The ABINIT Users Mailing List ( CLOSED )

[Physics fany <physicsfany@yahoo.com>]

Hello,

Thank you for the reply, please let me answer your kind questions as follows:

1. opensuse comes with gcc-4.3.2 (?) yes, it does.
2. but what kind of MPI implementation are you using? openmpi-1.2.8
3. A copy of your abinit configure or the head of the config.log would be useful. Please find it below.
4. Maybe you need to specify a transport with mpirun suitable for your hardware setup. in abinit 5.4.4 I made the abinip by manually enabling mpi and some libraries, I did the same for some libraries, still the made abinip does not work!

5. Do you receive the error message with one of the parallel test cases? yes, with at least 5 of them, I quit testing the rest.

 ==============================================================================
 === Overall startup                                                        ===
 ==============================================================================

checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking target system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
configure: M4 10411 - Autoconf 26200 - Automake 11001 - Libtool 20204
configure: reporting user interface changes:
configure:  * new option --enable-bindings is available
configure:  * new option --enable-error-handlers is available
configure:  * new option --enable-gw-dpc is available
configure:  * --enable-mpi has a new meaning
configure:    please check that enable-mpi="yes" is OK for you
configure:  * new option --enable-scalapack is available
configure:  * --with-fc-name renamed --with-fc-vendor
configure:  * new option --with-mpi-level is available
configure:  * new option --with-plugins-prefix is available
configure:  * new option --with-plugins-srcdir is available
configure:  * new option --with-scalapack-includes is available
configure:  * new option --with-scalapack-libs is available
configure:  * --enable-tricks has a new meaning
configure:    please check that enable-tricks="yes" is OK for you

 ==============================================================================
 === Option consistency checking                                            ===
 ==============================================================================

configure: checking consistency of MPI options
configure:  |---> all OK
configure:
configure: checking consistency of external prerequisite options
configure:  |---> all OK
configure:
configure: checking consistency of plug-in options
configure:  |---> all OK
configure:
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
configure: parsing command-line options

 ==============================================================================
 === MPI startup                                                            ===
 ==============================================================================

checking for MPI support requested... yes
configure: looking for MPI in /usr
checking for a usable MPI implementation... no
configure: looking for MPI in /usr/local
checking for a usable MPI implementation... yes
checking the type of MPI implementation we have... openmpi
configure: setting LD_LIBRARY_PATH

 ==============================================================================
 === Utilities                                                              ===
 ==============================================================================

checking whether make sets $(MAKE)... (cached) yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether ln -s works... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for gawk... (cached) gawk
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/grep -E
checking for sh... /usr/bin/sh
checking for perl... /usr/bin/perl
checking for python... /usr/bin/python
checking for rm... /bin/rm
checking for mv... /bin/mv
checking for tar... /bin/tar
checking for latex... /bin/false
checking for dvips... /bin/false
checking for dvipdf... /usr/bin/dvipdf
checking for ps2pdf... /usr/bin/ps2pdf
checking for markdown... no
checking for wget... /usr/bin/wget
configure: using internal version of MarkDown

 ==============================================================================
 === Preprocessing                                                          ===
 ==============================================================================

checking for style of include used by make... GNU
checking for gcc... /usr/local/bin/mpicc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/local/bin/mpicc accepts -g... yes
checking for /usr/local/bin/mpicc option to accept ISO C89... none needed
checking dependency style of /usr/local/bin/mpicc... gcc3
checking how to run the C preprocessor... /usr/local/bin/mpicc -E
checking for the true C preprocessor... /lib/cpp
checking for C preprocessor options... -P -std=c89

 ==============================================================================
 === C support                                                              ===
 ==============================================================================

checking for gcc... (cached) /usr/local/bin/mpicc
checking whether we are using the GNU C compiler... (cached) yes
checking whether /usr/local/bin/mpicc accepts -g... (cached) yes
checking for /usr/local/bin/mpicc option to accept ISO C89... (cached) none needed
checking dependency style of /usr/local/bin/mpicc... (cached) gcc3
checking which type of compiler we have... gcc gcc
configure: applying C compiler tricks (type: gcc, version: gcc)
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no

 ==============================================================================
 === C++ support                                                            ===
 ==============================================================================

checking whether we are using the GNU C++ compiler... yes
checking whether /usr/local/bin/mpic++ accepts -g... yes
checking dependency style of /usr/local/bin/mpic++... gcc3
checking which type of C++ compiler we have... gcc g++
configure: applying C++ compiler tricks (type: gcc, version: g++)

 ==============================================================================
 === Fortran support                                                        ===
 ==============================================================================

checking whether we are using the GNU Fortran compiler... yes
checking whether /usr/local/bin/mpif90 accepts -g... yes
checking which type of Fortran compiler we have... gcc GNU
checking whether the Fortran compiler accepts exit()... yes
checking whether the Fortran compiler accepts flush()... yes
configure: applying Fortran compiler tricks (type: gcc, version: GNU)
checking whether to use C clock for timings... no

 ==============================================================================
 === Libraries and linking                                                  ===
 ==============================================================================

checking for ar... /usr/bin/ar
checking for ranlib... ranlib

 ==============================================================================
 === 64-bit support                                                         ===
 ==============================================================================

configure: this section is still under development
checking for a 64-bit architecture... unknown

 ==============================================================================
 === Optimizations                                                          ===
 ==============================================================================

configure: applying optimisations for cc: gcc/all/all.standard
configure: applying optimisations for cxx: gcc/all/all.standard
configure: applying optimisations for fc: gcc/all/all.standard

 ==============================================================================
 === MPI support                                                            ===
 ==============================================================================

checking whether MPI is usable... yes
checking whether to build parallel code... yes
configure: MPI CPPFLAGS > -DMPI=1 -DMPI2=1   

 ==============================================================================
 === External prerequisites                                                 ===
 ==============================================================================

checking whether to use the FFTW library... no
configure: applying linear algebra tricks (type: abinit)
checking whether to build the LINALG library... yes

 ==============================================================================
 === Plug-ins                                                               ===
 ==============================================================================

configure: using tarball repository /home/sara/.abinit/tarballs
checking for a source tarball of BIGDFT... yes
checking whether to enable the BIGDFT plug-in... yes
checking whether to build the BIGDFT plug-in... yes
configure: applying BigDFT tricks (not needed yet)
checking whether to enable the NETCDF plug-in... no
checking whether to build the NETCDF plug-in... no
checking whether to enable the ETSF_IO plug-in... no
checking whether to build the ETSF_IO plug-in... no
checking whether to enable the ETSF_XC plug-in... no
checking whether to build the ETSF_XC plug-in... no
checking whether to enable the FOX plug-in... no
checking whether to build the FOX plug-in... no
checking whether to enable the XMLF90 plug-in... no
checking whether to build the XMLF90 plug-in... no
checking for a source tarball of WANNIER90... yes
checking whether to enable the WANNIER90 plug-in... yes
checking whether to build the WANNIER90 plug-in... yes
configure: applying compiler-specific Wannier90 tricks (type: gcc, version: GNU)

 ==============================================================================
 === Nightly builds                                                         ===
 ==============================================================================

checking whether to build Nightly code... no

 ==============================================================================
 === Experimental developments                                              ===
 ==============================================================================

checking whether to enable bindings... no
checking whether to enable error handlers... no
checking whether to enable GW double-precision calculations... no
checking whether to activate ScaLAPACK support... no

 ==============================================================================
 === Output                                                                 ===
 ==============================================================================

configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.py
config.status: creating config.sh
config.status: creating config.dump
config.status: creating config/wrappers/wrap-fc
config.status: creating plugins/xmlf90/build.mk
config.status: creating src/defs/defs_infos.F90
config.status: creating tests/tests.env
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/defs/Makefile
config.status: creating src/lib00macroav/Makefile
config.status: creating src/lib00numeric/Makefile
config.status: creating src/lib01fftnew/Makefile
config.status: creating src/lib01cg/Makefile
config.status: creating src/lib01hidempi/Makefile
config.status: creating src/00basis/Makefile
config.status: creating src/01manage_mpi/Makefile
config.status: creating src/11util/Makefile
config.status: creating src/11contract/Makefile
config.status: creating src/12spacepar/Makefile
config.status: creating src/12parser/Makefile
config.status: creating src/12geometry/Makefile
config.status: creating src/12ffts/Makefile
config.status: creating src/12nlstrain/Makefile
config.status: creating src/13xml/Makefile
config.status: creating src/13xc/Makefile
config.status: creating src/13recipspace/Makefile
config.status: creating src/13paw/Makefile
config.status: creating src/13iovars/Makefile
config.status: creating src/13nonlocal/Makefile
config.status: creating src/13psp/Makefile
config.status: creating src/13ionetcdf/Makefile
config.status: creating src/13io_mpi/Makefile
config.status: creating src/14poisson/Makefile
config.status: creating src/14wfs/Makefile
config.status: creating src/14wvl_wfs/Makefile
config.status: creating src/14iowfdenpot/Makefile
config.status: creating src/14bader/Makefile
config.status: creating src/14occeig/Makefile
config.status: creating src/15common/Makefile
config.status: creating src/15gw/Makefile
config.status: creating src/15recursion/Makefile
config.status: creating src/15rsprc/Makefile
config.status: creating src/16response/Makefile
config.status: creating src/16geomoptim/Makefile
config.status: creating src/17suscep/Makefile
config.status: creating src/17lwf/Makefile
config.status: creating src/17ddb/Makefile
config.status: creating src/18seqpar/Makefile
config.status: creating src/19cut3d/Makefile
config.status: creating src/21paral_md/Makefile
config.status: creating src/21drive/Makefile
config.status: creating src/21rdm/Makefile
config.status: creating src/main/Makefile
config.status: creating src/nightly/Makefile
config.status: creating prereqs/Makefile
config.status: creating prereqs/linalg/Makefile
config.status: creating plugins/Makefile
config.status: creating plugins/bigdft/Makefile
config.status: creating plugins/netcdf/Makefile
config.status: creating plugins/etsf_io/Makefile
config.status: creating plugins/etsf_xc/Makefile
config.status: creating plugins/fox/Makefile
config.status: creating plugins/wannier90/Makefile
config.status: creating plugins/xmlf90/Makefile
config.status: creating bindings/Makefile
config.status: creating bindings/parser/Makefile
config.status: creating doc/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing script-perms commands

        +--------------------------------------------------------------+
        | IMPORTANT NOTE                                               |
        +--------------------------------------------------------------+
        | You are using a generic MPI installation. In this case, for  |
        | consistency reasons, both sequential and parallel binaries   |
        | have to be built with the same compiler - the MPI-capable    |
        | one - which means that the sequential binaries will depend   |
        | on the MPI libraries, even though they do not make use of    |
        | them.                                                        |
        |                                                              |
        | This, in turn, means that you will not be able to run ABINIT |
        | binaries unless you properly set the LD_LIBRARY_PATH         |
        | environment variable. The configure script just did it now,  |
        | in order to perform its task seamlessly. Please read the     |
        | "Environment variables" section in the chapter dedicated to  |
        | the configure script of the ABINIT Build System Guide that   |
        | you will find in the ~abinit/doc/build/ subdirectory of the  |
        | source tree to make the proper settings more permanent.      |
        |                                                              |
        | Another solution might be to pass the "-static" flag         |
        | to the C, C++ and Fortran linkers respectively through the   |
        | "--with-cc-ld-optflags", "--with-cxx-ld-optflags" and        |
        | "--with-fc-ld-optflags" options of the configure script, but |
        | this cannot be done on all platforms.                        |
        +--------------------------------------------------------------+