > libmpi.a -Vaxlib
> > # Include blas, lapack, and any other libraries here
> >  LIBS_PAR=$(LIBS) $(MPI_A)
> >
> > # This is a last line in makefile_macros ----------
> >
> 

Mr. Xavier

  The input file is bellow. I did not made the parallel tests. I think that I
have to make a few modifications the script "Run" due to changes in MPI2
(mpdboot, etc). So I
try to run tA.in as a regular job, but I am waiting in the queue.

  Thanks for your attention.

Marcelo Garcia
===============================================================
# PPV slab with 3 cells in 100 direction
# we are considering 10 angstrom of vaccum
# Auto consistencia somente


#Definition of the unit cell
acell  34.2  6.05  6.54  angstrom  # Lattice parameters with 10 angstrom of
vaccum in x direction
rprim  1.0000000000  0.000000000000  0.000000000000
       0.0000000000  0.838670561983 -0.544639008264
       0.0000000000  0.000000000000  1.000000000000 

#SCF preconditioner
iprcel 45

#Definition of the k-point grid 
kptopt 1          # Option for the automatic generation of k points, taking
                  # into account the symmetry
ngkpt  3 3 1  
nshiftk 1
shiftk  0.5 0.5 0.5
 
#Exchange-Correlation functional
ixc 1             # LDA Teter Pade parametrization

#Definition of the planewave basis set
ecut  30.0         # Maximal kinetic energy cut-off, in Hartree

#Definition of the SCF procedure
nstep 3          # Maximal number of SCF cycles
toldfe 1.0d-6
     
#Definition of the atom types
ntypat 2          # There is only one type of atom
znucl 6 1         # The keyword "znucl" refers to the atomic number of the 
                  # possible type(s) of atom. The pseudopotential(s) 
                  # mentioned in the "files" file must correspond
                  # to the type(s) of atom. Here, the only type is Carbon and
Hydrogen
                         

#Definition of the atoms
natom 84               # threre are 52 atoms in the unit cell and some vacuum
typat 48*1 36*2        # These atoms are of type 6 and 1, that is, Carbon and 
                       # Hydrogen respectively
xangst
8.354   -0.091   2.901   # C   
7.686   1.027   2.358   # C   
7.616   1.207   1.001   # C   
8.192   0.284   0.100   # C   
8.859   -0.834   0.643   # C   
8.930   -1.014   2.001   # C   
8.497   -0.315   4.298   # C   
8.050   0.509   5.283   # C   
4.449   2.791   4.543   # C   
3.706   1.723   3.999   # C   
3.585   1.576   2.641   # C   
4.197   2.477   1.743   # C   
4.940   3.545   2.286   # C   
5.061   3.692   3.645   # C   
4.600   3.011   -0.640   # C   
4.046   2.257   0.347   # C   
0.454   -0.091   2.901   # C   
-0.214   1.027   2.358   # C   
-0.284   1.207   1.001   # C   
0.292   0.284   0.100   # C   
0.959   -0.834   0.643   # C   
1.030   -1.014   2.001   # C   
0.597   -0.315   4.298   # C   
0.150   0.509   5.283   # C   
20.249   2.791   4.543   # C   
19.506   1.723   3.999   # C   
19.385   1.576   2.641   # C   
19.997   2.477   1.743   # C   
20.740   3.545   2.286   # C   
20.861   3.692   3.645   # C   
20.400   3.011   -0.640   # C   
19.846   2.257   0.347   # C   
16.254   -0.091   2.901   # C   
15.586   1.027   2.358   # C   
15.516   1.207   1.001   # C   
16.092   0.284   0.100   # C   
16.759   -0.834   0.643   # C   
16.830   -1.014   2.001   # C   
16.397   -0.315   4.298   # C   
15.950   0.509   5.283   # C   
12.349   2.791   4.543   # C   
11.606   1.723   3.999   # C   
11.485   1.576   2.641   # C   
12.097   2.477   1.743   # C   
12.840   3.545   2.286   # C   
12.961   3.692   3.645   # C   
12.500   3.011   -0.640   # C   
11.946   2.257   0.347   # C   
13.541   4.527   -2.523   # H   
11.332   1.387   0.074   # H   
13.114   3.880   -0.367   # H   
9.465   -1.879   2.410   # H   
7.212   1.763   3.017   # H   
7.082   2.073   0.591   # H   
7.524   1.434   5.007   # H   
9.023   -1.240   4.574   # H   
5.432   4.266   1.626   # H   
3.214   1.002   4.660   # H   
3.005   0.741   2.229   # H   
9.334   -1.569   6.564   # H   
5.641   4.527   -2.523   # H   
3.432   1.387   0.074   # H   
5.214   3.880   -0.367   # H   
1.565   -1.879   2.410   # H   
-0.688   1.763   3.017   # H   
-0.818   2.073   0.591   # H   
-0.376   1.434   5.007   # H   
1.123   -1.240   4.574   # H   
21.232   4.266   1.626   # H   
19.014   1.002   4.660   # H   
18.805   0.741   2.229   # H   
1.434   -1.569   6.564   # H   
21.441   4.527   -2.523   # H   
19.232   1.387   0.074   # H   
21.014   3.880   -0.367   # H   
17.365   -1.879   2.410   # H   
15.112   1.763   3.017   # H   
14.982   2.073   0.591   # H   
15.424   1.434   5.007   # H   
16.923   -1.240   4.574   # H   
13.332   4.266   1.626   # H   
11.114   1.002   4.660   # H   
10.905   0.741   2.229   # H   
17.234   -1.569   6.564   # H   
===========================================================================