Thanks, I was able to compile without openmp now. The siesta-ldau bug I found is still there though (see next mail/thread).
Giovanni ________________________________________ De : siesta-l-requ...@uam.es [siesta-l-requ...@uam.es] de la part de Herbert Fruchtl [herbert.fruc...@st-andrews.ac.uk] Envoyé : mardi 13 mai 2014 14:55 À : siesta-l@uam.es Objet : Re: [SIESTA-L] compiling Siesta in parallel with intelmpi You need the sequential mkl. Here's my BLAS line: BLAS_LIBS= -L/usr/local/intel/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core Herbert On 13/05/14 13:42, Borghi Giovanni wrote: > Ok below an arch.make which works, and lets siesta run in parallel, > apparently -openmp is required, otherwise I get errors of the type (full > output included below the arch.make) > > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_dispatch_fini_8' > > kmpc appears to be library coming with openmp. > > *********************************************************************** > SIESTA_ARCH=x86_64-unknown-linux-gnu--Intel > > FPP= > FPP_OUTPUT= > FC=mpiifort > RANLIB=ranlib > > SYS=nag > > SP_KIND=4 > DP_KIND=8 > KINDS=$(SP_KIND) $(DP_KIND) > > FFLAGS=-g -check all -traceback -openmp > FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT > LDFLAGS=-static-intel -openmp > > ARFLAGS_EXTRA= > > FCFLAGS_fixed_f= > FCFLAGS_free_f90= > FPPFLAGS_fixed_F= > FPPFLAGS_free_F90= > > BLAS_LIBS=-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core > LAPACK_LIBS=-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core > BLACS_LIBS=-lmkl_blacs_lp64 -lmkl_blacs_intelmpi_lp64 > SCALAPACK_LIBS= -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 > > COMP_LIBS=dc_lapack.a > > NETCDF_LIBS= > NETCDF_INTERFACE= > > LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) > $(NETCDF_LIBS) > > #SIESTA needs an F90 interface to MPI > #This will give you SIESTA's own implementation > #If your compiler vendor offers an alternative, you may change > #to it here. > #MPI_INTERFACE=/opt/intel/impi/4.0.3.008/intel64/lib/libmpiif.a > MPI_INTERFACE=libmpi_f90.a > MPI_INCLUDE=. > > ************************************************************************************************************* > > siesta.o: In function `siesta': > /home/borghi/marzari/siesta/siesta-ldau/Src/siesta.F:1: undefined reference > to `__kmpc_begin' > /home/borghi/marzari/siesta/siesta-ldau/Src/siesta.F:37: undefined reference > to `__kmpc_end' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_ok_to_fork' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_end_single' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_ordered' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_for_static_init_8' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `omp_get_thread_num' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_barrier' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `omp_get_num_threads' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `omp_get_num_procs' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_dispatch_next_4' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_end_reduce_nowait' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_critical' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_dispatch_fini_8' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_atomic_cmplx8_add' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_atomic_float4_add' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_serialized_parallel' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_end_critical' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_dispatch_init_8' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `ompc_set_nested' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `omp_get_nested' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_dispatch_fini_4' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `omp_in_parallel' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_push_num_threads' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_reduce_nowait' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `omp_get_max_threads' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_for_static_init_4' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_end_serialized_parallel' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_flush' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_single' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_dispatch_next_8' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_atomic_float8_add' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_dispatch_init_4' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_global_thread_num' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_end_ordered' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_fork_call' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_atomic_fixed8_add' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_for_static_fini' > /opt/intel/composer_xe_2011_sp1.6.233/mkl/lib/intel64/libmkl_intel_thread.so: > undefined reference to `__kmpc_atomic_cmplx4_add' > > ________________________________________ > De : siesta-l-requ...@uam.es [siesta-l-requ...@uam.es] de la part de Nick > Papior Andersen [nickpap...@gmail.com] > Envoyé : mardi 13 mai 2014 10:57 > À : siesta-l@uam.es > Objet : Re: [SIESTA-L] compiling Siesta in parallel with intelmpi > > Add -DMPI to FPPFLAGS > and try again... > > > 2014-05-13 7:48 GMT+00:00 Borghi Giovanni > <giovanni.bor...@epfl.ch<mailto:giovanni.bor...@epfl.ch>>: > Dear all, > > I am trying to compile Siesta in parallel using intel mpi and mpiifort. > However, when running with > > mpirun -np 6 siesta_rootdir/Obj/siesta > > The code starts in serial mode. > Can anyone suggest me what is wrong? Does anyone have an example arch.make I > may > draw inspiration from? > I paste the main part of the arch.make below... > Thank you very much! > Giovanni > > ******************************************************************************* > SIESTA_ARCH=x86_64-unknown-linux-gnu--unknown > > FPP= > FPP_OUTPUT= > FC=mpiifort > RANLIB=ranlib > > SYS=nag > > SP_KIND=4 > DP_KIND=8 > KINDS=$(SP_KIND) $(DP_KIND) > > FFLAGS= -O2 -openmp > FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT > LDFLAGS= -static-intel -openmp > > ARFLAGS_EXTRA= > > FCFLAGS_fixed_f= > FCFLAGS_free_f90= > FPPFLAGS_fixed_F= > FPPFLAGS_free_F90= > > BLAS_LIBS=-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core > LAPACK_LIBS=-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core > BLACS_LIBS=-lmkl_blacs_lp64 -lmkl_blacs_intelmpi_lp64 > SCALAPACK_LIBS= -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 > > COMP_LIBS=dc_lapack.a > > NETCDF_LIBS= > NETCDF_INTERFACE= > > LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) > $(NETCDF_LIBS) > > #SIESTA needs an F90 interface to MPI > #This will give you SIESTA's own implementation > #If your compiler vendor offers an alternative, you may change > #to it here. > #MPI_INTERFACE=/opt/intel/impi/4.0.3.008/intel64/lib/libmpiif.a<http://4.0.3.008/intel64/lib/libmpiif.a> > MPI_INTERFACE=/usr/lib/openmpi/lib/libmpi_f90.a > MPI_INCLUDE=/opt/intel/impi/4.0.3.008/intel64/include/<http://4.0.3.008/intel64/include/> > > > > -- > Kind regards Nick > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532
