The ABINIT Users Mailing List ( CLOSED )

[mmgarcia@if.usp.br]

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 ----------