Yeah, that is something we need to address. Could you please add this to your arch.make file:
NETCDF_LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz Den tir. 16. feb. 2021 kl. 22.00 skrev I. Camps <ica...@gmail.com>: > Hi Nick, > > Thank you for your email. > > 1. We can't see your arch.make, so there may be problems related to that. >> > The used arch.make file is attached here. > I successfully compiled SIESTA, both v4.1.5 and PSML version, without any > errors with it > > >> 2. You shouldn't do any manual copies, so I bet your copy of the >> xmlparser folder causes problems. Could you please try from a clean >> pdosxml folder, it should only contain these files: >> total 196K >> -rw-r--r-- 1 nicpa nicpa 28K Oct 9 2019 f2kcli-manual.txt >> -rw-r--r-- 1 nicpa nicpa 141K Oct 9 2019 h2o_dos.PDOS >> -rw-r--r-- 1 nicpa nicpa 1.6K Feb 4 08:22 makefile >> -rw-r--r-- 1 nicpa nicpa 1.2K Nov 17 13:48 m_orbital_chooser.f90 >> -rw-r--r-- 1 nicpa nicpa 5.9K Feb 4 08:22 m_pdos.f90 >> -rw-r--r-- 1 nicpa nicpa 1.3K Feb 4 08:22 pdosxml.f90 >> -rw-r--r-- 1 nicpa nicpa 1.7K Oct 9 2019 README >> > This was Ok. > > 3. Utilities depend on the Obj directory. So if you hadn't done >> ../Src/obj_setup.sh in the Obj directory this may be the root cause of the >> problem. >> > This did the trick! But there following packages: > > > > > > > > > > > > > **** All failed directories: *** (Some programs have to be compiled after > compiling Siesta) ./WFS ./SiestaSubroutine/ProtoNEB/Src > ./SiestaSubroutine/SimpleTest/Src ./ON ./Grid ./Gen-basis > ./STM/simple-stm ./DensityMatrix ./MPI_test ./Helpers:* > > Had the same complaint finding NETCDF. For example, this is the output of > running *make* inside the WFS folder: > > > > > > > > > > > > > > > > > > > > > > > > > *fort -L/software/SIESTA-Libs/zlib-1.2.8/lib > -Wl,-rpath=/software/SIESTA-Libs/zlib-1.2.8/lib > -L/software/SIESTA-Libs/hdf5-1.8.12/lib > -Wl,-rpath=/software/SIESTA-Libs/hdf5-1.8.12/lib > -L/software/SIESTA-Libs/netcdf-4.4.1/lib > -Wl,-rpath=/software/SIESTA-Libs/netcdf-4.4.1/lib > -L/software/SIESTA-Libs/netcdf-fortran-4.4.4/lib > -Wl,-rpath=/software/SIESTA-Libs/netcdf-fortran-4.4.4/lib -static-intel > -L/software/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64 > -o wfsnc2wfsx wfsnc2wfsx.o ld: wfsnc2wfsx.o: in function > `MAIN__':wfsnc2wfsx.F90:(.text+0x66): undefined reference to > `netcdf_mp_nf90_open_'ld: wfsnc2wfsx.F90:(.text+0x97): undefined reference > to `netcdf_mp_nf90_inq_dimid_'ld: wfsnc2wfsx.F90:(.text+0xc4): undefined > reference to `netcdf_mp_nf90_inquire_dimension_'ld: > wfsnc2wfsx.F90:(.text+0xfe): undefined reference to > `netcdf_mp_nf90_inq_dimid_'ld: wfsnc2wfsx.F90:(.text+0x128): undefined > reference to `netcdf_mp_nf90_inquire_dimension_'ld: > wfsnc2wfsx.F90:(.text+0x155): undefined reference to > `netcdf_mp_nf90_inq_dimid_'ld: wfsnc2wfsx.F90:(.text+0x182): undefined > reference to `netcdf_mp_nf90_inquire_dimension_'ld: > wfsnc2wfsx.F90:(.text+0x1af): undefined reference to > `netcdf_mp_nf90_inq_dimid_'ld: wfsnc2wfsx.F90:(.text+0x1dc): undefined > reference to `netcdf_mp_nf90_inquire_dimension_'ld: > wfsnc2wfsx.F90:(.text+0x209): undefined reference to > `netcdf_mp_nf90_inq_dimid_'ld: wfsnc2wfsx.F90:(.text+0x236): undefined > reference to `netcdf_mp_nf90_inquire_dimension_'ld: > wfsnc2wfsx.F90:(.text+0x263): undefined reference to > `netcdf_mp_nf90_inq_varid_'ld: wfsnc2wfsx.F90:(.text+0x28d): undefined > reference to `netcdf_mp_nf90_inq_varid_'ld: wfsnc2wfsx.F90:(.text+0x1856): > undefined reference to `netcdf_mp_nf90_get_var_1d_fourbytereal_'ld: > wfsnc2wfsx.F90:(.text+0x19ec): undefined reference to > `netcdf_mp_nf90_get_var_1d_fourbytereal_'ld: wfsnc2wfsx.F90:(.text+0x1b3a): > undefined reference to `netcdf_mp_nf90_get_var_1d_fourbytereal_'ld: > wfsnc2wfsx.F90:(.text+0x1bf3): undefined reference to > `netcdf_mp_nf90_get_var_1d_fourbytereal_'ld: wfsnc2wfsx.F90:(.text+0x1d71): > undefined reference to `netcdf_mp_nf90_close_'ld: > wfsnc2wfsx.F90:(.text+0x1dcf): undefined reference to > `netcdf_mp_nf90_strerror_'ld: wfsnc2wfsx.o: in function > `wfsnc2wfsx_IP_check_':wfsnc2wfsx.F90:(.text+0x1f65): undefined reference > to `netcdf_mp_nf90_strerror_'make: *** [makefile:58: wfsnc2wfsx] Error 1* > > Regards, > > Camps > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- Kind regards Nick
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
