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Installation issues with netcdf, Yambo version 5.1.0
Posted: Fri Mar 24, 2023 2:53 pm
by stefan19rkc
Dear all,
I'm having issues compiling the newest version of Yambo. I'm using the same settings a colleague used for the previous version (5.0), but it doesn't work, either because of the version difference, or a different environment. I am using a HPC cluster and am trying to install it there.
The main problems that pop out when trying to "make yambo" are the following:
Code: Select all
chmod: cannot access ‘/home/bepsvelj/yambo/lib/external/intel/mpiifort/v4/serial/lib*/*netcdf*a’: No such file or directory
chmod: cannot access ‘/home/bepsvelj/yambo/lib/external/intel/mpiifort/v4/serial/lib*/*netcdff*a’: No such file or directory
chmod: cannot access ‘/home/bepsvelj/yambo/lib/external/intel/mpiifort/lib*/*xc*a’: No such file or directory
Please find the config.log file and the whole log folder attached and let me know if you need any additional information.
Kind regards,
Stefan Velja
PhD Student,
Carl von Ossietzky University Oldenburg
Re: Installation issues with netcdf, Yambo version 5.1.0
Posted: Fri Mar 24, 2023 3:54 pm
by Nicola Spallanzani
Dear Stefan,
try using the newer version 5.1.1
https://github.com/yambo-code/yambo/arc ... 1.1.tar.gz
and follow this procedure:
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export FC=ifort
export F77=ifort
export CPP="icc -E -ansi"
export CC=icc
export FPP="fpp -free -P"
export F90SUFFIX=".f90"
export MPIFC=mpiifort
export MPIF77=mpiifort
export MPICC=mpiicc
export MPICXX=mpiicpc
./configure \
--enable-open-mp --enable-mpi --enable-par-linalg \
--enable-msgs-comps --enable-time-profile --enable-memory-profile \
--with-blas-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" \
--with-lapack-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" \
--with-scalapack-libs="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64" \
--with-blacs-libs="-L${MKLROOT}/lib/intel64 -lmkl_blacs_intelmpi_lp64" \
--with-fft-includedir="${MKLROOT}/include" \
--with-fft-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" \
--with-extlibs-path=${HOME}/opt/yambo-ext-libs
make -j4 core
let me know if this works.
Best,
Nicola
Re: Installation issues with netcdf, Yambo version 5.1.0
Posted: Fri Mar 24, 2023 7:05 pm
by stefan19rkc
Dear Nicola,
Thank you very much for your very fast response! I tried several things, including copying your instructions exactly, but I keep getting the following errors:
gzip: stdin: unexpected end of file
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now
gtar: This does not look like a tar archive
gtar: Exiting with failure status due to previous errors
WARNING: I can't seem to be able to run `tar' with the given arguments.
You may want to install GNU tar or Free paxutils, or check the
command line arguments.
\t[libxc-5.1.5] configuration
\t[libxc-5.1.5] compilation
\t[libxc-5.1.5] installation
and
chmod: cannot access ‘/home/bepsvelj/opt/yambo-ext-libs/intel/mpiifort/lib*/*xc*a’: No such file or directory
Please note that I did use tar to extract the downloaded Yambo tar.gz file, so I assume it's already installed. You can find the new logs attached.
Thanks once again,
Stefan Velja
PhD Student,
Carl von Ossietzky University Oldenburg
Re: Installation issues with netcdf, Yambo version 5.1.0
Posted: Mon Mar 27, 2023 11:07 am
by stefan19rkc
Dear all,
Here's an update: there seems to have been some security measurements on the cluster which prevented the file from downloading correctly. I downloaded it to my PC and uploaded it from there. Then, after following Nicola's suggested steps, it compiled correctly. At least, I have 5 files in my bin folder (a2y, c2y, p2y, yambo, ypp).
Thank you very much once again Nicola for your advice.
Kind regards,
Stefan Velja
PhD Student,
Carl von Ossietzky University Oldenburg
Re: Installation issues with netcdf, Yambo version 5.1.0
Posted: Tue Mar 28, 2023 8:51 am
by Nicola Spallanzani
Dear Stefan,
you are right, now I understand what uppened. Few days ago there was an issue on the server hosting the libxc library releases.
The file downloaded in lib/archive/libxc-x.x.x.tar.gz probably is corrupted. And every time you try to use it the library compilation fails. But yambo will continue to try to use it because it is available.
So please delete it and try again the installation in the cluster with before a "make distclean".
Best,
Nicola
Re: Installation issues with netcdf, Yambo version 5.1.0
Posted: Thu Mar 20, 2025 8:27 am
by ezekiel
Dear Nicola,
I encountered similar problem. The solution you gave to the problem is not clear to me. Do l need to download libxc...gz again and reinstall?
Thank you.
Ezekiel
Re: Installation issues with netcdf, Yambo version 5.1.0
Posted: Thu Mar 20, 2025 10:26 am
by Nicola Spallanzani
Dear Ezekiel,
which version of Yambo are you using?
Because with the last version 5.3.0 it may happen a different issue related to libxc, only similar to this one.
If the problem is what I think you may need to check if all autotool packages are installed (autoconf, automake, libtool). How to install them it depends on the OS that you are using.
Let me know if you need more help. In that case send the content of the "log" directory and also the config.log file.
Best,
Nicola
Re: Installation issues with netcdf, Yambo version 5.1.0
Posted: Thu Mar 20, 2025 11:46 am
by ezekiel
Hi Nicola,
The version I'm installing is 5.1.1. A Log file is attached. Thank you
Re: Installation issues with netcdf, Yambo version 5.1.0
Posted: Thu Mar 20, 2025 11:58 am
by ezekiel
Hi Nicola,
The config.log file is attached
Re: Installation issues with netcdf, Yambo version 5.1.0
Posted: Tue Mar 25, 2025 12:12 pm
by Nicola Spallanzani
ezekiel wrote: ↑Thu Mar 20, 2025 11:46 am
Hi Nicola,
The version I'm installing is 5.1.1. A Log file is attached. Thank you
Ok, the problem is that the developers of the libxc libraries changed the repository where to download the tarball. Unfortunately they also changed the content of the tarball. So Yambo 5.1.1 is not anymore able to compile atomatically the library. You have two possible solutions:
1) download and install manually the libxc library from here
https://gitlab.com/libxc/libxc/-/archiv ... 2.3.tar.gz
and then link the library with the yambo configure flag "--with-libxc-path=/path/to/the/libxc/prefix"
2) download and install yambo 5.3.0
Best regards,
Nicola