ABINIT Discussion Forums

Hi, Sorry for the slow reaction... It is necessary to start from the beginning, i.e. know the environment From your batch script, can you run the following commands to fix the env : module load cdt/19.06 module load intel/18.0.0.128 module swap PrgEnv-cray PrgEnv-intel module load cray-fftw/3.3.8.3 ...

Hi,

configure: error: unrecognized option: `--with_mpi_prefix=/opt/cray/pe/craype/2.6.1/bin/

can you try with
or jmb

Hi, Officially, we do not build packages for Abinit... But, there are some possible sources anyway: - https://github.com/abinit/abiconda - under Ubuntu 18.04 (old version ) : apt search abinit abinit/bionic 8.0.8-4 amd64 package for electronic structure calculations abinit-data/bionic,bionic 8.0.8-4...

Hi,

Perhaps here : https://www.abinit.org/sites/default/fi ... tials.html

Hi,

Maybe some packages are missing depending on your OS

We find /usr/include/sys/socket.h :
- for Ubuntu 18 : libc6-dev-amd64
- for CentOS 7 : glibc-headers-2.17-323.el7_9.x86_64

Hello, there is obviously a problem with the generation of the XMLF90 v1.5.3.1 fallback doc Neither of the two necessary software ( Latex and doxygen ) was installed on our testfarm builders :? They could not have reported this bug... :? in the XMLF90 v1.5.4.0 version, the doc is no longer generated...

Hi, You can find this information : 1) on the ABINIT website : https://www.abinit.org/fallbacks 2) in the tarball : config/specs/fbversion.conf [9.2] atompaw = 4.1.0.6 bigdft = abinit-1.7.1.28 hdf5 = 1.10.6 libpsml = 1.1.7 libxc = 4.3.4 lapack = abinit_6.10 netcdf4 = 4.6.3 netcdf4_fortran = 4.5.2 wa...

Hi, This is not a YAML issue. The code aborts when we try to create a netcdf4 file with MPI-IO support so I believe the problem is not in the MPI library but in the hdf5/netcdf4/netcdf-fortran software stack (that depends on MPI). Perhaps one of these libraries has been compiled using different mpic...

Hi, I don't have access to a Cray ;) it seems that the lib contains blas/lapack, blacs/scalapack and fftw. maybe I can help you... usable with abinit 9.x we need to build this part of the configuration ( I guess the library is called libsci :? ) : # BLAS/LAPACK with_linalg_flavor="custom" LINALG_CPP...

Hi,

missing python cmd...

see this post :

viewtopic.php?f=3&t=4482#p13271

jmb

Hi,

there is a "syntax" error :

mpirun abinit -j 12 < files_file

Of course, don't forget to compile ABINIT with OMP support ( intel : -qopenmp , gnu : -fopenmp )

jmb

Hi, something strange... in your first post ( 24 Oct ), You used abinit 9.2.1 with_libxc=/home/sunlight/work/abinit/abinit-9.2.1/buildfallbacks/install/libxc-5.0.0 PS : We do not support libXC 5.0.0 yet. ! in your lst post, you used abinit 9.0.4 /home/sunlight/work/abinit/abinit-9.0.4/build/fallback...

Hi, in your ac file, there are a few unnecessary "extra" lines that may have produced the problem : # MPI settings FC="mpiifort" CC="mpiicc" CXX="mpiicpc" with_mpi="yes" enable_mpi_io="yes" # linear algebra settings with_linalg_flavor="mkl" LINALG_CPPFLAGS="-I${MKLROOT}/include" LINALG_FCFLAGS="-I${...

Hi,

= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 12136 RUNNING AT c29
= EXIT CODE: 6
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES

The error message is from the system, not Abinit.

Hi,

Where did you download the tarball?

Link found in abinit website :

https://www.abinit.org/sites/default/fi ... 2.1.tar.gz

The configure script is present !

A+

jmb

Hi,

use OpenMP and/or use THREADS with atlas

jmb

see viewtopic.php?f=3&t=4482#p13271
jmb

Hi,
need more infos...

the output of ./configure

jmb

Hi, these are the modules used : module load EasyBuild module load Python/3.6.6-intel-2018b module load intel/2018b module load iimpi/2018b module load HDF5/1.10.2-intel-2018b module load libxc/3.0.1-intel-2018b module load netCDF/4.6.1-intel-2018b module load netCDF-Fortran/4.4.4-intel-2018b module...

Hi, make check-local make[3]: Entering directory `/users/home/shiva/tools/abinit-8.10.3/build/tests' [ -f "runtests.py" ] && ./runtests.py fast -o1 --no-colors --no-logo || ../../tests/runtests.py fast -o1 --no-colors --no-logo --with-pickle=0 ... [fast][t00][np=1]: fldiff.pl fatal error: Unable to ...

Hi, your configure command reformatted for readability ;-) CC=mpiicc CXX=mpiicpc FC=mpiifort F77=mpiifort \ ../configure \ --with-mpi=/public1/soft/mpich/3.1.4 \ --with-linalg=/public1/soft/intel/2018/compilers_and_libraries_2018.2.199/linux/mkl \ --with-hdf5=/public1/home/sc30842/tarballs/hdf5-inst...

I'm sorry, my mistake...

it seems it's a problem with the linalg librairy !

I need more information

which options do you use for the ./configure?
if you use an ac file, what is the content?
the output at the end of the configure

jmb

Hi, concerning the config.log, I didn't see anything serious. most of the errors are expected: the configure tests the existence of a series of libraries, tools, system features... concerning make check which kind of errors ? concerning the errors libi40iw -i40iw_vmapped_qp: failed to pin memory for...

Hi, your ac9 file without comment : CC="mpicc" CFLAGS="-O2 -xCore-AVX512 -ftz -fp-speculation=safe -fp-model source -mkl=cluster" CXX="mpic++" CXXFLAGS="-O2 -xCore-AVX512 -ftz -fp-speculation=safe -fp-model source -mkl=cluster" FC="mpif90" FCFLAGS="-O2 -xCore-AVX512 -ftz -fp-speculation=safe -fp-mod...

Hi, I noticed that under Ubuntu >=18, the python command doesn't exist even if a python package ( 2.x or 3.x ) is installed... :shock: you have to manually create a symbolic link or use the os script : update-alternatives cd /usr/bin ln -s python3.6 python during the ./configure, there is a python s...