Yambo Community Forum

Dear Bramchari,

of course, the internal versions of netcdf/netcdff/hdf5 are supported, and there is no need to move to others.
The question is whether the compilation is actually working or not.

As a first step: try to have a clean and simple compilation (try specifying to configure as few options as possible) and check whether that is working.

If the problem persists, and we still believe the problem is related to netcdf, you may want to use existing netcdf libs available in the system, or, eventually to re-compile them yourself
(in this latter case you may want to take the lib tar balls from yambo/libs/archive). In these latter cases, you may want to ask for the support of your system admin (if not comfortable with lib compiling and alike)

take care
Andrea

Dear sir,
Thank you for the reply. I would like to know that how should I check that internal compilation of netcdf and hdf is correct or not after compilation. Could you tell me the file where the information will be stored?.

Regards,

Dear developers,
I configure yambo by giving few options to configure and recompile. However the problem persists when I run p2y.

[ERROR] Writing File ./SAVE//ns.db1; Variable NOT DEFINED; Permission denied.

Options are given below
./configure CC=icc PFC=mpiifort FC=ifort MPIFC=mpiifort MPIF77=ifort MPICC=mpiicc F77=ifort F90=ifort --with-fft-libs="-L$fftwdir/lib -lfftw3" --with-fft-path=$fftwdir --enable-int-linalg

I need help to rectify this error.
Regards,

At this point, here I'd need to try to reproduce the p2y error.
Can you send the scf and nscf input files (+ pseudopot in case) ?
Andrea

Dear Sir,
Thank you for replying again and again and helping me. Attached is the files scf, nscf and pseudo potential file for hBN. These files are used for testing the proper compilation of the Yambo-5.0.3.

Regards,

Dear Bramchari,

using yambo 5.0.3 compiled with ifort version 19.1.0.166 (either internal or external netcdf/hdf5)
and qe-6.8 (also compiled with the same intel compiler),
everything works fine in my case, and I am not able to reproduce the problem.

take care
Andrea

Dear Sir,
By following your suggestion I tried to install qe-6.8 with the same compiler that I have used for yambo. Configure works fine. But the following message appears during the make for qe-6.8.

force_hub_gpu.f90(1543): catastrophic error: **Internal compiler error: internal abort** Please report this error along with the circumstances in which it occurred in a Software Problem Report. Note: File and line given may not be explicit cause of this error.
compilation aborted for force_hub_gpu.f90 (code 1)
make[2]: *** [force_hub_gpu.o] Error 1
make[2]: Leaving directory `/home/bkhamari/Software/q-e-qe-6.8/PW/src'
make[1]: *** [pw-lib] Error 1
make[1]: Leaving directory `/home/bkhamari/Software/q-e-qe-6.8/PW'
make: *** [pwlibs] Error 1

Regards,

Dear Bramchari,

I mentioned qe-6.8 to be precise about my setup. Nevertheless, I've also tried qe-6.3 and qe-6.6 (all combined with y5.0.3) and all worked with me.
So, if any, I consider using a newer version of the intel compiler (eg >= psxe_2020 ).

Andrea

BTW:
For the sake of completeness, getting "internal compiler error" means that the compiler crashed unexpectedly, and this can be associated to a compiler bug.
Optimizations (as well as advanced features such as openmp support) are often at the origin of these behaviour.
A typical workaround is to lower the optimisation level (using -O0 instead of -O2 or -O3) just the for compilation of the specific file raising the problems (in QE you need to edit make.inc), then going back to the pristine optimisation level.

Dear Sir,
I have installed qe-6.6 with intel-19 and like to install yambo-5.0.3 with the same compiler. When I untar the tar file of yambo5, I got the empty yambo folder inside yambo5.0.3/lib. I do not have the internet access. So I put the required library in archive. Can you suggest steps to follow just to check whether I have followed the procedure properly in my earlier compilation.

Regards,

Dear Developers,

With the qe-6.6 and yambo-5.0.3 with intel-19 is also not working for me. Compilation of yambo is done by using internal netcdf and hdf5. The error remains as it is -Writing File ./SAVE//ns.db1; Variable NOT DEFINED; Permission denied when p2y is performed.

Now I am left with a option of installing the netcdf and hdf5 (manually) and linking them externally to configure. However, I am confuse with the netcdf.

Following itemize things I would like to know

i) Should I use netcdf-c-4.7.4.tar.gz or netcdf-fortran-4.5.3.tar.gz or both. Also like to know the version of hdf5.

ii) How to configure netcdf and hdf5 with intel.

iii) how to link while configuring Yambo.

Any help will be appreciated.

Regards,