(RESOLVED) Geogrid Error: error while loading shared libraries: libnetcdf.so.7

[ggp17mkm]

After setting my domain etc in the namelist.wps file, when I run the geogrid program, I get this error:
./geogrid.exe: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory

Any ideas why netcdf is having problems?

 

[kwerner]

Hi,
It could be possible that NetCDF has been updated since you built WPS. Check your netcdf path (echo $NETCDF) and see if that library exists there. If you happen to be using Cheyenne's supercomputer, try logging out and logging back in (it sounds silly, but this has gotten me past this error in the past).

 

[mgduda]

This might just be an issue of correctly setting the LD_LIBRARY_PATH environment variable to include the path to the netCDF shared library.

 

[ggp17mkm]

Hi,

Thanks for always helping out guys. I still cannot spot whats going wrong.
I tried echo$NETCDF. And I get this response:
echo/home/ggp17mkm/Build_WRF/LIBRARIES/libs/netcdf/: No such file or directory

I have treid logging out and in of my uni HPC several times. Doesn't solve the issue.
I have attached the screenshot of what I have in the netcdf folder.

Also, my .bashrc file has these paths set:

# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi

# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=

# User specific aliases and functions
export DIR="/home/ggp17mkm/Build_WRF/LIBRARIES/libs"
export CC="gcc"
export CXX="g++"
export FC="gfortran"
export FCFLAGS="-m64"
export F77="gfortran"
export FFLAGS="-m64"
export PATH="$DIR/netcdf/bin:$PATH"
#export HDF5="/usr/local/modulefiles/staging/eb/all/HDF5/"
export NETCDF="/home/ggp17mkm/Build_WRF/LIBRARIES/libs/netcdf/"
#export PATH="$DIR/mpich/bin:$PATH"
export LDFLAGS="-L$DIR/grib2/lib"
export CPPFLAGS="-I$DIR/grib2/include"
export JASPERLIB="$DIR/grib2/lib"
export JASPERINC="$DIR/grib2/include"

 

[kwerner]

Hi,
Can you put a space between 'echo' and $NETCDF'? The command should be:

echo $NETCDF

 

[ggp17mkm]

Hi,

Ahh I see. Sorry for that silly error. I get this path as response to echo $NETCDF
/home/ggp17mkm/Build_WRF/LIBRARIES/libs/netcdf/

 

[kwerner]

Thanks for sending that. As mgduda mentioned, you may just need to set your LD_LIBRARY_PATH. If it's not already included, add the NetCDF library to the path. Something like:

export LD_LIBRARY_PATH=/path-to-netcdf-library/lib:$LD_LIBRARY_PATH

Let me know if that makes any difference.

 

[ggp17mkm]

Hello,

As my netcdf path is: /home/ggp17mkm/Build_WRF/LIBRARIES/libs/netcdf/

I have added this to my .bashrc file:

LD_LIBRARY_PATH="home/ggp17mkm/Build_WRF/LIBRARIES/libs/netcdf:$LD_LIBRARY_PATH"
I logged out and in again, then issued ./geogrid.exe, but still have the same error.

 

[mgduda]

I think you may be missing the beginning "/" character, and you need to add the suffix "/lib" (assuming that agrees with the installation path of the files like "libnetcdf.a". Also, you need to export the variable. Can you try the following:

export LD_LIBRARY_PATH=/home/ggp17mkm/Build_WRF/LIBRARIES/libs/netcdf/lib:$LD_LIBRARY_PATH

? You can even run this export command directly in your shell to test.

 

[ggp17mkm]

Hi,
Thanks for all the help I really appreciate it. the netcdf error seems to have solved. However there are these errors now:

Processing domain 1 of 1
Processing XLAT and XLONG

Program received signal SIGSEGV: Segmentation fault - inavlid memory reference.

Backtrace for this error:

0x7FF23A97B697
0x7FF23A97BCDE
0x7FF239E763FF
0x7FF239FAAC11
0x7FF23AA59CC8
0x7FF23A97E13A
0x7F497F7E in ext_ncd_inquiry
0x43216A in_output_module_MOD_output_init
0x43B3E5 in_process_tile_module_MOD_process_tile
Segmentation fault

 

[kwerner]

Thanks for updating the post to let us know that the original error is corrected. Do you mind posting the new problem as a new topic inquiry, as the error is different now. It helps to keep topics separated, organized, and more searchable. When you do post it, please also attach your namelist.wps file, along with the full geogrid.log. Thanks!