Elio,
it seems /opt/intel/composer_xe_2013_sp1/bin/compilervars.sh is only
available on your login/frontend nodes,
but not on your compute nodes.
you might be luckier with
/opt/intel/mkl/bin/mklvars.sh
an other option is to
ldd /home/emoujaes/Elie/SPRKKR/bin/kkrscf6.3MPI
on your login node, and explicitly set the LD_LIBRARY_PATH in your PBS
script
if /opt/intel/composer_xe_2013_sp1/mkl/lib/intel64 is available on your
compute nodes, you might want to append
-Wl,-rpath,/opt/intel/composer_xe_2013_sp1/mkl/lib/intel64
to LIB
/* if you do that, keep in mind you might not automatically use the most
up to date mkl lib when they get upgraded by your sysadmin */
Cheers,
Gilles
On 3/24/2016 11:03 AM, Elio Physics wrote:
Dear all,
I have been trying ,for the last week, compiling a code (SPRKKR). the
compilation went through ok. however, there are problems with the
executable (kkrscf6.3MPI) not finding the MKL library links. i could
not fix the problem..I have tried several things but in vain..I will
post both the "make" file and the "PBS" script file. Please can anyone
help me in this? the error I am getting is:
/opt/intel/composer_xe_2013_sp1/bin/compilervars.sh: No such file or
directory
/home/emoujaes/Elie/SPRKKR/bin/kkrscf6.3MPI: error while loading
shared libraries: libmkl_intel_lp64.so: cannot open shared object
file: No such file or directory
/home/emoujaes/Elie/SPRKKR/bin/kkrscf6.3MPI: error while loading
shared libraries: libmkl_intel_lp64.so: cannot open shared object
file: No such file or directory
/home/emoujaes/Elie/SPRKKR/bin/kkrscf6.3MPI: error while loading
shared libraries: libmkl_intel_lp64.so: cannot open shared object
file: No such file or directory
_make file :_
_
_
###############################################################################
# Here the common makefile starts which does depend on the
OS ####
###############################################################################
#
# FC: compiler name and common options e.g. f77 -c
# LINK: linker name and common options e.g. g77 -shared
# FFLAGS: optimization e.g. -O3
# OP0: force nooptimisation for some routiens e.g. -O0
# VERSION: additional string for executable e.g. 6.3.0
# LIB: library names e.g. -L/usr/lib -latlas -lblas -llapack
# (lapack and blas libraries are needed)
# BUILD_TYPE: string "debug" switches on debugging options
# (NOTE: you may call, e.g. "make scf BUILD_TYPE=debug"
# to produce executable with debugging flags from
command line)
# BIN: directory for executables
# INCLUDE: directory for include files
# (NOTE: directory with mpi include files has to be
properly set
# even for sequential executable)
###############################################################################
BUILD_TYPE ?=
#BUILD_TYPE := debug
VERSION = 6.3
ifeq ($(BUILD_TYPE), debug)
VERSION := $(VERSION)$(BUILD_TYPE)
endif
BIN =~/Elie/SPRKKR/bin
#BIN=~/bin
#BIN=/tmp/$(USER)
LIB = -L/opt/intel/composer_xe_2013_sp1/mkl/lib/intel64
-lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_core
-lmkl_sequential
# Include mpif.h
INCLUDE =-I/usr/include/openmpi-x86_64
#FFLAGS
FFLAGS = -O2
FC = mpif90 -c $(FFLAGS) $(INCLUDE)
LINK = mpif90 $(FFLAGS) $(INCLUDE)
MPI=MPI
_PBS script:_
_
_
BIN =~/Elie/SPRKKR/bin
#BIN=~/bin
#BIN=/tmp/$(USER)
LIB = -L/opt/intel/composer_xe_2013_sp1/mkl/lib/intel64
-lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_core
-lmkl_sequential
# Include mpif.h
INCLUDE =-I/usr/include/openmpi-x86_64
#FFLAGS
FFLAGS = -O2
FC = mpif90 -c $(FFLAGS) $(INCLUDE)
LINK = mpif90 $(FFLAGS) $(INCLUDE)
MPI=MPI
[emoujaes@jlborges SPRKKR]$ cd Fe
[emoujaes@jlborges Fe]$ ls
Fe.inp Fe.pbs Fescf.e50505 Fescf.o50505
scf-50505.jlborges.fisica.ufmg.br.out
[emoujaes@jlborges Fe]$ more Fe.pbs
#PBS -S /bin/bash
#PBS -l nodes=1:ppn=8
#PBS -l walltime=70:00:00
#PBS -N Fescf
# procura o nome o input baseado no nome do job (linha #PBS -N xxx acima).
INP=Fe.inp
OUT=scf-$PBS_JOBID.out
## Configura o no de calculo
source /opt/intel/composer_xe_2013_sp1/bin/compilervars.sh
module load libraries/openmpi-1.5.4/gnu-4.4
#ormacoes do job no arquivo de saida
qstat -an -u $USER
cat $PBS_NODEFILE
########################################
#------- Inicio do trabalho ----- #
########################################
## executa o programa
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=1
mpirun ~/Elie/SPRKKR/bin/kkrscf6.3MPI $INP > $OUT
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