undefined reference to `netcdf_mp_nf90_var_par_access_

[MarkR_UoLeeds]

Hi CESM team, in response to a request from jim edwards...

I have started trying to create a machine file for arc4 and get the "undefined reference to `netcdf_mp_nf90_var_par_access_" message during the build of cesm. I have attached the bld log and this is the module show netcdf/4.6.3:

-------------------------------------------------------------------
/apps/Modules/developers/libraries/netcdf/4.6.3:

module-whatis NetCDF library (inc. pnetcdf 1.11.2 and hdf5 1.8.21)
prepend-path MODULE_DEPEND netcdf/4.6.3//class-compiler
prepend-path MODULE_DEPEND netcdf/4.6.3//class-mpi
prepend-path MODULE_FLAVOUR netcdf/4.6.3//1//intel-19.0.4-intelmpi-2019.4.243
setenv NETCDF_HOME /apps/developers/libraries/netcdf/4.6.3/1/intel-19.0.4-intelmpi-2019.4.243
prepend-path PATH /apps/developers/libraries/netcdf/4.6.3/1/intel-19.0.4-intelmpi-2019.4.243/bin
prepend-path CPATH /apps/developers/libraries/netcdf/4.6.3/1/intel-19.0.4-intelmpi-2019.4.243/include
prepend-path LIBRARY_PATH /apps/developers/libraries/netcdf/4.6.3/1/intel-19.0.4-intelmpi-2019.4.243/lib
prepend-path LD_LIBRARY_PATH /apps/developers/libraries/netcdf/4.6.3/1/intel-19.0.4-intelmpi-2019.4.243/lib
prepend-path CLASSPATH /apps/developers/libraries/netcdf/4.6.3/1/intel-19.0.4-intelmpi-2019.4.243/lib
prepend-path PKG_CONFIG_PATH /apps/developers/libraries/netcdf/4.6.3/1/intel-19.0.4-intelmpi-2019.4.243/lib/pkgconfig
prepend-path MANPATH /apps/developers/libraries/netcdf/4.6.3/1/intel-19.0.4-intelmpi-2019.4.243/man
prepend-path MANPATH /apps/developers/libraries/netcdf/4.6.3/1/intel-19.0.4-intelmpi-2019.4.243/share/man
prepend-path INFOPATH /apps/developers/libraries/netcdf/4.6.3/1/intel-19.0.4-intelmpi-2019.4.243/share/info

 

[jedwards]

You need a section like this one in your config_compilers.xml file, except it should be NETCDF_HOME instead of NETCDFHOME. You might also try adding a line <PNETCDF_PATH>$ENV{NETCDF_HOME}</PNETCDF_PATH> since it looks like you've included a pnetcdf build in your netcdf library.

 

[MarkR_UoLeeds]

Some good progress. But challenging now to work out finesse of SGE and what to put in the generic SGE definition and what to put in the specific machine batch definition. for example how to have several queue options. I inherited a chunk of the work so I think the previous worker put some compiler definitions in the machine rather than the compiler XML file. Latest is that there are "alien" strings i the job script so the submission fails. I am also unclear about where to start from when I make a mistake, adjust a file and want to repeat a step. Currently i am creating fresh case directory (case08 now). Alsonote I am on UTC+1 in UK so some lag in responses.