ABINIT Discussion Forums

Hi all,

I've just started learning to use ABINIT and Linux, and have a question regarding running the tutorial on the H2 atom.
I installed ABINIT 7.4.1 according to <http://www.youtube.com/watch?v=DppLQ-KQA68> and <http://forum.abinit.org/viewtopic.php?f=2&t=1391&p=4330&hilit=ubuntu+12.04+recipe#p4330> onto Ubuntu 12.04. I'm not sure if this is relevant but per the instructions of the video, there is a build directory within the extracted tar file where abinit-7.4.1 was downloaded where the ./configure and make commands were completed.

I've followed the tutorial and included the input files, but when the input file is passed through abinit, it is unable to complete the calculation. Instead I get a Fortran error: end of file associated with fort.9 that shows up as an empty file in the current directory; none of the expected output files (e.g. WFK, EIG files) are generated. If additional files or information would be helpful, please let me know.

Thanks for any help you can offer!
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Input used with ./configure options:
enable_mpi="yes"
enable_mpi_io="yes"
with_mpi_prefix="/usr"
with_netcdf_incs="-I/usr/include"
with_netcdf_libs="-L/usr/lib -lnetcdf -lnetcdff"
with_fft_flavor="fftw3"
with_fft_incs="-I/usr/include/"
with_fft_libs="-L/usr/lib -lfftw3 -lfftw3f"
with_linalg_flavor="atlas"
with_linalg_libs="-L/usr/lib/atlas-base/ -llapack -lf77blas -lcblas -latlas"
with_dft_flavor="atompaw+bigdft+libxc+wannier90"
enable_gw_dpc="yes"
enable_maintainer_checks="no"
enable_test_timeout="yes"
enable_gui_build="no"
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In terms of the config.log file, there were many instances of :
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "ABINIT-Test-Suite"
| #define PACKAGE_TARNAME "abinit-test"
| #define PACKAGE_VERSION "7.4.1"
| #define PACKAGE_STRING "ABINIT-Test-Suite 7.4.1"
| #define PACKAGE_BUGREPORT "https://bugs.launchpad.net/abinit/"
| #define PACKAGE_URL ""
| #define PACKAGE "abinit-test"
| #define VERSION "7.4.1"
| /* end confdefs.h. */

though the configuration exited as zero --> configure: exit 0
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Input file to abinit used, as per the tutorial:

tbase1_1.in
tbase1_1.out
tbase1_1i
tbase1_1o
tbase1_1
~/Programs/abinit-7.4.1/tests/Psps_for_tests/01h.psphgh
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Copied below is the log of the attempted calculation:

At line 112 of file ../../../src/57_iopsp_parser/inpspheads.F90 (unit = 9, file = 'fort.9')
Fortran runtime error: End of file
ABINIT

Give name for formatted input file:
tbase1_1.in
Give name for formatted output file:
tbase1_1.out
Give root name for generic input files:
tbase1_1i
Give root name for generic output files:
tbase1_1o
Give root name for generic temporary files:
tbase1_1

.Version 7.4.1 of ABINIT
.(MPI version, prepared for a x86_64_linux_gnu4.6 computer)

.Copyright (C) 1998-2013 ABINIT group .
ABINIT comes with ABSOLUTELY NO WARRANTY.
It is free software, and you are welcome to redistribute it
under certain conditions (GNU General Public License,
see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).

ABINIT is a project of the Universite Catholique de Louvain,
Corning Inc. and other collaborators, see ~abinit/doc/developers/contributors.txt .
Please read ~abinit/doc/users/acknowledgments.html for suggested
acknowledgments of the ABINIT effort.
For more information, see http://www.abinit.org .

.Starting date : Tue 27 Aug 2013.
- ( at 22h51 )


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

=== Build Information ===
Version : 7.4.1
Build target : x86_64_linux_gnu4.6
Build date : 20130827

=== Compiler Suite ===
C compiler : gnu4.6
CFLAGS : -g -O2 -mtune=native -march=native
C++ compiler : gnu4.6
CXXFLAGS : -g -O2 -mtune=native -march=native
Fortran compiler : gnu4.6
FCFLAGS : -g -ffree-line-length-none
FC_LDFLAGS :

=== Optimizations ===
Debug level : basic
Optimization level : standard
Architecture : unknown_unknown

=== MPI ===
Parallel build : yes
Parallel I/O : yes
Time tracing : no
GPU support : no

=== Connectors / Fallbacks ===
Connectors on : yes
Fallbacks on : yes
DFT flavor : libxc-fallback+atompaw-fallback+bigdft-fallback+wannier90-fallback
FFT flavor : fftw3
LINALG flavor : atlas
MATH flavor : none
TIMER flavor : abinit
TRIO flavor : none

=== Experimental features ===
Bindings : no
Exports : no
GW double-precision : yes

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
-O2 -mtune=native -march=native


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
CPP options activated during the build:

CC_GNU CXX_GNU FC_GNU

HAVE_DFT_ATOMPAW HAVE_DFT_BIGDFT HAVE_DFT_LIBXC

HAVE_DFT_WANNIER90 HAVE_FC_ALLOCATABLE_DT... HAVE_FC_COMMAND_LINE

HAVE_FC_CONTIGUOUS HAVE_FC_CPUTIME HAVE_FC_EXIT

HAVE_FC_FLUSH HAVE_FC_GAMMA HAVE_FC_GETENV

HAVE_FC_INT_QUAD HAVE_FC_IOMSG HAVE_FC_ISO_C_BINDING

HAVE_FC_LONG_LINES HAVE_FC_NULL HAVE_FC_STREAM_IO

HAVE_FFT HAVE_FFT_FFTW3 HAVE_FFT_MPI

HAVE_FFT_SERIAL HAVE_FORTRAN2003 HAVE_LINALG

HAVE_LINALG_SERIAL HAVE_MPI HAVE_MPI2

HAVE_MPI_IO HAVE_MPI_TYPE_CREATE_S... HAVE_OS_LINUX

HAVE_TIMER HAVE_TIMER_ABINIT HAVE_TIMER_MPI

HAVE_TIMER_SERIAL
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

- input file -> tbase1_1.in
- output file -> tbase1_1.out
- root for input files -> tbase1_1i
- root for output files -> tbase1_1o

-instrng : 68 lines of input have been read from file tbase1_1.in


iofn2 : Please give name of formatted atomic psp file
iofn2 : for atom type 1 , psp file is ~/Programs/abinit-7.4.1/tests/Psps_for_tests/01h.psphgh

Nevermind? I just tried it again, but with the path to the pseudopotential as /home/<usrname>/Programs/abinit-7.4.1/tests/Psps_for_tests/01h.pspgth instead of with the tilda... though I am still confused about why this happened (other than it couldn't find the psp file?)

Although tilde expansion is a shell feature, many Fortran compilers support csh like behavior. So Abinit OPEN statements should expand ~ to /home/<username> (if the $HOME variable is correctly set) and I'm surprised it apparently doesn't work here.

Alain

Sorry for the late reply- was moving to new school. Thanks for the confirmation! Explicitly listing the path to the pseudopotential file seems to work consistently through the tutorials, so I'll stick with that for now.

I can confirm many architectures do not support this. A complaint about fort.9 means your psp files are not readable/accessible by abinit - probably a bad path or file mount difference etc...

Matthieu

Having the same issue running in Windows. I get the exact same error message. Any suggestions?

Can you give us more details ?
Where are located your psp files (full path) ?
What is your files file ?
...

Jordan