Search found 355 matches
- Sun Jun 20, 2021 1:25 pm
- Forum: Configuring and compiling ABINIT
- Topic: MPI support for ABINIT 9.4.1 on a Cray XC40 cluster
- Replies: 3
- Views: 83323
Re: MPI support for ABINIT 9.4.1 on a Cray XC40 cluster
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 ...
- Thu Jun 03, 2021 1:46 pm
- Forum: Configuring and compiling ABINIT
- Topic: MPI support for ABINIT 9.4.1 on a Cray XC40 cluster
- Replies: 3
- Views: 83323
Re: MPI support for ABINIT 9.4.1 on a Cray XC40 cluster
Hi,
or
jmb
can you try withconfigure: error: unrecognized option: `--with_mpi_prefix=/opt/cray/pe/craype/2.6.1/bin/
Code: Select all
--with-mpi=/opt/cray/pe/craype/2.6.1/
Code: Select all
--with-mpi="yes"
export FC="mpifort"
export CC="mpicc"
export CXX="mpicxx"
- Tue May 11, 2021 10:48 am
- Forum: Link to other codes
- Topic: Package 'abinit' has no installation candidate [SOLVED]
- Replies: 1
- Views: 11874
Re: Package 'abinit' has no installation candidate [SOLVED]
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...
- Mon May 10, 2021 8:50 pm
- Forum: Link to other codes
- Topic: Where to find old NC PSP [SOLVED]
- Replies: 2
- Views: 12006
- Mon May 10, 2021 11:30 am
- Forum: Configuring and compiling ABINIT
- Topic: Compilation error for abinit-9.4.2
- Replies: 1
- Views: 8107
Re: Compilation error for abinit-9.4.2
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
Maybe some packages are missing depending on your OS
![Question :?:](./images/smilies/icon_question.gif)
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
- Tue Mar 16, 2021 2:34 pm
- Forum: Configuring and compiling ABINIT
- Topic: Error when compiling abinit-9.4.0 fallbacks
- Replies: 1
- Views: 7737
Re: Error when compiling abinit-9.4.0 fallbacks
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...
- Sat Jan 23, 2021 10:48 am
- Forum: Configuring and compiling ABINIT
- Topic: Running Abinit in virtual box Ubuntu [SOLVED]
- Replies: 5
- Views: 18186
Re: Running Abinit in virtual box Ubuntu [SOLVED]
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...
- Fri Dec 04, 2020 10:05 am
- Forum: Configuring and compiling ABINIT
- Topic: No YAML Error found abinit-9.2.2 [SOLVED]
- Replies: 5
- Views: 16224
Re: No YAML Error found abinit-9.2.2 [SOLVED]
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...
- Fri Nov 06, 2020 3:20 pm
- Forum: Configuring and compiling ABINIT
- Topic: CCE + Cray Libsci build
- Replies: 1
- Views: 7684
Re: CCE + Cray Libsci build
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...
- Fri Nov 06, 2020 2:52 pm
- Forum: Configuring and compiling ABINIT
- Topic: error while executing make for abinit-9.0.2 [SOLVED]
- Replies: 5
- Views: 16818
- Mon Nov 02, 2020 2:49 pm
- Forum: Configuring and compiling ABINIT
- Topic: Abinit uses small percentage of CPU [SOLVED]
- Replies: 4
- Views: 13576
Re: Abinit uses small percentage of CPU [SOLVED]
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
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
- Mon Nov 02, 2020 2:41 pm
- Forum: Configuring and compiling ABINIT
- Topic: why the HDF5 and libxc is enable but not work? [SOLVED]
- Replies: 5
- Views: 15841
Re: why the HDF5 and libxc is enable but not work? [SOLVED]
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...
- Mon Oct 26, 2020 8:37 pm
- Forum: Configuring and compiling ABINIT
- Topic: why the HDF5 and libxc is enable but not work? [SOLVED]
- Replies: 5
- Views: 15841
Re: why the HDF5 and libxc is enable but not work? [SOLVED]
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${MKLROOT}/include" LINALG_FCFLAGS="-I${...
- Mon Oct 26, 2020 8:27 pm
- Forum: Configuring and compiling ABINIT
- Topic: tutorial base1 and base2 [SOLVED]
- Replies: 2
- Views: 12735
Re: tutorial base1 and base2 [SOLVED]
Hi,
The error message is from the system, not Abinit.= 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
- Mon Oct 26, 2020 8:24 pm
- Forum: Configuring and compiling ABINIT
- Topic: A question for 9.2.1
- Replies: 3
- Views: 8085
Re: A question for 9.2.1
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
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
- Thu Oct 22, 2020 11:26 pm
- Forum: Configuring and compiling ABINIT
- Topic: Abinit uses small percentage of CPU [SOLVED]
- Replies: 4
- Views: 13576
Re: Abinit uses small percentage of CPU [SOLVED]
Hi,
use OpenMP and/or use THREADS with atlas
jmb
use OpenMP and/or use THREADS with atlas
jmb
- Thu Oct 22, 2020 11:21 pm
- Forum: Configuring and compiling ABINIT
- Topic: Error in Compiling and Make with Abinit-9.0.4
- Replies: 2
- Views: 7738
- Sun Oct 18, 2020 8:54 pm
- Forum: Configuring and compiling ABINIT
- Topic: Configure Error: Parallel version - removed option --enable-mpi [SOLVED]
- Replies: 7
- Views: 8230
Re: Configure Error: Parallel version - removed option --enable-mpi [SOLVED]
Hi,
need more infos...
the output of ./configure
jmb
need more infos...
the output of ./configure
jmb
- Thu Oct 08, 2020 11:02 am
- Forum: Configuring and compiling ABINIT
- Topic: error while executing make for abinit-9.2.1 on NIC4 cluster [SOLVED]
- Replies: 2
- Views: 4566
Re: error while executing make for abinit-9.2.1 on NIC4 cluster [SOLVED]
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...
- Wed Aug 26, 2020 12:39 pm
- Forum: Ground state
- Topic: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation [SOLVED]
- Replies: 8
- Views: 376299
Re: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation [SOLVED]
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 ...
- Thu Aug 20, 2020 3:51 pm
- Forum: Configuring and compiling ABINIT
- Topic: NetCDF Fortran is not WORKING in 9.0.4
- Replies: 3
- Views: 3913
Re: NetCDF Fortran is not WORKING in 9.0.4
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...
- Thu Aug 20, 2020 3:13 pm
- Forum: Configuring and compiling ABINIT
- Topic: Undefined reference to `dgesvd_' issue [SOLVED]
- Replies: 4
- Views: 5698
Re: Undefined reference to `dgesvd_' issue [SOLVED]
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
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
- Wed Aug 19, 2020 10:26 am
- Forum: Ground state
- Topic: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation [SOLVED]
- Replies: 8
- Views: 376299
Re: Segmentation fault - invalid memory reference error in abinit-8.10.3 when running ground state calculation [SOLVED]
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...
- Tue Aug 18, 2020 11:10 am
- Forum: Configuring and compiling ABINIT
- Topic: Abinit 9.0.4, linalg segfault on cluster [SOLVED]
- Replies: 2
- Views: 4451
Re: Abinit 9.0.4, linalg segfault on cluster [SOLVED]
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...
- Sun Aug 16, 2020 6:00 pm
- Forum: Configuring and compiling ABINIT
- Topic: Undefined reference to `dgesvd_' issue [SOLVED]
- Replies: 4
- Views: 5698
Re: Undefined reference to `dgesvd_' issue [SOLVED]
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...