[BUG/ISSUE] Necessity of LD_LIBRARY_PATH when building/running GEOS-Chem

[pkasibhatla]

What institution are you from?

Duke University

Description of the problem

I successfully downloaded and compiled GCClassic v13.4.1 on my cluster. But when I tried to perform a dry run with the command ./geos --dryrun > log.dryrun I get the message gcclassic: error while loading shared libraries: libnetcdff.so.7: cannot open shared object file: No such file or directory

Description of troubleshooting performed

I did not do any specific troubleshooting because the User's Guide says "If you are using GEOS-Chem 13.0.0 , you do not need to define any Unix environment variables other than the compiler variables (FC, CC, and CXX)."

GEOS-Chem version

v13.4.1

Description of modifications

None

Log files

• Build log (if applicable): I am attaching the CMakeCache.txt file CMakeCache.txt
• Run logs (if applicable):
• Run script (if applicable):

Software versions

• CMake version: 3.19.3
• Compilers (Intel or GNU, and version): GNU 9.4.0
• NetCDF version: 4.8.1

[yantosca]

Hi @pkasibhatla. It seems that CMake couldn't find your netCDF Fortran library.

From the cache file I see that these are the paths that the build process found.

//Location of nc-config utility
NC_CONFIG:FILEPATH=/opt/apps/rhel8/miniconda3/envs/gchp-env/bin/nc-config

//Directory containing "netcdf.h"
NETCDF_C_INCLUDE_DIR:PATH=/opt/apps/rhel8/miniconda3/envs/gchp-env/include

//Path to "libnetcdf"
NETCDF_C_LIBRARY:FILEPATH=/opt/apps/rhel8/miniconda3/envs/gchp-env/lib/libnetcdf.so

//Directory containing "netcdf.inc"
NETCDF_F77_INCLUDE_DIR:PATH=/opt/apps/rhel8/miniconda3/envs/gchp-env/include

//Directory containing "netcdf.mod"
NETCDF_F90_INCLUDE_DIR:PATH=/opt/apps/rhel8/miniconda3/envs/gchp-env/include

//Path to "libnetcdff"
NETCDF_F_LIBRARY:FILEPATH=/opt/apps/rhel8/miniconda3/envs/gchp-env/lib/libnetcdff.so

//Location of nf-config utility
NF_CONFIG:FILEPATH=/opt/apps/rhel8/miniconda3/envs/gchp-env/bin/nf-config

It did find the libnetcdff.so file (the shared library for netCDF-Fortran). Sometimes this is a symbolic link to another file in the same directory. Take a look in this folder: /opt/apps/rhel8/miniconda3/envs/gchp-env/lib/ and see if libnetcdff.so is symbolically linked to another library file there or if the link is broken.

Also note: we are updating our documentation and migrating it to geos-chem.readthedocs.io. We realize that some of the wiki docs are out of date. We'll have this finished by the 14.0.0 release.

[pkasibhatla]

Hi @yantosca, it is indeed symbolically linked to another file, but that file exists:

psk9@dcc-login-03 ~ $ cd /opt/apps/rhel8/miniconda3/envs/gchp-env/lib psk9@dcc-login-03 /opt/apps/rhel8/miniconda3/envs/gchp-env/lib $ ls -l libnetcdff.so lrwxrwxrwx. 1 tm103 rescomp 19 Jul 18 10:22 libnetcdff.so -> libnetcdff.so.7.1.0* psk9@dcc-login-03 /opt/apps/rhel8/miniconda3/envs/gchp-env/lib $ ls -l libnetcdff.so.7.1.0 -rwxrwxr-x. 3 tm103 rescomp 1760416 Jan 20 11:39 libnetcdff.so.7.1.0*

[pkasibhatla]

Hi again @yantosca,

I was able to run after executing the command:

export LD_LIBRARY_PATH=/opt/apps/rhel8/miniconda3/envs/gchp-env/lib:$LD_LIBRARY_PATH

But I thought with v13, we did not need to specify this environment variable.

[yantosca]

Normally you wouldn't need to specify LD_LIBRARY_PATH, as the CMake build process should find the library file. Am tagging @LiamBindle who knows more about the particulars of CMake than I do.

[pkasibhatla]

Adding -DCMAKE_PREFIX_PATH=/opt/apps/rhel8/miniconda3/envs/gchp-env/lib to the build initialization did not fix this problem - I still need to specify

export LD_LIBRARY_PATH=/opt/apps/rhel8/miniconda3/envs/gchp-env/lib:$LD_LIBRARY_PATH

to run the model, even though it compiles without LD_LIBRARY_PATH being set.

[LiamBindle]

If I understand correctly, you successfully compiled GC-Classic but when you try to run you get

gcclassic: error while loading shared libraries: libnetcdff.so.7: cannot open shared object file: No such file or directory

If that's the case, the problem is the shared library libnetcdff.so.7 cant be found when you execute ./geos. This isn't related to building GEOS-Chem. In linux, when a program starts, the dynamic linker loads all of the shared libraries that the program links. It does this by searching through a list of directories for a file with the right name. LD_LIBRARY_PATH is an environment variable that adds extra directories to this search list.

You can always run ldd ./geos to list the resolved paths to shared libraries loaded by the ./geos program. Before you set LD_LIBRARY_PATH, ldd it should say libnetcdff.so.7.1.0 isn't found. After you set LD_LIBRARY_PATH, it should show the path to the library. This is because your libnetcdff.so.7.1.0 is installed in a non-standard location (since you've installed it via conda rather than installing it system wide).

tldr: This is expected. Set LD_LIBRARY_PATH before you run ./geos. LD_LIBRARY_PATH is a list of directories that linux searches for shared libraries when you launch a program. If your netcdf libraries are in a non-standard directory (e.g., installed via conda as opposed to installed system-wide) then you usually need to set LD_LIBRARY_PATH.

[pkasibhatla]

Thanks for the explanation. Not sure why the Duke sys admin installed using conda, but I guess I am stuck with it. So yes, everything works fine once I set LD_LIBRARY_PATH.

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