Problems in Building Libraries

[wakefultrance]

Hello. It is my first time installing WRF on a Rocky Linux system. In building the required libraries, I ran into some problems installing HDF5 while following the steps listed in the 'Full WRF and WPS Installation (GNU)' page. Everything had pretty much proceeded without a hitch until I tried to execute the command 'make -j 4' in the Install HDF5 code section in the link. I attached a logfile containing the issues I encountered when I executed said command. In particular, I get hit with a warning stating that the wrf_dependencies/netcdf/include cannot be found (see line 9 in logfile).

I hope someone knowledgeable about these things could lend me a hand. Your help would be greatly appreciated.

Thank you.

 

[gdicker]

Hello, you seem to have posted within the MPAS section of the Forum instead of the WRF section. Sometimes our forum admins move these posts, but you may get a quicker response if you re-post this in the appropriate section and delete this one.

 

[islas]

@wakefultrance These errors can be safely ignored. The order of building the dependencies adds includes for where netCDF will be before it has been created. While this is technically incorrect, in an effort to simplify the directions include flags are set once for all dependencies even if not used. This results in HDF5 warning about a directory that has yet to even be created and thus cannot be searched.

Perhaps further revision is needed where flags are set only where necessary.. I'll take this into consideration.

 

[wakefultrance]

Hello, you seem to have posted within the MPAS section of the Forum instead of the WRF section. Sometimes our forum admins move these posts, but you may get a quicker response if you re-post this in the appropriate section and delete this one.

Thank you for letting me know. I will post my questions there in the future.

 

[wakefultrance]

@wakefultrance These errors can be safely ignored. The order of building the dependencies adds includes for where netCDF will be before it has been created. While this is technically incorrect, in an effort to simplify the directions include flags are set once for all dependencies even if not used. This results in HDF5 warning about a directory that has yet to even be created and thus cannot be searched.

Perhaps further revision is needed where flags are set only where necessary.. I'll take this into consideration.

Thank you for your response.

When I was tracking the progress of the build, the readouts made made me think that maybe something had gone wrong so thank you for clarifying. I was able to install all the wrf depdendencies up to the jasper code block in Full WRF and WPS Installation Example (GNU). Should I also execute the commands in the Build WRF and Build WPS block in that link before proceeding to the Library Compiling Tests phase?

Thanks again. I appreciate your help.

 

[islas]

The compilation test phase if done should be before WRF & WPS compilation as it is meant to catch certain configuration errors before potentially spending 40+ minutes compiling WRF only to find it didn't work.

 

[wakefultrance]

The compilation test phase if done should be before WRF & WPS compilation as it is meant to catch certain configuration errors before potentially spending 40+ minutes compiling WRF only to find it didn't work.

Hi @islas. I was able to get past TEST 1 of the Library Compatibility Tests stage but could not proceed to TEST 2 since the mpi executables are absent. After checking the logfile (created from running build_wrf_dependencies.sh) to track the progress of the build, I saw that no makefiles were created in the installation of mpich (lines 72 and 73 in the build_wrf_dependencies.sh script and lines 15863 and 15864 in the attached log file).

After seeing that, I redid the installation process in a new terminal and added unset F90 and unset F90FLAGS above line 15863 to avoid the configure error which seems to have fixed the issue since mpi was installed this time around. But the include files were no longer present in ${NETCDF}/include/ folder and the $DIR/mpich/include/

Do you have any suggestions on how to move forward?

Thanks for writing back. Your feedback is very much appreciated.

 

[wakefultrance]

Hi again @islas. Just thought I'd give a fresher update after I was able to successfully able to install mpich but there is still one problem when I try to complete the series of commands in TEST 2 in Library Compatibility Tests. This specifically has to do with the execution of the mpirun command as follows:

../wrf_dependencies/mpich/bin/./mpirun ./a.out

which is supposed to display this
C function called by Fortran
Values are xx = 2.00 and ii = 1
status = 2
SUCCESS test 2 fortran + c + netcdf + mpi

but instead displays this:
./a.out: error while loading shared libraries: libnetcdff.so.7: cannot open shared object file: No such file or directory
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 127
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================

Hi @islas. I was able to get past TEST 1 of the Library Compatibility Tests stage but could not proceed to TEST 2 since the mpi executables are absent. After checking the logfile (created from running build_wrf_dependencies.sh) to track the progress of the build, I saw that no makefiles were created in the installation of mpich (lines 72 and 73 in the build_wrf_dependencies.sh script and lines 15863 and 15864 in the attached log file).

After seeing that, I redid the installation process in a new terminal and added unset F90 and unset F90FLAGS above line 15863 to avoid the configure error which seems to have fixed the issue since mpi was installed this time around. But the include files were no longer present in ${NETCDF}/include/ folder and the $DIR/mpich/include/

Do you have any suggestions on how to move forward?

Thanks for writing back. Your feedback is very much appreciated.

 

[wakefultrance]

The compilation test phase if done should be before WRF & WPS compilation as it is meant to catch certain configuration errors before potentially spending 40+ minutes compiling WRF only to find it didn't work.

Hi again @islas. I was able to build WRF after realizing I made a small error. Thanks again for your help anyway.