Re: [SIESTA-L] List removal
If you want to unsubscribe from the mailing list you should follow these guidelines: http://departments.icmab.es/leem/siesta/Documentation/list.html Otherwise you may unsubscribe on this page: https://listas-correo.uam.es/sympa/sigrequest/siesta-l 2016-09-23 16:20 GMT+02:00 Salvador Cardona Serra: > Can you please remove me from the mail-list? > > Thanks. > > > -- Kind regards Nick
Re: [SIESTA-L] << compiling siesta-4.1-b1 with NetCDF >>
It should be placed at the end of the arch.make. Try the attached arch.make file. 2016-09-23 16:15 GMT+02:00 I. Camps: > Sorry, it didn't work :( > > > []'s, > > Camps > > On Fri, Sep 23, 2016 at 11:09 AM, Nick Papior > wrote: > >> Ah, ok. Now I see. >> >> You should (both) do this in your arch.make. >> >> You may track it on launchpad: https://bugs.launch >> pad.net/siesta/+bug/1627041 >> >> The easy fix is this: >> >> FFLAGS += $(INCFLAGS) $(NETCDF_INCFLAGS) >> >> which should work (disclaimer I haven't tested this). >> >> 2016-09-23 15:54 GMT+02:00 I. Camps : >> >>> Yes, I compiled everything with the same intel compiler. >>> >>> >>> []'s, >>> >>> Camps >>> >>> On Fri, Sep 23, 2016 at 10:51 AM, Nick Papior >>> wrote: >>> Have you compiled the netcdf and hdf5 with the same intel compiler? That is necessary. Sadly, this is one of the inconveniences of fortran. 2016-09-23 15:23 GMT+02:00 I. Camps : > Here is the arch.make: > ## > # source /opt/intel/parallel_studio_xe_2015/psxevars.sh > # source /opt/intel/parallel_studio_xe_2017.0.035/psxevars.sh > # source /opt/intel/Compiler/11.0/083/bin/ifortvars.sh intel64 > # source /opt/intel/impi_5.0.2/bin64/mpivars.sh > # This file is part of the SIESTA package. > # > # Copyright (c) Fundacion General Universidad Autonoma de Madrid: > # E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal > # and J.M.Soler, 1996- . > # > # Use of this software constitutes agreement with the full conditions > # given in the SIESTA license, as signed by all legitimate users. > # > # > # Description: > # Intel compiler/mkl V11 on atto > # OpenMPI with support for Intel compiler V11 > # MKL V11 libraries, including a version of BLACS provided > # by Intel for the openmpi framework, > # and Intel's own Scalapack, Lapack, and > BLAS. > # > # Execution: > # > # $(OPENMPI_ROOT)/bin in PATH > # $(OPENMPI_ROOT)/lib in LD_LIBRARY_PATH > # > # mpirun -np NPROCS siesta > # > SIESTA_ARCH=intel-mpi > # > # > FC=mpiifort > FC_SERIAL=ifort > > # > # You can play with other optimization options > # I am not sure whether the compiler attempts to multithread the code > # > FFLAGS= -w -O2 -mp > FFLAGS_CHECKS=-g -O0 -debug full -traceback -C > FFLAGS_DEBUG= -g > LDFLAGS= > #COMP_LIBS += libncdf.a libfdict.a > RANLIB=echo > # > # You might want to turn off FoX for Intel11 > # > DUMMY_FOX=--enable-dummy > # > # > NETCDF_ROOT=/software/lib/netcdf > NETCDF_INCFLAGS=-I$(NETCDF_ROOT)/include > NETCDF_LIBS=-L$(NETCDF_ROOT)/lib64 -lnetcdff -lnetcdf > HDF5_ROOT=/software/lib/hdf5 > LIBS +=-L$(HDF5_ROOT)/lib64 -lhdf5_fortran -lhdf5 -lz > FPPFLAGS_CDF=-DCDF -DNCDF_4 -DNCDF_PARALLEL > # > MPI_INTERFACE=libmpi_f90.a > MPI_INCLUDE=. # Note . for no-op > FPPFLAGS_MPI=-DMPI > > METIS_LIB=/software/lib/metis/lib/libmetis.a > FPPFLAGS += -DSIESTA__METIS > > # > # From the "Intel advisor" > # > #MKLPATH=/opt/intel/composer_xe_2015/mkl/lib/intel64 > #MKLPATH=/opt/intel/Compiler/11.0/083/mkl/lib/em64t > MKLPATH=/opt/intel/compilers_and_libraries_2017.0.098/linux/ > mkl/lib/intel64_lin > SUGGESTED_LIBS=$(MKLPATH)/libmkl_scalapack_lp64.a \ >-Wl,--start-group \ > $(MKLPATH)/libmkl_intel_lp64.a \ > $(MKLPATH)/libmkl_sequential.a \ > $(MKLPATH)/libmkl_core.a \ > $(MKLPATH)/libmkl_blacs_intelmpi_lp64.a \ >-Wl,--end-group \ >-lpthread > # > COMP_LIBS += libncdf.a libfdict.a > > LIBS=$(SUGGESTED_LIBS) $(NETCDF_LIBS) $(COMP_LIBS) $(METIS_LIB) > # > SYS=nag > FPPFLAGS= $(FPPFLAGS_CDF) $(FPPFLAGS_MPI) > INCFLAGS +=$(NETCDF_INCFLAGS) > # > .F.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< > .f.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $< > .F90.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< > .f90.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< > # > > ## > > > > []'s, > > Camps > > On Fri, Sep 23, 2016 at 2:58 AM, Nick Papior > wrote: > >> Please attach your entire arch.make file. There are a few unknowns in >> your compilation process. >> >> >> >> 2016-09-23 2:52 GMT+02:00 I. Camps : >> >>> Hello, >>> >>> I am trying to compile siesta-4.1-b1
[SIESTA-L] List removal
Can you please remove me from the mail-list? Thanks.
Re: [SIESTA-L] << compiling siesta-4.1-b1 with NetCDF >>
Sorry, it didn't work :( []'s, Camps On Fri, Sep 23, 2016 at 11:09 AM, Nick Papiorwrote: > Ah, ok. Now I see. > > You should (both) do this in your arch.make. > > You may track it on launchpad: https://bugs.launchpad.net/siesta/+bug/ > 1627041 > > The easy fix is this: > > FFLAGS += $(INCFLAGS) $(NETCDF_INCFLAGS) > > which should work (disclaimer I haven't tested this). > > 2016-09-23 15:54 GMT+02:00 I. Camps : > >> Yes, I compiled everything with the same intel compiler. >> >> >> []'s, >> >> Camps >> >> On Fri, Sep 23, 2016 at 10:51 AM, Nick Papior >> wrote: >> >>> Have you compiled the netcdf and hdf5 with the same intel compiler? That >>> is necessary. >>> >>> Sadly, this is one of the inconveniences of fortran. >>> >>> 2016-09-23 15:23 GMT+02:00 I. Camps : >>> Here is the arch.make: ## # source /opt/intel/parallel_studio_xe_2015/psxevars.sh # source /opt/intel/parallel_studio_xe_2017.0.035/psxevars.sh # source /opt/intel/Compiler/11.0/083/bin/ifortvars.sh intel64 # source /opt/intel/impi_5.0.2/bin64/mpivars.sh # This file is part of the SIESTA package. # # Copyright (c) Fundacion General Universidad Autonoma de Madrid: # E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal # and J.M.Soler, 1996- . # # Use of this software constitutes agreement with the full conditions # given in the SIESTA license, as signed by all legitimate users. # # # Description: # Intel compiler/mkl V11 on atto # OpenMPI with support for Intel compiler V11 # MKL V11 libraries, including a version of BLACS provided # by Intel for the openmpi framework, # and Intel's own Scalapack, Lapack, and BLAS. # # Execution: # # $(OPENMPI_ROOT)/bin in PATH # $(OPENMPI_ROOT)/lib in LD_LIBRARY_PATH # # mpirun -np NPROCS siesta # SIESTA_ARCH=intel-mpi # # FC=mpiifort FC_SERIAL=ifort # # You can play with other optimization options # I am not sure whether the compiler attempts to multithread the code # FFLAGS= -w -O2 -mp FFLAGS_CHECKS=-g -O0 -debug full -traceback -C FFLAGS_DEBUG= -g LDFLAGS= #COMP_LIBS += libncdf.a libfdict.a RANLIB=echo # # You might want to turn off FoX for Intel11 # DUMMY_FOX=--enable-dummy # # NETCDF_ROOT=/software/lib/netcdf NETCDF_INCFLAGS=-I$(NETCDF_ROOT)/include NETCDF_LIBS=-L$(NETCDF_ROOT)/lib64 -lnetcdff -lnetcdf HDF5_ROOT=/software/lib/hdf5 LIBS +=-L$(HDF5_ROOT)/lib64 -lhdf5_fortran -lhdf5 -lz FPPFLAGS_CDF=-DCDF -DNCDF_4 -DNCDF_PARALLEL # MPI_INTERFACE=libmpi_f90.a MPI_INCLUDE=. # Note . for no-op FPPFLAGS_MPI=-DMPI METIS_LIB=/software/lib/metis/lib/libmetis.a FPPFLAGS += -DSIESTA__METIS # # From the "Intel advisor" # #MKLPATH=/opt/intel/composer_xe_2015/mkl/lib/intel64 #MKLPATH=/opt/intel/Compiler/11.0/083/mkl/lib/em64t MKLPATH=/opt/intel/compilers_and_libraries_2017.0.098/linux/ mkl/lib/intel64_lin SUGGESTED_LIBS=$(MKLPATH)/libmkl_scalapack_lp64.a \ -Wl,--start-group \ $(MKLPATH)/libmkl_intel_lp64.a \ $(MKLPATH)/libmkl_sequential.a \ $(MKLPATH)/libmkl_core.a \ $(MKLPATH)/libmkl_blacs_intelmpi_lp64.a \ -Wl,--end-group \ -lpthread # COMP_LIBS += libncdf.a libfdict.a LIBS=$(SUGGESTED_LIBS) $(NETCDF_LIBS) $(COMP_LIBS) $(METIS_LIB) # SYS=nag FPPFLAGS= $(FPPFLAGS_CDF) $(FPPFLAGS_MPI) INCFLAGS +=$(NETCDF_INCFLAGS) # .F.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< .f.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $< .F90.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< .f90.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< # ## []'s, Camps On Fri, Sep 23, 2016 at 2:58 AM, Nick Papior wrote: > Please attach your entire arch.make file. There are a few unknowns in > your compilation process. > > > > 2016-09-23 2:52 GMT+02:00 I. Camps : > >> Hello, >> >> I am trying to compile siesta-4.1-b1 with NetCDF4 but I am getting >> into troubles :( >> >> The errors are (my system info is bellow): >> >> mpiifort -E -P -x c -DCDF -DNCDF_4 -DMPI -DNCDF_PARALLEL -I. >> -I/home/icamps/Temp/SIESTA/siesta-4.1-b1/Src/NCDF/src >>
Re: [SIESTA-L] << compiling siesta-4.1-b1 with NetCDF >>
Yes, I compiled everything with the same intel compiler. []'s, Camps On Fri, Sep 23, 2016 at 10:51 AM, Nick Papiorwrote: > Have you compiled the netcdf and hdf5 with the same intel compiler? That > is necessary. > > Sadly, this is one of the inconveniences of fortran. > > 2016-09-23 15:23 GMT+02:00 I. Camps : > >> Here is the arch.make: >> ## >> # source /opt/intel/parallel_studio_xe_2015/psxevars.sh >> # source /opt/intel/parallel_studio_xe_2017.0.035/psxevars.sh >> # source /opt/intel/Compiler/11.0/083/bin/ifortvars.sh intel64 >> # source /opt/intel/impi_5.0.2/bin64/mpivars.sh >> # This file is part of the SIESTA package. >> # >> # Copyright (c) Fundacion General Universidad Autonoma de Madrid: >> # E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal >> # and J.M.Soler, 1996- . >> # >> # Use of this software constitutes agreement with the full conditions >> # given in the SIESTA license, as signed by all legitimate users. >> # >> # >> # Description: >> # Intel compiler/mkl V11 on atto >> # OpenMPI with support for Intel compiler V11 >> # MKL V11 libraries, including a version of BLACS provided >> # by Intel for the openmpi framework, >> # and Intel's own Scalapack, Lapack, and BLAS. >> # >> # Execution: >> # >> # $(OPENMPI_ROOT)/bin in PATH >> # $(OPENMPI_ROOT)/lib in LD_LIBRARY_PATH >> # >> # mpirun -np NPROCS siesta >> # >> SIESTA_ARCH=intel-mpi >> # >> # >> FC=mpiifort >> FC_SERIAL=ifort >> >> # >> # You can play with other optimization options >> # I am not sure whether the compiler attempts to multithread the code >> # >> FFLAGS= -w -O2 -mp >> FFLAGS_CHECKS=-g -O0 -debug full -traceback -C >> FFLAGS_DEBUG= -g >> LDFLAGS= >> #COMP_LIBS += libncdf.a libfdict.a >> RANLIB=echo >> # >> # You might want to turn off FoX for Intel11 >> # >> DUMMY_FOX=--enable-dummy >> # >> # >> NETCDF_ROOT=/software/lib/netcdf >> NETCDF_INCFLAGS=-I$(NETCDF_ROOT)/include >> NETCDF_LIBS=-L$(NETCDF_ROOT)/lib64 -lnetcdff -lnetcdf >> HDF5_ROOT=/software/lib/hdf5 >> LIBS +=-L$(HDF5_ROOT)/lib64 -lhdf5_fortran -lhdf5 -lz >> FPPFLAGS_CDF=-DCDF -DNCDF_4 -DNCDF_PARALLEL >> # >> MPI_INTERFACE=libmpi_f90.a >> MPI_INCLUDE=. # Note . for no-op >> FPPFLAGS_MPI=-DMPI >> >> METIS_LIB=/software/lib/metis/lib/libmetis.a >> FPPFLAGS += -DSIESTA__METIS >> >> # >> # From the "Intel advisor" >> # >> #MKLPATH=/opt/intel/composer_xe_2015/mkl/lib/intel64 >> #MKLPATH=/opt/intel/Compiler/11.0/083/mkl/lib/em64t >> MKLPATH=/opt/intel/compilers_and_libraries_2017.0.098/linux/ >> mkl/lib/intel64_lin >> SUGGESTED_LIBS=$(MKLPATH)/libmkl_scalapack_lp64.a \ >>-Wl,--start-group \ >> $(MKLPATH)/libmkl_intel_lp64.a \ >> $(MKLPATH)/libmkl_sequential.a \ >> $(MKLPATH)/libmkl_core.a \ >> $(MKLPATH)/libmkl_blacs_intelmpi_lp64.a \ >>-Wl,--end-group \ >>-lpthread >> # >> COMP_LIBS += libncdf.a libfdict.a >> >> LIBS=$(SUGGESTED_LIBS) $(NETCDF_LIBS) $(COMP_LIBS) $(METIS_LIB) >> # >> SYS=nag >> FPPFLAGS= $(FPPFLAGS_CDF) $(FPPFLAGS_MPI) >> INCFLAGS +=$(NETCDF_INCFLAGS) >> # >> .F.o: >> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< >> .f.o: >> $(FC) -c $(FFLAGS) $(INCFLAGS) $< >> .F90.o: >> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< >> .f90.o: >> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< >> # >> >> ## >> >> >> >> []'s, >> >> Camps >> >> On Fri, Sep 23, 2016 at 2:58 AM, Nick Papior >> wrote: >> >>> Please attach your entire arch.make file. There are a few unknowns in >>> your compilation process. >>> >>> >>> >>> 2016-09-23 2:52 GMT+02:00 I. Camps : >>> Hello, I am trying to compile siesta-4.1-b1 with NetCDF4 but I am getting into troubles :( The errors are (my system info is bellow): mpiifort -E -P -x c -DCDF -DNCDF_4 -DMPI -DNCDF_PARALLEL -I. -I/home/icamps/Temp/SIESTA/siesta-4.1-b1/Src/NCDF/src /home/icamps/Temp/SIESTA/siesta-4.1-b1/Src/NCDF/src/nf_ncdf.F90 | sed -e 's/NEWLINE/\n/g;/^$/d;/^\!.*&/d; s/[[:space:]]*##[[:space:]]*\([^[:space:]]*\)/\1/g; s/[[:space:]]*#\([^i][^[:space:]]*\)/"\1"/g; s:/ /://:g; s/"endif"/\n#endif/g' > nf_ncdf.f90 #2> /dev/null ifort: command line warning #10155: ignoring option '-x'; argument required ifort: error #10236: File not found: 'c' mpiifort -c -w -O2 -mp -I../../nf_ncdf.f90 nf_ncdf.f90(59): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [NETCDF] use netcdf --^ nf_ncdf.f90(95): error #8237: The character length in a component declaration shall either be a colon, be an initialization expression, or be a specification
Re: [SIESTA-L] << compiling siesta-4.1-b1 with NetCDF >>
Have you compiled the netcdf and hdf5 with the same intel compiler? That is necessary. Sadly, this is one of the inconveniences of fortran. 2016-09-23 15:23 GMT+02:00 I. Camps: > Here is the arch.make: > ## > # source /opt/intel/parallel_studio_xe_2015/psxevars.sh > # source /opt/intel/parallel_studio_xe_2017.0.035/psxevars.sh > # source /opt/intel/Compiler/11.0/083/bin/ifortvars.sh intel64 > # source /opt/intel/impi_5.0.2/bin64/mpivars.sh > # This file is part of the SIESTA package. > # > # Copyright (c) Fundacion General Universidad Autonoma de Madrid: > # E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal > # and J.M.Soler, 1996- . > # > # Use of this software constitutes agreement with the full conditions > # given in the SIESTA license, as signed by all legitimate users. > # > # > # Description: > # Intel compiler/mkl V11 on atto > # OpenMPI with support for Intel compiler V11 > # MKL V11 libraries, including a version of BLACS provided > # by Intel for the openmpi framework, > # and Intel's own Scalapack, Lapack, and BLAS. > # > # Execution: > # > # $(OPENMPI_ROOT)/bin in PATH > # $(OPENMPI_ROOT)/lib in LD_LIBRARY_PATH > # > # mpirun -np NPROCS siesta > # > SIESTA_ARCH=intel-mpi > # > # > FC=mpiifort > FC_SERIAL=ifort > > # > # You can play with other optimization options > # I am not sure whether the compiler attempts to multithread the code > # > FFLAGS= -w -O2 -mp > FFLAGS_CHECKS=-g -O0 -debug full -traceback -C > FFLAGS_DEBUG= -g > LDFLAGS= > #COMP_LIBS += libncdf.a libfdict.a > RANLIB=echo > # > # You might want to turn off FoX for Intel11 > # > DUMMY_FOX=--enable-dummy > # > # > NETCDF_ROOT=/software/lib/netcdf > NETCDF_INCFLAGS=-I$(NETCDF_ROOT)/include > NETCDF_LIBS=-L$(NETCDF_ROOT)/lib64 -lnetcdff -lnetcdf > HDF5_ROOT=/software/lib/hdf5 > LIBS +=-L$(HDF5_ROOT)/lib64 -lhdf5_fortran -lhdf5 -lz > FPPFLAGS_CDF=-DCDF -DNCDF_4 -DNCDF_PARALLEL > # > MPI_INTERFACE=libmpi_f90.a > MPI_INCLUDE=. # Note . for no-op > FPPFLAGS_MPI=-DMPI > > METIS_LIB=/software/lib/metis/lib/libmetis.a > FPPFLAGS += -DSIESTA__METIS > > # > # From the "Intel advisor" > # > #MKLPATH=/opt/intel/composer_xe_2015/mkl/lib/intel64 > #MKLPATH=/opt/intel/Compiler/11.0/083/mkl/lib/em64t > MKLPATH=/opt/intel/compilers_and_libraries_2017.0.098/ > linux/mkl/lib/intel64_lin > SUGGESTED_LIBS=$(MKLPATH)/libmkl_scalapack_lp64.a \ >-Wl,--start-group \ > $(MKLPATH)/libmkl_intel_lp64.a \ > $(MKLPATH)/libmkl_sequential.a \ > $(MKLPATH)/libmkl_core.a \ > $(MKLPATH)/libmkl_blacs_intelmpi_lp64.a \ >-Wl,--end-group \ >-lpthread > # > COMP_LIBS += libncdf.a libfdict.a > > LIBS=$(SUGGESTED_LIBS) $(NETCDF_LIBS) $(COMP_LIBS) $(METIS_LIB) > # > SYS=nag > FPPFLAGS= $(FPPFLAGS_CDF) $(FPPFLAGS_MPI) > INCFLAGS +=$(NETCDF_INCFLAGS) > # > .F.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< > .f.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $< > .F90.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< > .f90.o: > $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< > # > > ## > > > > []'s, > > Camps > > On Fri, Sep 23, 2016 at 2:58 AM, Nick Papior wrote: > >> Please attach your entire arch.make file. There are a few unknowns in >> your compilation process. >> >> >> >> 2016-09-23 2:52 GMT+02:00 I. Camps : >> >>> Hello, >>> >>> I am trying to compile siesta-4.1-b1 with NetCDF4 but I am getting into >>> troubles :( >>> >>> The errors are (my system info is bellow): >>> >>> mpiifort -E -P -x c -DCDF -DNCDF_4 -DMPI -DNCDF_PARALLEL -I. >>> -I/home/icamps/Temp/SIESTA/siesta-4.1-b1/Src/NCDF/src >>> /home/icamps/Temp/SIESTA/siesta-4.1-b1/Src/NCDF/src/nf_ncdf.F90 | sed >>> -e 's/NEWLINE/\n/g;/^$/d;/^\!.*&/d; >>> s/[[:space:]]*##[[:space:]]*\([^[:space:]]*\)/\1/g; >>> s/[[:space:]]*#\([^i][^[:space:]]*\)/"\1"/g; s:/ /://:g; >>> s/"endif"/\n#endif/g' > nf_ncdf.f90 #2> /dev/null >>> ifort: command line warning #10155: ignoring option '-x'; argument >>> required >>> ifort: error #10236: File not found: 'c' >>> mpiifort -c -w -O2 -mp -I../../nf_ncdf.f90 >>> nf_ncdf.f90(59): error #7002: Error in opening the compiled module >>> file. Check INCLUDE paths. [NETCDF] >>> use netcdf >>> --^ >>> nf_ncdf.f90(95): error #8237: The character length in a component >>> declaration shall either be a colon, be an initialization expression, or be >>> a specification expression. [GRP] >>> character(len=NF90_MAX_NAME) :: grp = " " >>> -^ >>> nf_ncdf.f90(95): error #6404: This name does not have a type, and must >>> have an explicit type. [NF90_MAX_NAME] >>> character(len=NF90_MAX_NAME) :: grp = " " >>> ---^ >>>
Re: [SIESTA-L] << compiling siesta-4.1-b1 with NetCDF >>
Here is the arch.make: ## # source /opt/intel/parallel_studio_xe_2015/psxevars.sh # source /opt/intel/parallel_studio_xe_2017.0.035/psxevars.sh # source /opt/intel/Compiler/11.0/083/bin/ifortvars.sh intel64 # source /opt/intel/impi_5.0.2/bin64/mpivars.sh # This file is part of the SIESTA package. # # Copyright (c) Fundacion General Universidad Autonoma de Madrid: # E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal # and J.M.Soler, 1996- . # # Use of this software constitutes agreement with the full conditions # given in the SIESTA license, as signed by all legitimate users. # # # Description: # Intel compiler/mkl V11 on atto # OpenMPI with support for Intel compiler V11 # MKL V11 libraries, including a version of BLACS provided # by Intel for the openmpi framework, # and Intel's own Scalapack, Lapack, and BLAS. # # Execution: # # $(OPENMPI_ROOT)/bin in PATH # $(OPENMPI_ROOT)/lib in LD_LIBRARY_PATH # # mpirun -np NPROCS siesta # SIESTA_ARCH=intel-mpi # # FC=mpiifort FC_SERIAL=ifort # # You can play with other optimization options # I am not sure whether the compiler attempts to multithread the code # FFLAGS= -w -O2 -mp FFLAGS_CHECKS=-g -O0 -debug full -traceback -C FFLAGS_DEBUG= -g LDFLAGS= #COMP_LIBS += libncdf.a libfdict.a RANLIB=echo # # You might want to turn off FoX for Intel11 # DUMMY_FOX=--enable-dummy # # NETCDF_ROOT=/software/lib/netcdf NETCDF_INCFLAGS=-I$(NETCDF_ROOT)/include NETCDF_LIBS=-L$(NETCDF_ROOT)/lib64 -lnetcdff -lnetcdf HDF5_ROOT=/software/lib/hdf5 LIBS +=-L$(HDF5_ROOT)/lib64 -lhdf5_fortran -lhdf5 -lz FPPFLAGS_CDF=-DCDF -DNCDF_4 -DNCDF_PARALLEL # MPI_INTERFACE=libmpi_f90.a MPI_INCLUDE=. # Note . for no-op FPPFLAGS_MPI=-DMPI METIS_LIB=/software/lib/metis/lib/libmetis.a FPPFLAGS += -DSIESTA__METIS # # From the "Intel advisor" # #MKLPATH=/opt/intel/composer_xe_2015/mkl/lib/intel64 #MKLPATH=/opt/intel/Compiler/11.0/083/mkl/lib/em64t MKLPATH=/opt/intel/compilers_and_libraries_2017.0.098/linux/mkl/lib/intel64_lin SUGGESTED_LIBS=$(MKLPATH)/libmkl_scalapack_lp64.a \ -Wl,--start-group \ $(MKLPATH)/libmkl_intel_lp64.a \ $(MKLPATH)/libmkl_sequential.a \ $(MKLPATH)/libmkl_core.a \ $(MKLPATH)/libmkl_blacs_intelmpi_lp64.a \ -Wl,--end-group \ -lpthread # COMP_LIBS += libncdf.a libfdict.a LIBS=$(SUGGESTED_LIBS) $(NETCDF_LIBS) $(COMP_LIBS) $(METIS_LIB) # SYS=nag FPPFLAGS= $(FPPFLAGS_CDF) $(FPPFLAGS_MPI) INCFLAGS +=$(NETCDF_INCFLAGS) # .F.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< .f.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $< .F90.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< .f90.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $< # ## []'s, Camps On Fri, Sep 23, 2016 at 2:58 AM, Nick Papiorwrote: > Please attach your entire arch.make file. There are a few unknowns in your > compilation process. > > > > 2016-09-23 2:52 GMT+02:00 I. Camps : > >> Hello, >> >> I am trying to compile siesta-4.1-b1 with NetCDF4 but I am getting into >> troubles :( >> >> The errors are (my system info is bellow): >> >> mpiifort -E -P -x c -DCDF -DNCDF_4 -DMPI -DNCDF_PARALLEL -I. >> -I/home/icamps/Temp/SIESTA/siesta-4.1-b1/Src/NCDF/src >> /home/icamps/Temp/SIESTA/siesta-4.1-b1/Src/NCDF/src/nf_ncdf.F90 | sed -e >> 's/NEWLINE/\n/g;/^$/d;/^\!.*&/d; >> s/[[:space:]]*##[[:space:]]*\([^[:space:]]*\)/\1/g; >> s/[[:space:]]*#\([^i][^[:space:]]*\)/"\1"/g; s:/ /://:g; >> s/"endif"/\n#endif/g' > nf_ncdf.f90 #2> /dev/null >> ifort: command line warning #10155: ignoring option '-x'; argument >> required >> ifort: error #10236: File not found: 'c' >> mpiifort -c -w -O2 -mp -I../../nf_ncdf.f90 >> nf_ncdf.f90(59): error #7002: Error in opening the compiled module file. >> Check INCLUDE paths. [NETCDF] >> use netcdf >> --^ >> nf_ncdf.f90(95): error #8237: The character length in a component >> declaration shall either be a colon, be an initialization expression, or be >> a specification expression. [GRP] >> character(len=NF90_MAX_NAME) :: grp = " " >> -^ >> nf_ncdf.f90(95): error #6404: This name does not have a type, and must >> have an explicit type. [NF90_MAX_NAME] >> character(len=NF90_MAX_NAME) :: grp = " " >> ---^ >> nf_ncdf.f90(255): error #6404: This name does not have a type, and must >> have an explicit type. [NF90_MPIIO] >> par = iand(NF90_MPIIO,this%mode) == NF90_MPIIO >> ---^ >> nf_ncdf.f90(255): error #6363: The intrinsic data types of the arguments >> must be the same. [IAND] >> par = iand(NF90_MPIIO,this%mode) == NF90_MPIIO >> --^ >> nf_ncdf.f90(255): error #6404: This name does not have a type, and
[SIESTA-L] non symmetric values of current for symmetric junction
Dear all, is it "normal" to get non symmetric valus of current for symmetric junction? symmetric here means left electrode is the same as right electrode. i am getting different absolute values; i.e == Results: Voltage, Current(A) = 7.9145E-01 8.76143710E-10 == == Results: Voltage, Current(A) = -7.9145E-01 -4.98629217E-10 == best regards taoufik
Re: [SIESTA-L] << compiling siesta-4.1-b1 with NetCDF >>
Please attach your entire arch.make file. There are a few unknowns in your compilation process. 2016-09-23 2:52 GMT+02:00 I. Camps: > Hello, > > I am trying to compile siesta-4.1-b1 with NetCDF4 but I am getting into > troubles :( > > The errors are (my system info is bellow): > > mpiifort -E -P -x c -DCDF -DNCDF_4 -DMPI -DNCDF_PARALLEL -I. > -I/home/icamps/Temp/SIESTA/siesta-4.1-b1/Src/NCDF/src > /home/icamps/Temp/SIESTA/siesta-4.1-b1/Src/NCDF/src/nf_ncdf.F90 | sed -e > 's/NEWLINE/\n/g;/^$/d;/^\!.*&/d; > s/[[:space:]]*##[[:space:]]*\([^[:space:]]*\)/\1/g; > s/[[:space:]]*#\([^i][^[:space:]]*\)/"\1"/g; s:/ /://:g; > s/"endif"/\n#endif/g' > nf_ncdf.f90 #2> /dev/null > ifort: command line warning #10155: ignoring option '-x'; argument required > ifort: error #10236: File not found: 'c' > mpiifort -c -w -O2 -mp -I../../nf_ncdf.f90 > nf_ncdf.f90(59): error #7002: Error in opening the compiled module file. > Check INCLUDE paths. [NETCDF] > use netcdf > --^ > nf_ncdf.f90(95): error #8237: The character length in a component > declaration shall either be a colon, be an initialization expression, or be > a specification expression. [GRP] > character(len=NF90_MAX_NAME) :: grp = " " > -^ > nf_ncdf.f90(95): error #6404: This name does not have a type, and must > have an explicit type. [NF90_MAX_NAME] > character(len=NF90_MAX_NAME) :: grp = " " > ---^ > nf_ncdf.f90(255): error #6404: This name does not have a type, and must > have an explicit type. [NF90_MPIIO] > par = iand(NF90_MPIIO,this%mode) == NF90_MPIIO > ---^ > nf_ncdf.f90(255): error #6363: The intrinsic data types of the arguments > must be the same. [IAND] > par = iand(NF90_MPIIO,this%mode) == NF90_MPIIO > --^ > nf_ncdf.f90(255): error #6404: This name does not have a type, and must > have an explicit type. [IAND] > par = iand(NF90_MPIIO,this%mode) == NF90_MPIIO > --^ > nf_ncdf.f90(257): error #6404: This name does not have a type, and must > have an explicit type. [NF90_MPIPOSIX] > par = iand(NF90_MPIPOSIX,this%mode) == NF90_MPIPOSIX > ---^ > nf_ncdf.f90(259): error #6404: This name does not have a type, and must > have an explicit type. [NF90_PNETCDF] > par = iand(NF90_PNETCDF,this%mode) == NF90_PNETCDF > ---^ > nf_ncdf.f90(297): error #6404: This name does not have a type, and must > have an explicit type. [NF90_64BIT_OFFSET] >this%mode = IOR(this%mode,NF90_64BIT_OFFSET) > -^ > nf_ncdf.f90(297): error #6363: The intrinsic data types of the arguments > must be the same. [IOR] >this%mode = IOR(this%mode,NF90_64BIT_OFFSET) > -^ > nf_ncdf.f90(311): error #6404: This name does not have a type, and must > have an explicit type. [NF90_SHARE] > if ( iand(NF90_SHARE,mode) /= NF90_SHARE ) & > ---^ > nf_ncdf.f90(311): error #6363: The intrinsic data types of the arguments > must be the same. [IAND] > if ( iand(NF90_SHARE,mode) /= NF90_SHARE ) & > --^ > nf_ncdf.f90(311): error #6404: This name does not have a type, and must > have an explicit type. [IAND] > if ( iand(NF90_SHARE,mode) /= NF90_SHARE ) & > --^ > nf_ncdf.f90(359): error #6404: This name does not have a type, and must > have an explicit type. [NF90_FORMAT_CLASSIC] >case ( NF90_FORMAT_CLASSIC ) > --^ > nf_ncdf.f90(359): error #6601: In a CASE statement, the case-value must be > a constant expression. [NF90_FORMAT_CLASSIC] >case ( NF90_FORMAT_CLASSIC ) > --^ > nf_ncdf.f90(359): error #6612: In a CASE statement, the case-value must be > of type INTEGER, CHARACTER, or LOGICAL. [NF90_FORMAT_CLASSIC] >case ( NF90_FORMAT_CLASSIC ) > --^ > nf_ncdf.f90(359): error #6611: The case-value must be of the same type as > the case-expr. [NF90_FORMAT_CLASSIC] >case ( NF90_FORMAT_CLASSIC ) > --^ > nf_ncdf.f90(361): error #6404: This name does not have a type, and must > have an explicit type. [NF90_FORMAT_64BIT] >case ( NF90_FORMAT_64BIT ) > --^ > nf_ncdf.f90(361): error #6601: In a CASE statement, the case-value must be > a constant expression. [NF90_FORMAT_64BIT] >case ( NF90_FORMAT_64BIT ) > --^ > nf_ncdf.f90(361): error #6612: In a CASE statement, the case-value must be > of type INTEGER, CHARACTER, or LOGICAL. [NF90_FORMAT_64BIT] >case ( NF90_FORMAT_64BIT ) > --^ > nf_ncdf.f90(361): error #6611: The case-value must be of the same type as > the case-expr. [NF90_FORMAT_64BIT] >case ( NF90_FORMAT_64BIT ) > --^ > nf_ncdf.f90(363): error #6404: This name does not have a type, and must > have an explicit type. [NF90_FORMAT_NETCDF4] >