case.build fails with the netCDF library

[nlaureanti]

Describe your problem or question:

Dear all,
I'm facing problems compiling CESM on a new Intel machine. The errors indicate mainly that the netCDF include is not available:

/p/tmp/nicolela/my_cesm_sandbox/cime/src/share/util/shr_ncread_mod.F90(39): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [NETCDF]
use netcdf
------^

This is weird, since I have the paths listed in the config_*.xml files (see attached). This is my first time compiling this model, and I'm also trying to set up the flags, which I've noticed are different from those for other Intel machines. Does anyone have a hint for fixing this problem?
I appreciate any advice.
Nicole

---

What version of the code are you using?
> git describe
cime5.8.32.9
release-cesm2.2.2

> ./manage_externals/checkout_externals --status --verbose

Processing externals description file : Externals.cfg (/p/tmp/nicolela/my_cesm_sandbox)
Processing externals description file : Externals_CAM.cfg (/p/tmp/nicolela/my_cesm_sandbox/components/cam)
Processing externals description file : .gitmodules (/p/tmp/nicolela/my_cesm_sandbox/components/cdeps)
Processing externals description file : ../Externals_cime.cfg (/p/tmp/nicolela/my_cesm_sandbox/cime)
Processing externals description file : Externals_CISM.cfg (/p/tmp/nicolela/my_cesm_sandbox/components/cism)
Processing externals description file : Externals_CLM.cfg (/p/tmp/nicolela/my_cesm_sandbox/components/clm)
Processing externals description file : Externals_POP.cfg (/p/tmp/nicolela/my_cesm_sandbox/components/pop)
Checking local status of required & optional components: cam, chem_proc, carma, cosp2, clubb, silhs, pumas, atmos_phys, atmos_cubed_sphere, cice, cdeps, fox, cime, cmeps, cism, source_cism, clm, fates, fms, mom, mosart, pop, cvmix, marbl, rtm, ww3,
M ./cime
modified sandbox, on cime5.8.32.9
e-o ./cime/src/drivers/nuopc/
-, not checked out -->
./components/cam
clean sandbox, on cam_cesm2_2_rel_09
./components/cam/chem_proc
clean sandbox, on tools/proc_atm/chem_proc/release_tags/chem_proc5_0_04
./components/cam/src/atmos_phys
clean sandbox, on version0_00_007
./components/cam/src/dynamics/fv3/atmos_cubed_sphere
clean sandbox, on fv3_cesm.04
./components/cam/src/physics/carma/base
clean sandbox, on carma/release_tags/carma3_49_rel
./components/cam/src/physics/clubb
clean sandbox, on clubb_release_b76a124_20200220_c20200320
./components/cam/src/physics/cosp2/src
clean sandbox, on v2.1.4cesm
./components/cam/src/physics/pumas
clean sandbox, on pumas_cam-release_v1.3
./components/cam/src/physics/silhs
clean sandbox, on silhs_clubb_release_b76a124_20200220_c20200320
./components/cdeps
clean sandbox, on d808b7c6f78a2d5dcfeb1da0d1a452a9b66e08c8
./components/cdeps/fox
clean sandbox, on 7b9488446b193192dd3f0378541e71099cb4e8a8
./components/cice
clean sandbox, on cice5-cesm2.2.2-20231220
./components/cism
clean sandbox, on cism2_1_69_b
./components/cism/source_cism
clean sandbox, on release-cesm2.2.2-f1a88d6derecho
./components/clm
clean sandbox, on release-cesm2.2.04
./components/clm/src/fates
clean sandbox, on sci.1.30.0_api.8.0.0
e-o ./components/mom
-, not checked out --> mi_20200908
./components/mosart
clean sandbox, on mosart1_0_37_1
./components/pop
clean sandbox, on pop2_cesm2_2_rel_n01
./components/pop/externals/CVMix
clean sandbox, on v0.98-beta
./components/pop/externals/MARBL
clean sandbox, on cesm2.2-n00
./components/rtm
clean sandbox, on rtm1_0_72
./components/ww3
clean sandbox, on ww3_200710
e-o ./libraries/FMS
-, not checked out --> fi_20200609_cesm2.2_231205

Have you made any changes to files in the source tree?
See attached


Describe every step you took leading up to the problem:

./create_newcase --case ~/work/cesm_exp/b.e21.B1850.f09_g17.CMIP6-esm-piControl.001.test --compset B1850 --res f09_g17 --machine foote --compiler intel --pecount 128 --walltime 24:00:00 -q standard --project tipmip  --output-root ~/work/cesm_exp/ --run-unsupported

./case.setup && ./case.build

If this is a port to a new machine: Please attach any files you added or changed for the machine port (e.g., config_compilers.xml, config_machines.xml, and config_batch.xml) and tell us the compiler version you are using on this machine.
Please attach any log files showing error messages or other useful information.
see attached csm_share.bldlog.250707-093232.txt

mpiifort --version
ifort (IFORT) 2021.10.0 20230609

 

[jedwards]

Where is the file netcdf.mod located? It is a fortran file - did you install netcdf fortran in /p/system/packages/libraries/netcdf-c/4.9.2//include ?

 

[nlaureanti]

This is under /p/system/packages/libraries/netcdf-fortran/4.6.1/include/
I added this to the /config_compilers.xml, like so:

<NETCDF_C_PATH>/p/system/packages/libraries/netcdf-c/4.9.2/</NETCDF_C_PATH>
  <NETCDF_FORTRAN_PATH>/p/system/packages/libraries/netcdf-fortran-intel/4.6.1/</NETCDF_FORTRAN_PATH>
  <PNETCDF_PATH>/p/system/packages/libraries/pnetcdf/1.12.3/</PNETCDF_PATH>

And it passed the first error. But there are still some errors in the compilation pointing to the pnetcdf application.

It looks like this:

/p/system/packages/libraries/pnetcdf/1.12.3//lib/libpnetcdf.a(ncmpio_close.o): In function `ncmpio_close_files':
/p/system/modulefiles/pnetcdf-1.12.3/src/drivers/ncmpio/ncmpio_close.c:62: undefined reference to `ompi_mpi_file_null'
/p/system/modulefiles/pnetcdf-1.12.3/src/drivers/ncmpio/ncmpio_close.c:68: undefined reference to `ompi_mpi_file_null'
/p/system/packages/libraries/pnetcdf/1.12.3//lib/libpnetcdf.a(ncmpio_create.o): In function `ncmpio_create':
/p/system/modulefiles/pnetcdf-1.12.3/src/drivers/ncmpio/ncmpio_create.c:145: undefined reference to `ompi_mpi_int'

Do you know what this is about? Should I reinstall pnetcdf?

 

[jedwards]

Try settng MOD_NETCDF to NETCDF_FORTRAN_PATH/include

 

[nlaureanti]

Still not working, same message

 

[jedwards]

The message in the cesm.log file is that you built pnetcdf with openmpi but you are trying to link with intel-mpi, you will need to rebuild pnetcdf with the same mpi library,.