Dear Gilles,
thanks for your reply and your options. I have tried the first option, hich for me basically is the easiest. I have compiled using "make.inc" but now setting LIB = -L/opt/intel/mkl/lib/intel64 -lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential Every went well. Then I tried the PBS script wjere I have added these two lines: source /opt/intel/mkl/bin/mklvars.sh export LD_LIBRARY_PATH=/opt/intel/mkl/bin/mklvars.sh But i still get the same error: /opt/intel/mkl/bin/mklvars.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 I just cannot understand why is it giving the same error and why it could not find the file : /opt/intel/mkl/bin/mklvars.sh although the link is true! Any advice please? Thanks ________________________________ From: users <users-boun...@open-mpi.org> on behalf of Gilles Gouaillardet <gil...@rist.or.jp> Sent: Thursday, March 24, 2016 12:22 AM To: Open MPI Users Subject: Re: [OMPI users] Problems in compiling a code with dynamic linking 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 _______________________________________________ users mailing list us...@open-mpi.org<mailto:us...@open-mpi.org> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users Link to this post: http://www.open-mpi.org/community/lists/users/2016/03/28812.php
