The ABINIT Users Mailing List ( CLOSED )

[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 ----------