Search found 346 matches

by jbeuken
Mon Oct 26, 2020 8:37 pm
Forum: Configuration
Topic: why the HDF5 and libxc is enable but not work?
Replies: 2
Views: 48

Re: why the HDF5 and libxc is enable but not work?

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${MKLROOT}/include" LINALG_FCFLAGS="-I${...
by jbeuken
Mon Oct 26, 2020 8:27 pm
Forum: Configuration
Topic: tutorial base1 and base2
Replies: 1
Views: 29

Re: tutorial base1 and base2

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.
by jbeuken
Mon Oct 26, 2020 8:24 pm
Forum: Configuration
Topic: A question for 9.2.1
Replies: 3
Views: 39

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
by jbeuken
Thu Oct 22, 2020 11:26 pm
Forum: Configuration
Topic: Abinit uses small percentage of CPU
Replies: 1
Views: 41

Re: Abinit uses small percentage of CPU

Hi,

use OpenMP and/or use THREADS with atlas

jmb
by jbeuken
Sun Oct 18, 2020 8:54 pm
Forum: Configuration
Topic: Configure Error: Parallel version - removed option --enable-mpi [SOLVED]
Replies: 7
Views: 582

Re: Configure Error: Parallel version - removed option --enable-mpi [SOLVED]

Hi,
need more infos...

the output of ./configure

jmb
by jbeuken
Thu Oct 08, 2020 11:02 am
Forum: Configuration
Topic: error while executing make for abinit-9.2.1 on NIC4 cluster [SOLVED]
Replies: 2
Views: 837

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...
by jbeuken
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: 1331

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 ...
by jbeuken
Thu Aug 20, 2020 3:51 pm
Forum: Configuration
Topic: NetCDF Fortran is not WORKING in 9.0.4
Replies: 3
Views: 497

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...
by jbeuken
Thu Aug 20, 2020 3:13 pm
Forum: Configuration
Topic: Undefined reference to `dgesvd_' issue [SOLVED]
Replies: 4
Views: 551

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
by jbeuken
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: 1331

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...
by jbeuken
Tue Aug 18, 2020 11:10 am
Forum: Configuration
Topic: Abinit 9.0.4, linalg segfault on cluster [SOLVED]
Replies: 2
Views: 990

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...
by jbeuken
Sun Aug 16, 2020 6:00 pm
Forum: Configuration
Topic: Undefined reference to `dgesvd_' issue [SOLVED]
Replies: 4
Views: 551

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...
by jbeuken
Mon Aug 03, 2020 10:27 am
Forum: Configuration
Topic: Configure Error: Parallel version - removed option --enable-mpi [SOLVED]
Replies: 7
Views: 582

Re: Configure Error: Parallel version - removed option --enable-mpi [SOLVED]

Hi, I noticed that during the minimum ( or standard ) installation of Ubuntu 19 or 20, the python cmd is not "defined". python3 is installed by default, but the link "python" to "python3" is not made . However, during configure, a python script is executed with : #!/usr/bin/env python one way to sol...
by jbeuken
Mon Jul 20, 2020 10:56 am
Forum: Configuration
Topic: Configure Error: Parallel version - removed option --enable-mpi [SOLVED]
Replies: 7
Views: 582

Re: Configure Error: Parallel version - removed option --enable-mpi [SOLVED]

Hi,

the youtube video is very old and not applicable with abinit 9..x version

As an attachment, a beta version of a document explaining
the instatllation on Ubuntu 19 but which is adapted for Ubuntu 20.

jmb
by jbeuken
Sat Jul 18, 2020 10:19 pm
Forum: Configuration
Topic: OpenMP Support with Intel 19.1 Compiler
Replies: 1
Views: 266

Re: OpenMP Support with Intel 19.1 Compiler

Hi, 1/ I am not able to build ABINIT v8.10.3 with openMP support. enable_openmp="yes" is not working. Seems like adding this to config file is causing the build system to start looking for gfortran compiler. If I switch this off then build goes forward fine. abinit 8.10.3 has never been officially t...
by jbeuken
Fri Jul 17, 2020 3:05 pm
Forum: Pseudopotentials and PAW datasets
Topic: The eigenvector with band 1 has zero norm
Replies: 5
Views: 740

Re: The eigenvector with band 1 has zero norm

Hi Miro, but set the parameter "pawecutdg" sorry, forgot to add pawecutdg 50 in tpaw1_1.in :? :? now ../../../src/98_main/abinit < tpaw1_1.files > log 2> err cat err no error... then, there's a problem with your abinit binary which version of MPI do you use ? can you create an ac file ( file.ac ) : ...
by jbeuken
Thu Jul 16, 2020 10:38 pm
Forum: Pseudopotentials and PAW datasets
Topic: The eigenvector with band 1 has zero norm
Replies: 5
Views: 740

Re: The eigenvector with band 1 has zero norm

Hi Miro, I compile abinit 8.10.3 with intel 17 >module list Currently Loaded Modulefiles: 1) intel/compiler/17.0.3 2) OpenMPI/2.0.2-intel-17.0 cd tests/tutorial/Input >cat tpaw1_1.files tpaw1_1.in tpaw1_1.out tpaw1_1i tpaw1_1o tpaw1_1tmp ../../Psps_for_tests/6c.pspnc ../../../src/98_main/abinit < tp...
by jbeuken
Thu Jul 09, 2020 12:51 pm
Forum: Configuration
Topic: Recompiling Abinit with multicore support [SOLVED]
Replies: 16
Views: 828

Re: Recompiling Abinit with multicore support [SOLVED]

with OpenMPI 4.0.3 compiled by me with GNU 8.3.1, all tests succeeded :)

Code: Select all

Suite   failed  passed  succeeded  skipped  disabled  run_etime  tot_etime
paral        0      11         30       75         0     428.21     435.52
the openmpi package is too old and/or not complete :?
by jbeuken
Thu Jul 09, 2020 12:03 pm
Forum: Configuration
Topic: Recompiling Abinit with multicore support [SOLVED]
Replies: 16
Views: 828

Re: Recompiling Abinit with multicore support [SOLVED]

concerning the parallel tests... No YAML Error found in [paral][t77_MPI4][np=4] I also observed that some tests ( 21,22,24,26,41,51,77) crashed, all with the same error... :cry: this is caused either to the compiler version ( GNU 8.3.1 ) or a problem with OpenMPI 2.1.1 ( old ;) ) [paral][t80_MPI1][n...
by jbeuken
Thu Jul 09, 2020 11:54 am
Forum: Configuration
Topic: Recompiling Abinit with multicore support [SOLVED]
Replies: 16
Views: 828

Re: Recompiling Abinit with multicore support [SOLVED]

Sorry, I didn't know the actual core count of your machine... so it's better to use -j 4 or -n 4 -j 1 for parallel jobs concerning the GPU, it's quite complicated to install the tools to use a GPU ( CUDA, MAGMA, kernel driver,... ). And finally, not to gain in performance... it's a matter of a speci...
by jbeuken
Wed Jul 08, 2020 7:36 pm
Forum: Configuration
Topic: Recompiling Abinit with multicore support [SOLVED]
Replies: 16
Views: 828

Re: Recompiling Abinit with multicore support [SOLVED]

there are a lot of mistakes/typos in this cmd ./configure --with-dft-flavor="libxc" --enable-linalg=yes --with-trio-flavor="netcdf" --enable-openmpi="yes" with_openmpi="yes" with_mpi="yes" --enable-mpi="yes" try this ( now , really tested under Fedora 29 ;) ): yum install -y openmpi openmpi-devel mo...
by jbeuken
Wed Jul 08, 2020 4:09 pm
Forum: Configuration
Topic: Configure says HDF5 and netCDF have MPI support but the code doesn't (v9.0.4)
Replies: 3
Views: 291

Re: Configure says HDF5 and netCDF have MPI support but the code doesn't (v9.0.4)

With all packages installed, ABINIT's build system (BS) detects serial and parallel installed versions of HDF5 and netCDF . Unfortunately, the design of the packages is badly configured... :cry: In addition, there are toxic dependencies... :cry: e.g., installation of parallel netCDF implies installa...
by jbeuken
Wed Jul 08, 2020 12:38 pm
Forum: Configuration
Topic: Configure says HDF5 and netCDF have MPI support but the code doesn't (v9.0.4)
Replies: 3
Views: 291

Re: Configure says HDF5 and netCDF have MPI support but the code doesn't (v9.0.4)

Hi Martin,

which OS ?
if ubuntu, output of :

Code: Select all

dpkg -l | egrep -E "openmpi|hdf5|netcdf"
by jbeuken
Fri Jul 03, 2020 8:40 pm
Forum: Configuration
Topic: Recompiling Abinit with multicore support [SOLVED]
Replies: 16
Views: 828

Re: Recompiling Abinit with multicore support [SOLVED]

Dear ssh77, * C compiler : gnu version 8.3 * Fortran compiler: gnu version 8.3 * architecture : unknown unknown (64 bits) ... * OpenMP enabled : no (collapse: ignored) * MPI enabled : no * MPI-IO enabled : no * GPU enabled : no (flavor: none) still no MPI support -> "MPI enable : no " :roll: which m...