The ABINIT Users Mailing List ( CLOSED )

[Doug Ritchie <ritchie@neon.sao.nrc.ca>]

Hi Alexey,

I was just about to post the same problem to see if anyone else has
experienced it before submitting a bug report to PGI.  I too get a
segmentation fault with the serial test1 run as well as others.

I too have tried various versions of abinit as well as reducing the
compiler optimization levels, but to no avail.  As well, the problem
is not limited to 64 bit Opteron systems but occurs on IA32 ones.

Since I knew I had had working versions with the PGI compiler, I tried 
going back to older versions of the compiler.  The problem started
with version 5.2-1 and continues through 6.0-5, but both abinis and
abinip run fine with version 5.1-6 of the PGI compiler.

I will proceed to report this to PGI unless someone has figured it out.

Regards,
Doug

-------------------------------------------------------------------------------
Douglas Ritchie
Research Computing Support Group  Groupe de soutien informatique a la 
recherche
IMSB                              DSGI
National Research Council Canada  Conseil national de recherches Canada
100 Sussex Drive, Room 2025       100 promenade Sussex, piece 2025
Ottawa, ON  K1A 0R6               Ottawa, ON  K1A 0R6
613-998-5691   Fax: 613-993-3127  613-998-5691   Fax: 613-993-3127
Douglas.Ritchie@nrc-cnrc.gc.ca    Douglas.Ritchie@nrc-cnrc.gc.ca
http://www.nrc-cnrc.gc.ca         http://www.cnrc-nrc.gc.ca
Government of Canada              Gouvernement du Canada
-------------------------------------------------------------------------------

On Thu, Oct 20, 2005 at 02:07:20PM +0200, dick@fhi-berlin.mpg.de wrote:
> Dear all,
> 
> I am also trying to get running parallel v4.5.4 on a 64-bit Opteron
> (makefile_macros file is attached, system: SuSe Linux 9.3, Opteron 250,
> PGI 6.0, MPICH 1.2.6, MPICH Device: ch_p4). Before proceeding to parallel
> version i tried to compile serial one. It compiles nicely, but fails to
> run: whatever input is it stops with "Segmentation fault" message. For
> instance the output for Test 1 is:
> ***
> Starting date : Thu 20 Oct 2005.
> 
> - input  file    -> test1.in
> - output file    -> test1.outA
> - root for input  files -> test1i
> - root for output files -> test1o
> 
>  instrng :    38 lines of input have been read
> 
>  iofn2 : Please give name of formatted atomic psp file
>  iofn2 : for atom type   1 , psp file is ../Psps_for_tests/01h.pspgth
>   read the values zionpsp=  1.0 , pspcod=   2 , lmax=   0
> 
>  iofn2 : deduce mpsang  =   1, n1xccc  =   0.
> 
>  invars1m : enter jdtset=     0
> Segmentation fault (core dumped)
> ***
> 
> The produced log-file is empty. I also tried to compile v4.4.4 and v4.6.4
> - the symptoms are the same.
> 
> I would appreciate any advice how to overcome the problem.
> 
> With best regards,
> Alexey
>  --
> _______________________________________________________________________________________
> 
>    Alexey Dick
>    Max-Planck-Institut für Eisenforschung GmbH       tel:  +49 (0211)
> 6792-283
>    Abteilung Computer-Gestütztes Material-Design     fax:  +49 (0211)
> 6792-465
>    Max-Planck-Str. 1                                 mail: dick@mpie.de
>    D-40237 Düsseldorf, Germany                       web: 
> http://www.sfhingx.de/dick/
> _______________________________________________________________________________________
> 
> 
> > I am trying to install 4.5.3 on a 64-bit Opteron running Linux and am
> > using the Portland Group Fortran compiler, v. 6.0. Abinit seems to install
> > without errors but cannot complete Test 1. The error message is test1
> > status: no such file or directory. Any guidance on troubleshooting or
> > leads on a makefile_macros file that works for this configuration would be
> > much appreciated.
> >
> > Thanks.
> >
> > Mark
> > Mark T. Lusk
> > Professor and Chair
> > Mechanical Engineering Program
> > Colorado School of Mines
> > (303) 273-3675
> > mlusk@mines.edu
> >

> 
> # This file contains the definitions needed for every possible script
> # to be used with the ABINIT makefiles.  It is very much machine-dependent.
> # It is read by makemake and makearch.
> 
> # This version for dummy based on a Pentium IV, bi-procs
> # Explanations about this file can be found in the  makefile_macros_help 
> file,
> # in the Infos subdirectory
> 
> ####################################################################
> # For the sequential version 
> 
> # Machine type
> MACHINE=P6
> # Fortran optimized compilation
> FC=/opt/pgi/linux86-64/6.0/bin/pgf90 -tp=k8-64 -Bstatic
> FFLAGS=-Mextend -Mfree -O2
> FFLAGS_LIBS = -O2
> 
> # C preprocessor, used to preprocess the fortran source.
> CPP=/lib/cpp 
> CPP_FLAGS=-P -traditional -DCONTRACT
> 
> # C optimized compilation.
> CC=cc
> CFLAGS=-O
> 
> # Location of perl . Used to generate the script fldiff, in 
> ~ABINIT/Utilities .
> PERL=/usr/bin/perl
> 
> # List of machine-dependent routines
> MACHINE_DEP_C_SEQ_SUBS_LIST=etime.o
> 
> # Use the ABINIT default libraries.
> # For dynamical link, uncomment this line
> #LIBS= $(LAPACK) $(BLAS) $(NETCDF)
> 
> NC_CC=cc
> NC_FC=/opt/pgi/linux86-64/6.0/bin/pgf77
> NC_F90=/opt/pgi/linux86-64/6.0/bin/pgf90
> NC_CPPFLAGS=-DpgiFortran
> 
> ####################################################################
> # For the parallel version 
> 
> # Compiler flags and definitions
> FFLAGS_PAR= $(FFLAGS) -I /opt/mpich/ch-p4/include
> # List of machine-dependent routines
> MACHINE_DEP_C_PAR_SUBS_LIST=etime.par
> 
> # Location of the MPI library
> MPI_A=/opt/mpich/ch-p4/lib64/libfmpich.a /opt/mpich/ch-p4/lib64/libmpich.a
> # Include blas, lapack, and any other libraries here
>  LIBS_PAR=$(LIBS) $(MPI_A)
> 
> # Command for automatic tests in parallel (optional)
>  COMMAND_PAR= /usr/local/mpi-pgi/bin/mpirun -np 2 -machinefile 
> dummy.pcpm.ucl.ac.be:2 ../../abinip 
> 
> ####################################################################
> # For integration of netcdf
> 
> # The following lines may be uncommented if the ./configure script for
> # netcdf doesn't find the appropriate tools.
> # The script Lib_netcdf/src/nc_configure will strip the NC_ prefix,
> # set the appropriate environment variables
> # and call the standard netcdf ./configure script
> # Note that in this example, the CFLAGS is given to define the "compiler 
> platform"
> # as expected by netcdf (not always required, the compiler may define
> # the adequate environment variable or configur may find it).
> # For examples of environment variables used on different platforms see:
> # http://www.unidata.ucar.edu/packages/netcdf/INSTALL.html
> 
> NC_FC=/opt/pgi/linux86/6.0/bin/pgf90
> NC_F90=/opt/pgi/linux86/6.0/bin/pgf90
> NC_CPPFLAGS='-DNDEBUG -DpgiFortran'
> #NC_CC=
> #NC_CFLAGS=
> #NC_FFLAGS=
> #NC_F90FLAGS=
> 
> # This is a last line in makefile_macros ----------