-
Notifications
You must be signed in to change notification settings - Fork 13
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
[BUG/ISSUE] "-lhdf5_hl -lhdf5" flags break compilation #37
Comments
I saw no hard-coded
which gives you this annoying $ $(spack location -i netcdf-fortran)/bin/nf-config --flibs
-L/home/centos/spack/opt/spack/linux-centos7-x86_64/intel-19.0.4/netcdf-fortran-4.4.5-tuuki3kp5ngtji3m54zjw3bkh7ri2num/lib -lnetcdff -L/home/centos/spack/opt/spack/linux-centos7-x86_64/intel-19.0.4/netcdf-4.7.0-sale32bbd3tize6jgjq6npfvgrfeyw65/lib -lnetcdf -lnetcdf -lhdf5_hl -lhdf5 -lz -lm |
Same problem with 12.5.0. See geoschem/GCHP#17 (comment) for a log containing this HDF5 error. |
I can confirm this will also be the case for GEOS-Chem Classic when generating the final This is specified in NC_LINK_CMD := $(shell $(GC_F_BIN)/nf-config --flibs)
|
In a container environment (with almost no pre-installed libraries), the |
Now 12.3.2 can be successfully compiled. Ref: geoschem/GCHP#37 (comment)
@jimmielin @JiaweiZhuang Have either of you verified if this issue is still an open issue when using CMake? I also wonder about using the latest GCHP which has an updated ESMF. |
I am closing this issue since there has been no responses. The problematic code is in Makefiles that will be retired in the next version (13.0). |
Describe the bug
During compilation, some commands contain
-lhdf5_hl -lhdf5
but don't specify the HDF5 library path via-L
:Full compile log: compile_hdf5_error.log
This can be solved by a dirty fix that copies HDF5 libraries into NetCDF directory:
Successful compile log: compile_success.log
To Reproduce
spack -v install netcdf-fortran %intel ^hdf5+fortran+hl ^intel-mpi
make build_all
The environment config is:
Environment
The text was updated successfully, but these errors were encountered: