after upgrade of my ubuntu I had to recompile abinit with the new gcc.
The compilation went well…but when I started running abinit I’ve got an error message:
— !ERROR
src_file: m_nctk.F90
src_line: 2788
mpi_rank: 0
message: |
nf90_def_var - NetCDF library returned: NetCDF: Name contains illegal characters
the hdf5 and Netcdf I am using are those of the fallbacks.
I thought the problem comes from the parallelization of theses libraries…but the summary of the configuration says that hdf5 and Netcdf are both parallel.
I don’t know your Ubuntu version
but here is a recipe with a fresh Ubuntu 23.10 with abinit 9.10.3 built with Ubuntu fallbacks !
Checks if python exists :
which python
if not but python3 exists then :
cd /etc
ln -s python3 python
apt install python3-dev
Packages to be installed ( gcc (Ubuntu 13.2.0-4ubuntu3) )
apt install gfortran
apt install openmpi-common openmpi-bin
apt install libhdf5-openmpi-fortran-102 libhdf5-openmpi-dev
apt install libnetcdf-dev libnetcdff-dev
apt install libnetcdf-mpi-dev
apt install libpnetcdf-dev libnetcdf-pnetcdf-dev
Linalg : OpenBLAS
export OPENBLAS_NUM_THREADS=1
export GOTO_NUM_THREADS=1
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
apt install libopenblas-dev
LibXC
caution : The LibXC package does not provide the 3rd derivatives of energy!
You should recompile it using --enable-kxc configure option.
Otherwise Abinit will not be able to provide nonlinear response properties (Raman intensities, ...).
apt install libxc-dev
Need for parallel NetCDF
export CPPFLAGS_EXTRA="-I/usr/lib/x86_64-linux-gnu/netcdf/pnetcdf/include"
Building abinit
wget https://www.abinit.org/sites/default/files/packages/abinit-9.10.3.tar.gz
cd abinit-9.10.3 && mkdir -p build && cd build
../configure
Core build parameters
---------------------
* C compiler : gnu version 13.2
* Fortran compiler : gnu version 13.2
* architecture : intel xeon (64 bits)
* debugging : basic
* optimizations : standard
* OpenMP enabled : no (collapse: ignored)
* MPI enabled : yes (flavor: none)
* MPI in-place : no
* MPI-IO enabled : yes
* HDF5 enabled : yes (MPI support: yes)
* NetCDF enabled : yes (MPI support: yes)
* NetCDF-F enabled : yes (MPI support: yes)
* FFT flavor : goedecker (libs: auto-detected)
* LINALG flavor : netlib+openblas (libs: auto-detected)
* SCALAPACK enabled : no
* FCFLAGS : -g -ffree-line-length-none -fallow-argument-mismatch
Compilation
make -j 12
Testsuite
../../runtests.py fast -j 12 --no-logo
Thanks a lot for your help.
Concerning the libxc, I am using the one from the fallbacks (version 6.0.0)…do I have to recompile it as well with --enable-kxc or it’s already compiled with that option.
Many many thanks,
Samir
Let’s assume that you have already compiled abinit-9.10.3 in the build/ folder.
cd build/fallbacks
A priori, you should find the following files:
INSTALL
Makefile
README
abinit-fallbacks-9.8
build-abinit-fallbacks.sh
install_fb
you need to edit the file build-abinit-fallbacks.sh
and add after the line: "–disable-libpsml --disable-xmlf90 "
--disable_hdf5 --disable-netcdf4 --disable-netcdf4_fortran \
( this compiles only the libXC fallback )
then run the command :
./build-abinit-fallbacks.sh
when libXC compilation is complete, the script displays a line like ( corrects the beginning of path! ):
with_libxc=/root/WorkSpace/abinit-9.10.3/build/fallbacks/install_fb/gnu/13.2/libxc/6.0.0
go to the build dir :
cd ..
copy this line to a file : my_config.ac9
and restart the full compilation :
make clean
../configure --with-config-file='my_config.ac9'
make -j 12
cd tests
../../tests/runtests.py fast libxc -j 12 --no-logo
Suite failed passed succeeded skipped disabled run_etime tot_etime
fast 0 2 9 0 0 86.75 87.77
libxc 0 14 22 0 0 847.71 850.54
PS : in the configure output, you must see :
checking whether the LibXC library works... yes
checking whether the LibXC was compiled with Kxc derivatives... yes
I checked that LibXC was compiled with Kxc and I thought every thing will run smoothly!!!
Unfortunately, and as you see in the configuration summary below, I followed the steps you recommended one by one, I am still having the problem of parallelization for hdf5, NETCDF and NETCDF-Fortran:
- C compiler : gnu version 13.2
-
Fortran compiler : gnu version 13.2
-
architecture : intel core_i7 (64 bits)
-
debugging : basic
-
optimizations : standard
-
OpenMP enabled : no (collapse: ignored)
-
MPI enabled : yes (flavor: auto)
-
MPI in-place : no
-
MPI-IO enabled : yes
-
GPU enabled : no (flavor: none)
-
LibXML2 enabled : yes
-
LibPSML enabled : no
-
XMLF90 enabled : no
-
HDF5 enabled : yes (MPI support: no)
-
NetCDF enabled : yes (MPI support: no)
-
NetCDF-F enabled : yes (MPI support: no)
-
FFT flavor : fftw3-threads (libs: auto-detected)
-
LINALG flavor : none (libs: ignored)
-
SCALAPACK enabled : no
-
ELPA enabled : no
-
MAGMA enabled : unknown (magma version >= 1.5 ? )
-
FCFLAGS : -g -ffree-line-length-none -fallow-argument-mismatch -fno-frontend-optimize -O2 -g -Wall -Wno-maybe-uninitialized -fbacktrace -pedantic -fcheck=all -I/usr/lib/x86_64-linux-gnu/netcdf/pnetcdf/include -I/usr/lib/x86_64-linux-gnu/include
-
NVCC_CFLAGS :
-
CPATH :
-
Build workflow : monolith
-
Did you see my remark in the first post :
Need for parallel NetCDF
export CPPFLAGS_EXTRA="-I/usr/lib/x86_64-linux-gnu/netcdf/pnetcdf/include"
copy/paste this line in shell
and restart configure
I noticed a small difference in the MPI :
in my config :
MPI enabled : yes (flavor: none)
in your config
MPI enabled : yes (flavor: auto)
can you execute this command :
dpkg -l | egrep "openmpi|hdf5|netcdf"
the result for my env :
ii hdf5-helpers 1.10.8+repack1-1ubuntu1
ii libcaf-openmpi-3:amd64 2.10.1-1
ii libcoarrays-openmpi-dev:amd64 2.10.1-1
ii libhdf5-103-1:amd64 1.10.8+repack1-1ubuntu1
ii libhdf5-cpp-103-1:amd64 1.10.8+repack1-1ubuntu1
ii libhdf5-dev 1.10.8+repack1-1ubuntu1
ii libhdf5-fortran-102:amd64 1.10.8+repack1-1ubuntu1
ii libhdf5-hl-100:amd64 1.10.8+repack1-1ubuntu1
ii libhdf5-hl-cpp-100:amd64 1.10.8+repack1-1ubuntu1
ii libhdf5-hl-fortran-100:amd64 1.10.8+repack1-1ubuntu1
ii libhdf5-mpi-dev 1.10.8+repack1-1ubuntu1
ii libhdf5-openmpi-103-1:amd64 1.10.8+repack1-1ubuntu1
ii libhdf5-openmpi-cpp-103-1:amd64 1.10.8+repack1-1ubuntu1
ii libhdf5-openmpi-dev 1.10.8+repack1-1ubuntu1
ii libhdf5-openmpi-fortran-102:amd64 1.10.8+repack1-1ubuntu1
ii libhdf5-openmpi-hl-100:amd64 1.10.8+repack1-1ubuntu1
ii libhdf5-openmpi-hl-cpp-100:amd64 1.10.8+repack1-1ubuntu1
ii libhdf5-openmpi-hl-fortran-100:amd64 1.10.8+repack1-1ubuntu1
ii libnetcdf-dev 1:4.9.2-2ubuntu1
ii libnetcdf-mpi-19:amd64 1:4.9.0-1ubuntu1
ii libnetcdf-mpi-dev:amd64 1:4.9.0-1ubuntu1
ii libnetcdf-pnetcdf-19:amd64 1:4.9.0-1ubuntu1
ii libnetcdf-pnetcdf-dev:amd64 1:4.9.0-1ubuntu1
ii libnetcdf19:amd64 1:4.9.2-2ubuntu1
ii libnetcdff-dev 4.6.0+really4.5.4+ds-3
ii libnetcdff7:amd64 4.6.0+really4.5.4+ds-3
ii libopenmpi-dev:amd64 4.1.5-3ubuntu1
ii libopenmpi3:amd64 4.1.5-3ubuntu1
ii libpnetcdf-dev:amd64 1.12.3-2
ii libpnetcdf0d:amd64 1.12.3-2
ii openmpi-bin 4.1.5-3ubuntu1
ii openmpi-common 4.1.5-3ubuntu1
for the parallel NetCDF environment variable CPPFLAGS_EXTRA exported it again but still the same problem…
the command line dpkg -l | egrep "openmpi|hdf5|netcdf" gives:
ii hdf5-helpers 1.10.8+repack1-1ubuntu1 amd64 HDF5 - Helper tools
ii libcaf-openmpi-3:amd64 2.10.1-1 amd64 Co-Array Fortran libraries (OpenMPI)
ii libcoarrays-openmpi-dev:amd64 2.10.1-1 amd64 Co-Array Fortran libraries - development files (OpenMPI)
ii libhdf5-103-1:amd64 1.10.8+repack1-1ubuntu1 amd64 HDF5 C runtime files - serial version
ii libhdf5-cpp-103-1:amd64 1.10.8+repack1-1ubuntu1 amd64 HDF5 - C++ runtime files - serial version
ii libhdf5-dev 1.10.8+repack1-1ubuntu1 amd64 HDF5 - development files - serial version
ii libhdf5-fortran-102:amd64 1.10.8+repack1-1ubuntu1 amd64 HDF5 Fortran runtime files - serial version
ii libhdf5-hl-100:amd64 1.10.8+repack1-1ubuntu1 amd64 HDF5 High Level runtime files - serial version
ii libhdf5-hl-cpp-100:amd64 1.10.8+repack1-1ubuntu1 amd64 HDF5 High Level C++ runtime files - serial version
ii libhdf5-hl-fortran-100:amd64 1.10.8+repack1-1ubuntu1 amd64 HDF5 High Level Fortran runtime files - serial version
ii libhdf5-mpi-dev 1.10.8+repack1-1ubuntu1 amd64 HDF5 - development files - default MPI version
ii libhdf5-openmpi-103-1:amd64 1.10.8+repack1-1ubuntu1 amd64 HDF5 - C runtime files - OpenMPI version
ii libhdf5-openmpi-cpp-103-1:amd64 1.10.8+repack1-1ubuntu1 amd64 HDF5 - C++ runtime files - OpenMPI version - unsupported
ii libhdf5-openmpi-dev 1.10.8+repack1-1ubuntu1 amd64 HDF5 - development files - OpenMPI version
ii libhdf5-openmpi-fortran-102:amd64 1.10.8+repack1-1ubuntu1 amd64 HDF5 Fortran runtime files - OpenMPI version
ii libhdf5-openmpi-hl-100:amd64 1.10.8+repack1-1ubuntu1 amd64 HDF5 High Level runtime files - OpenMPI version
ii libnetcdf-dev 1:4.9.2-2ubuntu1 amd64 creation, access, and sharing of scientific data
ii libnetcdf-mpi-19:amd64 1:4.9.0-1ubuntu1 amd64 Interface for scientific data access to large binary data
ii libnetcdf-mpi-dev:amd64 1:4.9.0-1ubuntu1 amd64 creation, access, and sharing of array-oriented scientific data
ii libnetcdf-pnetcdf-19:amd64 1:4.9.0-1ubuntu1 amd64 Interface for scientific data access to large binary data
ii libnetcdf-pnetcdf-dev:amd64 1:4.9.0-1ubuntu1 amd64 creation, access, and sharing of array-oriented scientific data
ii libnetcdf19:amd64 1:4.9.2-2ubuntu1 amd64 Interface for scientific data access to large binary data
ii libnetcdff-dev 4.6.0+really4.5.4+ds-3 amd64 creation, access, and sharing of scientific data in Fortran
ii libnetcdff7:amd64 4.6.0+really4.5.4+ds-3 amd64 Fortran interface for scientific data access to large binary data
ii libopenmpi-dev:amd64 4.1.5-3ubuntu1 amd64 high performance message passing library – header files
ii libopenmpi3:amd64 4.1.5-3ubuntu1 amd64 high performance message passing library – shared library
ii libpnetcdf-dev:amd64 1.12.3-2 amd64 Development files for the parallel netCDF library
ii libpnetcdf0d:amd64 1.12.3-2 amd64 Libraryfor reading and writing parallel NetCDF files
ii openmpi-bin 4.1.5-3ubuntu1 amd64 high performance message passing library – binaries
ii openmpi-common 4.1.5-3ubuntu1 all high performance message passing library – common files
the auto for my openmpi configuration may come from the fact that I am configuring with --with-mpi : …/configure --with-mpi --with-config-file=‘my_config.ac9’
Otherwise abinit cannot find my mpi and it stops with:
configure: error: invalid MPI settings
Can you sent me the config.log ?
jmb
At the beginning of the config.log :
PATH: /home/samir/anaconda3/condabin
Ha! you use anaconda3: Right?
If some libraries are installed under the OS and also under Conda, it can cause some problems…
Give me some time to test under conda…
jmb
I am not sure that I’ve got your point!!!
Yes I used anaconda for some time but as far as I know the only think that is common between anaconda and abinit is python…and there is no a special setting for python in anaconda…so I don’t see how can this affect the setting/libraries needed for abinit?
many many thanks,
Samir
Perhaps I wasn’t precise: is conda activated when you run ./configure?
I once had a configuration in which the OS packages were installed ( e.g. :apt install hdf5 ) AND the packages installed in conda ( conda install hdf5 ) : the ./configure found the OS libs while make found the libs installed by conda…
my config only installs OS packages ( no conda installed )
Now I understand…
No, Conda is not activated when I configure abinit.
Samir
I finally successfully installed abinit-9.10.5 with parallel hdf5 and netcdf.
But I still have:
WARNING: unrecognized options: --enable-kxc
Or should we compile this version (9.10.5) without this option?
Many thanks
1 Like
I installed libxc from : apt install libxc-dev
then I make: …/configure --enable-kxc
but in the config.log I get:
checking whether the LibXC library works
result: yes
checking whether the LibXC was compiled with Kxc derivatives
result: no
the libxc-dev library in ubuntu 23 has not been compiled with the kxc option!
libxc 6.x.y must be compiled from source with the option: --enable-kxc
with intel compilers, add :
CFLAGS_LIBXC=“${CFLAGS_LIBXC} -traceback -Wall -O0 -fp-model=precise”
Is CFLAGS_LIBC the same for the gfortran wrapper (mpif90)?
no need to use CFLAGS_LIBXC with gfortran
jmb