Yambo Community Forum

Dear Yambo Developers,
I installed the Intel one API suite (lBaseKit_p_2022.3.0.8767_offline.sh and lHPCKit_p_2022.3.0.8751_offline.sh) on the CentOS 7 system (Intel(R) Xeon(R) CPU E5-2686 v4 ). I tried to compile yambo5.1.1 using the following command (Use root account),
./configure --enable-uspp --enable-memory-profile --enable-options-check --with-blas-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-lapack-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-blacs-libs="-lmkl_blacs_intelmpi_lp64" --with-scalapack-libs="-lmkl_scalapack_lp64" --with-fft-libs="-mkl" FCFLAGS="-O2 -limf -assume bscc -nofor_main"
make all
The final display shows the following error:
make[2]: *** [mod_pars.o] Error 1
mod_pars.f90(26): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [NETCDF]
[driver] yambo (checking work to be done)
yambo linking failed. Check log/compile_yambo.log
mod_pars.f90(26): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [NETCDF]
make[1]: *** [yambo] Error 1
yambo build failed

All external libraries have been manually downloaded and placed on yambo-5.1.1.lib/archive
(This folder contains blacs.tar.gz hdf5-1.12.0.tar.gz package.list
etsf_io-1.0.4.tar.gz iotk-y1.2.2.tar.gz petsc-3.14.6.tar.gz
fftqe.tar.gz lapack-3.9.1.tar.gz pnetcdf-1.12.1.tar.gz
fftw-3.3.6-pl1.tar.gz libxc-5.1.5.tar.gz scalapack-2.1.0.tar.gz
futile-yambo.tar.gz Makefile.loc slepc-3.14.2.tar.gz
git.list netcdf-c-4.7.4.tar.gz yaml-0.2.2.tar.gz
git.list.in netcdf-fortran-4.5.3.tar.gz Ydriver-1.1.0.tar.gz
)

Please see the attached log files.
Any suggestions or help will be greatly appreciated!!
Best wishes,
YuLong

Dear YuLong,
please sign your posts with your name and affiliation, this is a rule of the forum, and you can do once for all by filling your user profile.

The error reported in the compile_yambo.log shows that there was a issue on the compilation of the netcdf libraries.
Please, send all the file .log that you have in the log directory.

Best,
Nicola

Nicola Spallanzani wrote: Tue Jul 01, 2025 3:28 pm Dear YuLong,
please sign your posts with your name and affiliation, this is a rule of the forum, and you can do once for all by filling your user profile.

The error reported in the compile_yambo.log shows that there was a issue on the compilation of the netcdf libraries.
Please, send all the file .log that you have in the log directory.

Best,
Nicola

Dear Nicola,
Thank you for your prompt response and reminder. I uploaded all the log files, and at the same time, I found this prompt during the make all process
\t[netcdf-fortran-4.5.3] configuration
\t[netcdf-fortran-4.5.3] compilation
\t[netcdf-fortran-4.5.3] installation
chmod: cannot access ‘/root/Downloads/yambo-5.1.1/lib/external/intel/mpiifort/v4/parallel/lib*/*netcdff*a’: No such file or directory

Best,
Yu Long, PhD
College of Chemistry and Chemical Engineering
Yangzhou University, Yangzhou, P. R. China

Dear YuLong,
I'm really sorry for the very late reply.
From the file configure_netcdf-c-4.7.4.log, I see that the configure procedure is not able to find the z library.
So please checks in the modules of the cluster if the library is already installed and load it before the yambo installation. Otherwise, if you are the administrator of the machine, you can install the z library from the package repository of the OS. Make sure you install also the header files of the z library (usually in a *-dev package).
Unfortunately you will also need to delete the hdf5 installation because is done without the z library and netcdf will complain that.

So before to restart the installation delete this directory:
/root/Downloads/yambo-5.1.1/lib/external/intel/mpiifort/v4/parallel/

and launch the command
make distclean

After that restart the installation from the launch of the configure line.

Best,
Nicola