[SIESTA-L] Compiling siesta 4.1.b4 and 4.1.5 with intel tools fails at iogrid_netcdf.F90
Hello,
Any help will be really appreciated. Many thanks in advance
I have modified line 33 of Makefile regarding a recipe that used to work for
Siesta
#add in Makefile line 33: lib: libfdict.a libncdf.a libSiestaXC.a libfdf.a
libSiestaForces.a
System information: Centos 7.8
Loaded modules
intel/19.1.1.217
netCDF/4.4.1.1-intel
HDF5/1.8.10-intel
PnetCDF/1.8.1-intel
metis/5.1.0-intel
Compilation output: [Full_PATH]/Src/iogrid_netcdf.F90(133): error #7002: Error
in opening the compiled module file. Check INCLUDE paths. [NETCDF] use netcdf
[Full_PATH]/Src/iogrid_netcdf.F90(272): error #7002: Error in opening the
compiled module file. Check INCLUDE paths. [NETCDF] use netcdf ^
[Full_PATH]/Src/iogrid_netcdf.F90(391): error #7002: Error in opening the
compiled module file. Check INCLUDE paths. [NETCDF] use netcdf, only:
nf90_noerr, nf90_strerror ^ [Full_PATH]/Src/iogrid_netcdf.F90(157): error
#6404: This name does not have a type, and must have an explicit type.
[NF90_SHARE] iret =
nf90_create(trim(name)//".grid.nc",NF90_SHARE+NF90_WRITE,ncid)
Arch.make as follows
#
# Copyright (C) 1996-2016 The SIESTA group
# This file is distributed under the terms of the
# GNU General Public License: see COPYING in the top directory
# or http://www.gnu.org/copyleft/gpl.txt.
# See Docs/Contributors.txt for a list of contributors.
#
#---
# arch.make file for gfortran compiler.
# To use this arch.make file you should rename it to
# arch.make
# or make a sym-link.
# For an explanation of the flags see DOCUMENTED-TEMPLATE.make
.SUFFIXES:
.SUFFIXES: .f .F .o .c .a .f90 .F90
SIESTA_ARCH=x86_64-unknown-linux-intel
CC = icc
FPP = $(FC) -E -P
FC = mpiifort
#FC_SERIAL = ifort
#FFLAGS = -O2 -fPIC -fp-model source
#AR = ar
RANLIB = ranlib
SYS = nag
SP_KIND = 4
DP_KIND = 8
KINDS = $(SP_KIND) $(DP_KIND)
#LDFLAGS =
FFLAGS= -qopenmp -I/opt/shared/apps/netCDF/4.4.1.1-intel/include/
-I/opt/apps/Siesta/siesta-4.1.5/Obj
FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DSIESTA__NO_MRRR
LDFLAGS= -qopenmp
ARFLAGS_EXTRA=
FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=
BLACS_LIBS= -L${MKLROOT}/lib/intel64 -libmkl_scalapack_lp64 -libmkl_intel_lp64
-libmkl_intel_thread -libmkl_core -libmkl_blacs_intelmpi_lp64 -liomp5 -lpthread
-lm -ldl
SCALAPACK_LIBS= -L${MKLROOT}/lib/intel64 -libmkl_scalapack_lp64
-libmkl_intel_lp64 -libmkl_intel_thread -libmkl_core
-libmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl
INTEL_LIBS = $MKLROOT/lib/intel64/libmkl_intel_lp64.a \
$(MKLROOT)/lib/intel64/libmkl_sequential.a \
$(MKLROOT)/lib/intel64/libmkl_core.a \
$(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a \
$(MKLROOT)/lib/intel64/libmkl_scalapack_lp64.a
MPI_LIBS =
-L/opt/intel/compilers_and_libraries_2020.1.217/linux/mpi/intel64/lib -lmpi
MPI_INCLUDE =
-I/opt/intel/compilers_and_libraries_2020.1.217/linux/mpi/intel64/include
#COMP_LIBS=dc_lapack.a liblapack.a libblas.a
export NETCDF=/opt/shared/apps/netCDF/4.4.1.1-intel
NETCDF_LIBS= -L$(NETCDF)/lib -L/opt/shared/apps/PnetCDF/1.7.0-intel/include
-L/opt/shared/apps/HDF5/1.8.19-intel/lib -lnetcdff -lnetcdf -lhdf5_fortran
-lhdf5 -lz -liomp5
NETCDF_INTERFACE=-I/apps/PNETCDF/1.8.1/INTEL/IMPI/include
HDF5_ROOT=/opt/shared/apps/HDF5/1.8.19-intel/
NETCDF_INCFLAGS = -I$(NETCDF)/include
HDF5_INCFLAGS = -I$(HDF5_ROOT)/include
LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS)
-L/apps/METIS/5.1.0/INTEL/lib -lmetis
#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=libmpi_f90.a
INCFLAGS = $(NETCDF_INCFLAGS) $(HDF5_INCFLAGS) $(MPI_INCLUDE) $(MKL_INCLUDE)
# Dependency rules -
FFLAGS_DEBUG = -g -O1 -fp-model source # your appropriate flags here...
# The atom.f code is very vulnerable. Particularly the Intel compiler
# will make an erroneous compilation of atom.f with high optimization
# levels.
atom.o: atom.F
$(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
state_analysis.o: state_analysis.F
$(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.c.o:
$(CC) -c $(CFLAGS) $(INCFLAGS) $(CPPFLAGS) $<
.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<
--
SIESTA is supported by the Spanish Research Agency (AEI) and by the European
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L] Compiling siesta 4.1.b4 and 4.1.5 with intel tools fails at siesta_cmlsubs.F90
Hello Hello, Issue compiling 4.1.b4. The error appears executing make lib compilation aborted for /opt/apps/Siesta/siesta-4.1-b4/Src/siesta_cmlsubs.F90 (code 1) make: *** [siesta_cmlsubs.o] Error 1 Any help will be really appreciated. Many thanks in advance mpiifort -c -qopenmp -I/opt/shared/apps/netCDF/4.4.1.1-intel/include/ -I/opt/apps/Siesta/siesta-4.1-b4/Obj -I/opt/shared/apps/netCDF/4.4.1.1-intel/include -I/opt/shared/apps/netCDF/4.4.1.1-intel/include -I/opt/shared/apps/HDF5/1.8.19-intel/include -I/opt/intel/compilers_and_libraries_2020.1.217/linux/mpi/intel64/include -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DSIESTA__NO_MRRR /opt/apps/Siesta/siesta-4.1-b4/Src/siesta_cmlsubs.F90 /opt/apps/Siesta/siesta-4.1-b4/Src/siesta_cmlsubs.F90(26): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [VERSION_INFO] Use version_info --^ /opt/apps/Siesta/siesta-4.1-b4/Src/siesta_cmlsubs.F90(62): error #6285: There is no matching specific subroutine for this generic subroutine call. [CMLADDMETADATA] Call cmlAddMetadata(mainXML, name='siesta:Version', content=version_str) --^ /opt/apps/Siesta/siesta-4.1-b4/Src/siesta_cmlsubs.F90(63): error #6285: There is no matching specific subroutine for this generic subroutine call. [CMLADDMETADATA] Call cmlAddMetadata(mainXML, name='siesta:Arch', content=siesta_arch) --^ /opt/apps/Siesta/siesta-4.1-b4/Src/siesta_cmlsubs.F90(64): error #6285: There is no matching specific subroutine for this generic subroutine call. [CMLADDMETADATA] Call cmlAddMetadata(mainXML, name='siesta:Flags', content=fflags) --^ /opt/apps/Siesta/siesta-4.1-b4/Src/siesta_cmlsubs.F90(65): error #6285: There is no matching specific subroutine for this generic subroutine call. [CMLADDMETADATA] Call cmlAddMetadata(mainXML, name='siesta:PPFlags', content=fppflags) --^ compilation aborted for /opt/apps/Siesta/siesta-4.1-b4/Src/siesta_cmlsubs.F90 (code 1) make: *** [siesta_cmlsubs.o] Error 1 -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
RE: [SIESTA-L] Compiling siesta 4.1.b4 and 4.1.5 with intel tools fails at iogrid_netcdf.F90
Many thanks for your response
It worked.
Everything is fine unless 2 warning that I want to check
Best Regards
Jorge
-Mensaje original-
De: siesta-l-requ...@uam.es En nombre de Alberto
Garcia
Enviado el: martes, 13 de julio de 2021 8:35
Para: siesta-l
Asunto: Re: [SIESTA-L] Compiling siesta 4.1.b4 and 4.1.5 with intel tools fails
at iogrid_netcdf.F90
Hi,
In your arch.make you have defined the symbol NETCDF_INTERFACE, but the symbol
whose value you append to INCFLAGS is NETCDF_INCLAGS.
Please change NETCDF_INTERFACE to NETCDF_INCFLAGS.
Also, regarding your related post: 'make lib' should not be used to compile
Siesta. Just use 'make'.
Alberto
- El 12 de Jul de 2021, a las 09:32, Jimenez Alfaro, Jorge (NASERTIC)
jjime...@nasertic.es escribió:
| Hello,
|
| Any help will be really appreciated. Many thanks in advance
|
| I have modified line 33 of Makefile regarding a recipe that used to
| work for Siesta
|
| #add in Makefile line 33: lib: libfdict.a libncdf.a libSiestaXC.a
| libfdf.a libSiestaForces.a
|
| System information: Centos 7.8
|
| Loaded modules
|
| intel/19.1.1.217
|
| netCDF/4.4.1.1-intel
|
| HDF5/1.8.10-intel
|
| PnetCDF/1.8.1-intel
|
| metis/5.1.0-intel
|
| Compilation output: [Full_PATH]/Src/iogrid_netcdf.F90(133): error
| #7002: Error in opening the compiled module file. Check INCLUDE paths.
| [NETCDF] use netcdf
|
| [Full_PATH]/Src/iogrid_netcdf.F90(272): error #7002: Error in opening
| the compiled module file. Check INCLUDE paths. [NETCDF] use netcdf
| ^
| [Full_PATH]/Src/iogrid_netcdf.F90(391): error #7002: Error in opening
| the compiled module file. Check INCLUDE paths. [NETCDF] use netcdf, only:
| nf90_noerr, nf90_strerror ^
| [Full_PATH]/Src/iogrid_netcdf.F90(157): error
| #6404: This name does not have a type, and must have an explicit type.
| [NF90_SHARE] iret =
| nf90_create(trim(name)//".grid.nc",NF90_SHARE+NF90_WRITE,ncid)
|
| Arch.make as follows
|
|
|
|
|
| #
|
| # Copyright (C) 1996-2016 The SIESTA group
|
| # This file is distributed under the terms of the
|
| # GNU General Public License: see COPYING in the top directory
|
| # or http://www.gnu.org/copyleft/gpl.txt.
|
| # See Docs/Contributors.txt for a list of contributors.
|
| #
|
| #---
|
| # arch.make file for gfortran compiler.
|
| # To use this arch.make file you should rename it to
|
| # arch.make
|
| # or make a sym-link.
|
| # For an explanation of the flags see DOCUMENTED-TEMPLATE.make
|
|
|
| .SUFFIXES:
|
| .SUFFIXES: .f .F .o .c .a .f90 .F90
|
|
|
| SIESTA_ARCH=x86_64-unknown-linux-intel
|
|
|
| CC = icc
|
| FPP = $(FC) -E -P
|
| FC = mpiifort
|
| #FC_SERIAL = ifort
|
|
|
| #FFLAGS = -O2 -fPIC -fp-model source
|
|
|
|
|
| #AR = ar
|
| RANLIB = ranlib
|
|
|
| SYS = nag
|
|
|
| SP_KIND = 4
|
| DP_KIND = 8
|
| KINDS = $(SP_KIND) $(DP_KIND)
|
|
|
| #LDFLAGS =
|
|
|
|
|
| FFLAGS= -qopenmp -I/opt/shared/apps/netCDF/4.4.1.1-intel/include/
| -I/opt/apps/Siesta/siesta-4.1.5/Obj
|
|
|
| FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF
| -DSIESTA__NO_MRRR
|
|
|
| LDFLAGS= -qopenmp
|
|
|
| ARFLAGS_EXTRA=
|
|
|
| FCFLAGS_fixed_f=
|
| FCFLAGS_free_f90=
|
| FPPFLAGS_fixed_F=
|
| FPPFLAGS_free_F90=
|
| BLACS_LIBS= -L${MKLROOT}/lib/intel64 -libmkl_scalapack_lp64
| -libmkl_intel_lp64 -libmkl_intel_thread -libmkl_core
| -libmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl
|
| SCALAPACK_LIBS= -L${MKLROOT}/lib/intel64 -libmkl_scalapack_lp64
| -libmkl_intel_lp64 -libmkl_intel_thread -libmkl_core
| -libmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl
|
|
|
| INTEL_LIBS = $MKLROOT/lib/intel64/libmkl_intel_lp64.a \
|
| $(MKLROOT)/lib/intel64/libmkl_sequential.a \
|
| $(MKLROOT)/lib/intel64/libmkl_core.a \
|
| $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a \
|
| $(MKLROOT)/lib/intel64/libmkl_scalapack_lp64.a
|
| MPI_LIBS =
| -L/opt/intel/compilers_and_libraries_2020.1.217/linux/mpi/intel64/lib
| -lmpi
|
| MPI_INCLUDE =
| -I/opt/intel/compilers_and_libraries_2020.1.217/linux/mpi/intel64/incl
| ude
|
|
|
|
|
| #COMP_LIBS=dc_lapack.a liblapack.a libblas.a
|
| export NETCDF=/opt/shared/apps/netCDF/4.4.1.1-intel
|
| NETCDF_LIBS= -L$(NETCDF)/lib
| -L/opt/shared/apps/PnetCDF/1.7.0-intel/include
| -L/opt/shared/apps/HDF5/1.8.19-intel/lib -lnetcdff -lnetcdf
| -lhdf5_fortran
| -lhdf5 -lz -liomp5
|
| NETCDF_INTERFACE=-I/apps/PNETCDF/1.8.1/INTEL/IMPI/include
|
| HDF5_ROOT=/opt/shared/apps/HDF5/1.8.19-intel/
|
|
|
| NETCDF_INCFLAGS = -I$(NETCDF)/include
|
| HDF5_INCFLAGS = -I$(HDF5_ROOT)/include
|
|
|
|
|
| LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS)
| $(NETCDF_LIBS) -L/apps/METIS/5.1.0/INTEL/lib -lmetis
|
|
|
| #SIESTA needs an F90 interface to MPI
|
| #This will give you SIESTA's own implementation
|
| #If your compiler vendor offers an alternati
