The ABINIT Users Mailing List ( CLOSED )

[rsaha@pas.rochester.edu]

Hi ABINITioners,

 My abinip installation works fine and compares well with the references for
 tparal_1 and tparal_2. However, tparal_3 run as


  mpirun -np 2 abinip < tparal_3.files >& m.log 

 hangs with the following error

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source    
         
libc.so.6          0000002A95CE27E4  Unknown               Unknown  Unknown
libc.so.6          0000002A95CE4019  Unknown               Unknown  Unknown
abinip             0000000000E931D7  Unknown               Unknown  Unknown
abinip             0000000000EA5C9F  Unknown               Unknown  Unknown
abinip             0000000000EA5C43  Unknown               Unknown  Unknown
abinip             0000000000C6E563  Unknown               Unknown  Unknown
abinip             000000000094E8B0  Unknown               Unknown  Unknown
abinip             0000000000915830  Unknown               Unknown  Unknown
abinip             000000000040858C  Unknown               Unknown  Unknown
abinip             0000000000405A3A  Unknown               Unknown  Unknown
libc.so.6          0000002A95C95E5D  Unknown               Unknown  Unknown
abinip             000000000040596A  Unknown               Unknown  Unknown

if wfoptflag 1 and nbdblock is 2 as needed for band parallelisation. However, 
nbdblock 1 leads to a smooth execution. I am using a 24-node cluster of  dual 
processor AMD opteron 246 machines running SUSE Linux. Could somebody please 
look at my build.ac file, suggest where I am going wrong ?

#
# Generic config file for ABINIT (documented template)
#
# After editing this file to suit your needs, you may save it as
# "~/.abinit/build/<hostname>.ac" to save these parameters as per-user
# defaults. Just replace "<hostname>" by the name of your machine,
# excluding the domain name.
#
# Example: if your machine is called "myhost.mydomain", you will save
#          this file as "~/.abinit/build/myhost.ac".
#
# You may put this file at the top level of an ABINIT source tree as well,
# in which case its definitions will apply to this particular tree only.
#
# Hint: If you do not know the name of your machine, just type "hostname".
#

#
# IMPORTANT NOTES
#
# 1. It may happen that this file is outdated. In such a case, the best is
#    to refer to the command-line options of the "configure" script.
#
#    To have a complete list of these options, just type "./configure --help"
#    from the top source directory of ABINIT.
#
# 2. Setting CPPFLAGS, CFLAGS, CXXFLAGS, or FCFLAGS manually is not
#    recommended and will override any other mechanism involved in
#    their configuration. Use at your own risks.
#
#    A more gentle way to do is to use the "--with-*-optflags" command-line
#    options of the "configure" script. See below for details.
#
# 3. Do not forget to remove the leading "#" on a line when you customize
#    an option.
#

# 
---------------------------------------------------------------------------- #
# Global build options                                                        
 #
# 
---------------------------------------------------------------------------- #

# Enable 64-bit compiler flags (default is no)
# Note: when necessary, fine-grained tuning may be achieved by setting
#  the *FLAGS_64BITS variables manually.
#
#enable_64bit_flags="yes"

# Enable debug mode (default is no)
#
#enable_debug="yes"

# Allow the use of external libraries (default is yes)
# Disable this to force the use of internal versions
#
#enable_extlibs="no"

# Enable advanced configuration features (default is no)
#
# Notes:
#
#     * known to make the configure script crash in some (rare) cases
#     * required for NQXC library support
# 
#enable_smart_config="no"

# Enable compiler tricks (default is yes)
#
#enable_tricks="no"

# Where to install ABINIT (default is /opt/etsf)
#
prefix="/home/rsaha/abinit"

# 
---------------------------------------------------------------------------- #
# Preprocessing                                                               
 #
# 
---------------------------------------------------------------------------- #

# C preprocessor (should not be set in most cases)
#
#CPP="/usr/bin/cpp"

# Set preprocessing options (overrides auto-detection)
# Use with care!
#
#with_cppflags="-DFOO"

# 
---------------------------------------------------------------------------- #
# C support                                                                   
 #
# 
---------------------------------------------------------------------------- #

# C compiler
#
#CC="gcc"

# Set optimizations for C source files (overrides auto-detection)
#
#with_cc_optflags="-O3"

# Add link flags for C binaries (default is unset)
#
#with_cc_ldflags=""

# 
---------------------------------------------------------------------------- #
# C++ support                                                                 
 #
# 
---------------------------------------------------------------------------- #

# C++ compiler
#
#CXX="g++"

# Set optimizations for C++ source files (overrides auto-detection)
#
#with_cxx_optflags="-O3"

# Add link flags for C++ binaries (default is unset)
#
#with_cxx_ldflags=""

# 
---------------------------------------------------------------------------- #
# Fortran support                                                             
 #
# 
---------------------------------------------------------------------------- #

# Fortran compiler
#
FC="/opt/intel/fce/9.0/bin/ifort"

# Set optimizations for Fortran source files (overrides auto-detection)
#
with_fc_optflags="-O2"

# Add link flags for Fortran binaries (default is unset)
#
#with_fc_ldflags=""

# Choose whether to read file lists from standard input or "ab.files"
# (default is yes = standard input)
#
#enable_stdin="no"

# Wrap Fortran compiler calls (default is auto-detected)
# Combine this option with enable_debug="yes" to keep preprocessed source
# files (they are removed by default, except if their build fails)
#
#enable_fc_wrapper="yes"

# Set per-directory Fortran optimizations (useful when a Fortran compiler
# crashes during the build)
# Note: this option is not available through the command line
#
#fcflags_opt_21drive="-O0"

# Use C clock instead of Fortran clock for timings
#
#enable_cclock="yes"

# 
---------------------------------------------------------------------------- #
# MPI support                                                                 
 #
# 
---------------------------------------------------------------------------- #

# Determine whether to build parallel code (default is yes)
#
#  * enable_mpi=manual : specify MPI settings manually
#  * enable_mpi=yes    : let the "configure" auto-detect MPI support
#  * enable_mpi=no     : disable MPI support
#
# Note: If "enable_mpi" is set to "yes", all "with_*" MPI options but
#       "with_mpi_prefix" will be ignored. On the other hand, setting
#       "enable_mpi" to "manual" will bypass auto-detection and the
#       "with_mpi_prefix" option will be ignored.
#
#enable_mpi="yes"

# Activate parallel FFT (default is no)
# WARNING: this feature is still under development
#
#enable_mpi_fft="yes"

# Activate parallel I/O (default is no)
# WARNING: this feature is still under development
#
#enable_mpi_io="yes"

# Activate MPI time tracing (default is no)
# WARNING: this feature is still under development
#
#enable_mpi_trace="yes"

# Look for the MPI library in <prefix>/lib (default is unset)
# This is required for MPI support if your Fortran compiler has no native
# MPI support
#
with_mpi_prefix="/home/rsaha/mpich2-install/"

#
# If your MPI installation is not detected, you may set the following
# variables manually (please make sure that "enable_mpi" is set to "manual")
#

# Set MPI C preprocessor (default is unset)
#
#with_mpi_cpp="/usr/local/bin/mpicpp"

# Set MPI-specific preprocessing flags (default is unset)
#
#with_mpi_cppflags=""

# Set MPI C compiler (default is unset)
#
#with_mpi_cc="/usr/local/bin/mpicc"

# Set MPI-specific C compile flags (default is unset)
#
#with_mpi_cflags=""

# Set MPI-specific C link flags (default is unset)
#
#with_mpi_cc_ldflags="-lmpi"

# Set MPI C++ compiler (default is unset)
#
#with_mpi_cxx="/usr/local/bin/mpic++"

# Set MPI-specific C++ compile flags (default is unset)
#
#with_mpi_cxxflags=""

# Set MPI-specific C++ link flags (default is unset)
#
#with_mpi_cxx_ldflags="-lmpi++"

# Set MPI Fortran 90 compiler (default is unset)
#
#with_mpi_fc="/home/rsaha/mpich2-install/bin/mpif90"

# Set MPI-specific Fortran compile flags (default is unset)
#
#with_mpi_fcflags="-I/home/rsaha/mpich2-install/include"

# Set MPI-specific Fortran link flags (default is unset)
#
#with_mpi_fc_ldflags="-lmpichf90"

# Set MPI Runner for tests (default is unset)
#
#with_mpi_run="/home/rsaha/mpich2-install/bin/mpirun"

# 
---------------------------------------------------------------------------- #
# External libraries                                                          
 #
# 
---------------------------------------------------------------------------- #

# Enable FFTW library support (default is no)
#
#enable_fftw="no"

# Enable threaded FFTW library support (default is no)
# Note: will be ignored if "enable_fftw" is set to "no"
#
#enable_fftw_threads="no"

# Enable BLAS and LAPACK linear algebra libraries support (default is yes)
# Note: disabling them might break the build
#
#enable_linalg="no"

# Link flags for BLAS and LAPACK linear algebra libraries (default is unset)
#
#with_linalg_ldflags="-L/usr/local/lib -lblas -llapack"

# Type of linear algebra libraries to use (default is unset)
# Under development - USE AT YOUR OWN RISKS!
#
# Supported libraries:
#
#    * acml      (not implemented)
#    * asl       (not implemented)
#    * atlas     (untested)
#    * cxml      (not implemented)
#    * essl      (should work)
#    * mkl       (not implemented)
#    * mlib      (not implemented)
#    * sgimath   (not implemented)
#    * sunperf   (not implemented)
#
#with_linalg_type="atlas"

# Enable NetCDF support (default is no)
#
enable_netcdf="yes"

# Include path for the NetCDF library (default is unset)
#
#with_netcdf_include="-I/usr/local/include/netcdf"

# Link flags for the NetCDF library (default is unset)
#
#with_netcdf_ldflags="/usr/local/lib/netcdf"

# Enable Nanoquanta/ETSF I/O library support (default is no)
#
enable_etsf_io="yes"

# Include path for the Nanoquanta/ETSF I/O library (default is unset)
#
#with_etsf_io_include="-I/opt/etsf/include"

# Link flags for the Nanoquanta/ETSF I/O library (default is unset)
#
#with_etsf_io_ldflags="-L/opt/etsf/lib -letsf_io"

# Enable Nanoquanta/ETSF XC library support (default is no)
# Will be forced to "no" if smart config is disabled (see the
# "build environment" section above)
#
#enable_etsf_xc="yes"

# Include path for the Nanoquanta/ETSF XC library (default is unset)
#
#with_etsf_xc_include="-I/opt/etsf/include"

# Link flags for the Nanoquanta/ETSF XC library (default is unset)
#
#with_etsf_xc_ldflags="-L/opt/etsf/lib -letsf_xc"

# Enable XMLF90 library support (default is no)
#
#enable_xmlf90="yes"

# Include path for the XMLF90 library (default is unset)
#
#with_xmlf90_include="-I${HOME}/include/xmlf90"

# Link flags for the XMLF90 library (default is unset)
#
#with_xmlf90_ldflags="-L${HOME}/lib/xmlf90 -lxmlf90"

# 
---------------------------------------------------------------------------- #
# Maintainer options                                                          
 #
# 
---------------------------------------------------------------------------- #

# Enable dependency tracking (Automake feature)
# Though the exact outcome of this is not known at present, you may
# turn it on if you have a taste for adventure ;-)
#
#enable_dependency_tracking="yes"

I would really appreciate some help.

Rajdeep