Port machine to Ubuntu error

[aatreyee_iirs]

I ran nm libpnetcdf.a and the output of that command is attached herewith. I could not quite understand what the output meant, but I could find some of the listed symbols except for the following,
`gptlget_memusage'
`gptlprint_memusage'
`shr_reprosumx86_fix_end'
`shr_reprosumx86_fix_start'
'gptlfinalize'
'gptldisable'
'gptlenable'
'gptlstartstop_vals'
`gptlstop'
`gptlstart'
`gptlpr_query_write'
`gptlpr_set_append'
`gptlpr_summary_file'
`gptlpr_file'
`gptlpr_set_write'
`gptlstamp'
`gptldisable'
`gptlevent_name_to_code'
`gptlenable'
`gptlevent_name_to_code'
`gptlsetutr'
`gptlsetoption'
`gptlinitialize'
`gptlsetoption'

While building pnetcdf, I did not come across any errors and the tests were successful. Could it be an issue with the version of the libraries? I am using the following (GCC and gfortran 9.4.0)
zlib-1.2.13
hdf5-1.10.5
netcdf-c-4.9.0
netcdf-fortran-4.6.0
mpich-3.3.1
pnetcdf-1.12.3
LAPACK and BLAS 3.11

Thank you

 

[jedwards]

Using this command -

mpif90 -o /home/ubuntuvm/projects/cesm/scratch/testrun2/bld/cesm.exe cime_comp_mod.o cime_driver.o component_mod.o component_type_mod.o cplcomp_exchange_mod.o map_glc2lnd_mod.o map_lnd2glc_mod.o map_lnd2rof_irrig_mod.o mrg_mod.o prep_aoflux_mod.o prep_atm_mod.o prep_glc_mod.o prep_ice_mod.o prep_lnd_mod.o prep_ocn_mod.o prep_rof_mod.o prep_wav_mod.o seq_diag_mct.o seq_domain_mct.o seq_flux_mct.o seq_frac_mct.o seq_hist_mod.o seq_io_mod.o seq_map_mod.o seq_map_type_mod.o seq_rest_mod.o t_driver_timers_mod.o -L/home/ubuntuvm/projects/cesm/scratch/testrun2/bld/lib/ -latm -L/home/ubuntuvm/projects/cesm/scratch/testrun2/bld/lib/ -lice -L/home/ubuntuvm/projects/cesm/scratch/testrun2/bld/lib/ -llnd -L/home/ubuntuvm/projects/cesm/scratch/testrun2/bld/lib/ -locn -L/home/ubuntuvm/projects/cesm/scratch/testrun2/bld/lib/ -lrof -L/home/ubuntuvm/projects/cesm/scratch/testrun2/bld/lib/ -lglc -L/home/ubuntuvm/projects/cesm/scratch/testrun2/bld/lib/ -lwav -L/home/ubuntuvm/projects/cesm/scratch/testrun2/bld/lib/ -lesp -L../../gnu/mpich/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/lib -lcsm_share -L../../gnu/mpich/nodebug/nothreads/lib -lpio -lgptl -lmct -lmpeu -L/home/ubuntuvm/CESM_Library -lnetcdff -L/home/ubuntuvm/CESM_Library -lnetcdf -lm -lnetcdf -lhdf5_hl -lhdf5 -lpnetcdf -ldl -lm -lz -Wl,-rpath -Wl,/home/ubuntuvm/CESM_Library -L/home/ubuntuvm/CESM_Library -lpnetcdf -L/usr/local/lib -llapack -L/usr/local/lib -lblas -L/home/ubuntuvm/CESM/CESM_Library/lib -lpnetcdf -L/home/ubuntuvm/CESM_Library/lib


rearrange the location of the -lpnetcdf until you don't see the nfmpi_ commands in the link error message any longer. Once you have that figured out move on to the timing library (gptl) I don't understand why your system is being so particular about library order - if there is a system admin you can consult on your system you should ask.

 

[aatreyee_iirs]

Thank you for your reply, I am trying what you have suggested and will update about the outcomes.

 

[aatreyee_iirs]

I have another doubt regarding the order of the libraries.
I built the libraries in the order>>>> Pnetcdf, HDF5, Netcdf-C and then Netcdf-Fortran.
So my doubt is, if library A depends on library B, which one should be linked first?

 

[jedwards]

This is not a problem we have with modern compilers and linkers, I don't really understand why you are seeing it, but:
The dependent library should come on the left, and the library which provides said dependency should come on the right.

 

[aatreyee_iirs]

Thank you for your reply. I am trying to rearrange the location of lpnetcdf and I will update about the results.