Running WPS in HPC cron

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elliottardif
Posts: 12
Joined: Tue Jan 07, 2020 4:52 pm

Running WPS in HPC cron

Post by elliottardif » Fri Jan 10, 2020 7:47 pm

Hi everyone, I've run into another issue with running WPS in a cron environment on my HPC cluster. I am writing a wrapper script in Perl to run WPS and WRF; thus far I have incorporated all the WPS processes into the script and I have run it successfully when I type the command for the script manually, but when I go to run the same script in cron, it gives me the following error (in this case, for geogrid):
./geogrid.exe: error while loading shared libraries: libnetcdff.so.6: cannot open shared object file: No such file or directory

What would cause this issue in cron vs running the script myself?

Thanks for any help,

Elliot Tardif

Ming Chen
Posts: 1398
Joined: Mon Apr 23, 2018 9:42 pm

Re: Running WPS in HPC cron

Post by Ming Chen » Fri Jan 10, 2020 10:59 pm

The Unix operating system usually looks at the environment variable LD_LIBRARY_PATH to search the directories in the path for the library. Try issuing these commands:
echo $LD_LIBRARY_PATH
If the path /usr/local/netcdf/lib is not included, then (in ksh, for example) please type:
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/netcdf/lib"
WRF Help Desk

elliottardif
Posts: 12
Joined: Tue Jan 07, 2020 4:52 pm

Re: Running WPS in HPC cron

Post by elliottardif » Tue Jan 14, 2020 10:11 pm

Hi Ming, thank you for your note. You were right: I had gotten my $LD_LIBRARY_PATH messed up and needed to fix it, which I did along with my intel compiler directory path reference, and these resolved the problem. This said, I noted that I couldn't run the Perl script itself in cron, I had to write a three line wrapper script in csh to kick off the Perl script I had written. Thank you for your time!

Elliot Tardif

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