Yambo Community Forum

Posted: **Thu May 29, 2025 6:59 am**

Dear all

I recently rebuild server with oneapi2025 and fail to complie yambo5.30. I read viewtopic.php?t=2822 and try ./configure, the output as follows:

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 ./configure CC=icx FC=ifx F77=ifx FPP="ifx -E -free -P" CPP="icx -E -ansi" MPICC=mpiicx MPIFC=mpiifx MPIF77=mpiifx   --enable-time-profile --enable-memory-profile --enable-mpi --enable-open-mp   --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-fft-libs="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl"   --with-fft-includedir=${MKLROOT}/include   --enable-slepc-linalg --enable-par-linalg   --with-blacs-libs="-L${MKLROOT}/lib/intel64 -lmkl_blacs_intelmpi_lp64"   --with-scalapack-libs="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64"
checking for vim... vim
checking for gcc... icx
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether icx accepts -g... no
checking for icx option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for malloc.h... yes
checking for struct mallinfo.arena... yes
checking for git... yes
fatal: not a git repository (or any of the parent directories): .git
checking for malloc.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for string.h... (cached) yes
checking for sys/time

Posted: **Thu May 29, 2025 8:04 am**

Dear Tang,
the problem is that the hdf5 library was not compiled properly, and consequentially the installation of netcdf-c and netcdf-fortran fail. So, in order to understand why, could you please send me the config.log file contained in the directory lib/hdf5/hdf5-1.12.2 ?

Also the files config/report and config/setup.

Finally I suggest to you to use the flag --with-extlibs-path in order to save the libraries in an external directory, so you don't need to rebuild them every time.

Best,
Nicola

Posted: **Thu May 29, 2025 10:44 am**

Dear Nicola,
Happy to hear your relpy
for unsolvable network problem, I do "make -f Makefile.loc" at "/lib/archive" as last compilation did(before rebiuld my server). It seems that I successfully download all the packages yambo need.

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jk@JK:~/opt/yambo-5.3.0/lib/archive$ ls
Makefile.loc             fftqe.tar.gz         git.list.in           libxc-5.2.3.tar.gz           petsc-3.22.0.tar.gz
blacs.tar.gz             fftw-3.3.10.tar.gz   hdf5-1.12.2.tar.gz    netcdf-c-4.9.0.tar.gz        scalapack-2.2.1.tar.gz
devicexlib-0.8.5.tar.gz  futile-yambo.tar.gz  iotk-y1.2.2.tar.gz    netcdf-fortran-4.6.0.tar.gz  slepc-3.22.0.tar.gz
etsf_io-1.0.4.tar.gz     git.list             lapack-3.12.0.tar.gz  package.list                 yaml-0.2.2.tar.gz

Here are the 3 files: config.log report setup

up.zip

Posted: **Fri May 30, 2025 8:38 am**

Dear Tang,
I found the same issue in the hdf5 github repository:
https://github.com/HDFGroup/hdf5/issues/2563

So probably they solved the issue in a newer release. You can ask to yambo to change the version of hdf5 from this file:
lib/archive/package.list

change the version like this (for example):
version_hdf5=1.14.6

Before to restart the compilation remember to run a distclean and then the configure again:

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make distclean
./configure [...] --with-extlibs-path=...  
make -j core

Let me know if this works.

Best,
Nicola

Posted: **Sun Jun 01, 2025 4:52 am**

Dear Nicola,
sorry to reply so late.

I have try the newest version version_hdf5. It seems that netcdf packages do not work under ifx and icx. As a result, automatic installation does not work So I try oneAPI2023 which has both ifx/icx and ifort/icc, and manage to install hdf5 and netcdf-c/fortran manually. I then add lib with "--with-netcdf-include=" "--with-netcdf-lib=". And it finally work.

All the installations mentioned are done with ifort and icc, I need ifx and icx for other uses.

Thanks for telling me the issue of ifx

Best
Tang
BNU

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