netcdf-c

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This is on NOAA's HPC system (hera), which I believe is CentOS.

In config.log I see:

configure:22699: checking size of off_t
configure:22704: gcc -o conftest  -fno-strict-aliasing -I//scratch2/BMC/gsienkf/whitaker/conda-envs/mpi4py/include -L/scratch2/BMC/gsienkf/whitaker/conda-envs/mpi4py/lib conftest.c -ldl -lbz2 -lzstd -lxml2 -lcurl  >&5
configure:22704: $? = 0
configure:22704: ./conftest
./conftest: error while loading shared libraries: libzstd.so.1: cannot open shared object file: No such file or directory
configure:22704: $? = 127
configure: program exited with status 127

and then

configure:22708: error: in `/scratch2/BMC/gsienkf/whitaker/python/netcdf-c':
configure:22710: error: cannot compute sizeof (off_t)
See `config.log' for more details

So the sizeof (off_t) test is failing because of an error loading the libzstd shared lib?

I'm also seeing this in some of the github actions runners for netcdf4-python.

.> /conftest: error while loading shared libraries: libzstd.so.1: cannot open shared object file: No such file or directory

This would indicate to me that libzstd did not get installed correctly.

could be, but the mystery then is why the test for zstd passed

configure:6676: gcc -o conftest  -fno-strict-aliasing -I//scratch2/BMC/gsienkf/whitaker/conda-envs/mpi4py/include -L/scratch2/BMC/gsienkf/whitaker/conda-envs/mpi4py/lib conftest.c -lzstd  -lxml2 -lcurl  >&5
configure:6676: $? = 0
configure:6693: result: -lzstd
configure:6705: checking whether libzstd library is available
configure:6707: result: yes

No idea what is going on.

I bumped into the same issue... - the system zstd is not installed, but the gcc got built with a separate zstd, and somehow the path to this libzstd "got lost". So adding this directory with the libzstd to LDFLAGS "fixes" this problem (at. least for me) ./configure ......... LDFLAGS="-L/lib/ -Wl,-rpath,/lib/" (this is scientific linux 7.7 here - hope it helps as an inspiration ;-))

Thanks for the insight.

Thanks @sb22bs for share it.