(1) the compiler (vendor and release: e.g. intel 10.1): intel/fce/10.1.012/
(2) the architecture (e.g. 64-bit IBM SP5) : 64-bit Intel(R) Xeon(R)
(3) if the problems occur compiling in serial/in parallel: parallel
(4) the version of ABINIT (revision number/major release version): 6.4.3
I use the following commands:
../configure --with-mpi-prefix="/homes/renyu/pkgs/lam-7.1.4" --enable-mpi=”yes” --program-suffix="-mpi"
However it seems that I could not get mpi to work. Here are some suspicious contents in the log:
configure: Initializing MPI support
configure: looking for MPI in /homes/renyu/pkgs/lam-7.1.4
checking for a MPI C compiler... /homes/renyu/pkgs/lam-7.1.4/bin/mpicc
checking for a MPI C++ compiler... /homes/renyu/pkgs/lam-7.1.4/bin/mpic++
checking for a MPI Fortran compiler... none found
checking for a MPI runner... /homes/renyu/pkgs/lam-7.1.4/bin/mpirun
configure: GPU support disabled from command-line
checking whether MPI is usable... no
configure: WARNING: MPI support is broken!
Does anyone know where might be wrong? Thanks a lot for your help! Below is the full log file.
Renyu
Code: Select all
==============================================================================
=== Overall startup ===
==============================================================================
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-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
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for gawk... (cached) gawk
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
configure: not loading options (no config file available)
==============================================================================
=== Build-system information ===
==============================================================================
configure: ABINIT version 6.4.3
configure: M4 010414 - Autoconf 026500 - Automake 011100 - Libtool 020204
configure: reporting user interface changes:
configure: * new option --enable-bse-unpacked is available
configure: * new option --enable-dft is available
configure: * --enable-etsf-io-test removed
configure: * new option --enable-fast-check is available
configure: * --enable-fftw renamed --enable-fft
configure: * --enable-fftw-threads removed
configure: * --enable-cuda renamed --enable-gpu
configure: * new option --enable-gw-cutoff is available
configure: * new option --enable-gw-optimal is available
configure: * new option --enable-gw-wrapper is available
configure: * new option --enable-linalg is available
configure: * new option --enable-maintainer-checks is available
configure: * --enable-gsl renamed --enable-math
configure: * new option --enable-smp is available
configure: * --enable-nightly renamed --enable-test-timeout
configure: * --enable-papi renamed --enable-timer
configure: * new option --enable-trio is available
configure: * new option --enable-vdwxc is available
configure: * --with-64bit-flags removed
configure: * --with-ar-dbgflags removed
configure: * --with-ar-optflags removed
configure: * --with-cc-dbgflags removed
configure: * --with-cc-ld-dbgflags removed
configure: * --with-cc-ld-dbglibs removed
configure: * --with-cc-ld-optflags removed
configure: * --with-cc-ld-optlibs removed
configure: * --with-cc-optflags removed
configure: * --with-cpp-dbgflags removed
configure: * --with-cpp-optflags removed
configure: * --with-cxx-dbgflags removed
configure: * --with-cxx-ld-dbgflags removed
configure: * --with-cxx-ld-dbglibs removed
configure: * --with-cxx-ld-optflags removed
configure: * --with-cxx-ld-optlibs removed
configure: * --with-cxx-optflags removed
configure: * new option --with-dft-flavor is available
configure: * new option --with-dft-includes is available
configure: * new option --with-dft-libs is available
configure: * --with-etsf-io-test-includes removed
configure: * --with-etsf-io-test-libs removed
configure: * --with-fc-dbgflags removed
configure: * --with-fc-ld-dbgflags removed
configure: * --with-fc-ld-dbglibs removed
configure: * --with-fc-ld-optflags removed
configure: * --with-fc-ld-optlibs removed
configure: * --with-fc-optflags removed
configure: * new option --with-fft-flavor is available
configure: * --with-fftw-includes renamed --with-fft-includes
configure: * --with-fftw-libs renamed --with-fft-libs
configure: * new option --with-gpu-cflags is available
configure: * new option --with-gpu-cppflags is available
configure: * new option --with-gpu-flavor is available
configure: * --with-cuda-includes renamed --with-gpu-includes
configure: * new option --with-gpu-ldflags is available
configure: * --with-cuda-libs renamed --with-gpu-libs
configure: * new option --with-gpu-prefix is available
configure: * --with-linalg-type renamed --with-linalg-flavor
configure: * new option --with-math-flavor is available
configure: * --with-gsl-includes renamed --with-math-includes
configure: * --with-gsl-libs renamed --with-math-libs
configure: * --with-mpi-runner removed
configure: * --with-scalapack-includes removed
configure: * --with-scalapack-libs removed
configure: * --with-timeout renamed --with-test-timeout
configure: * new option --with-timer-flavor is available
configure: * --with-papi-includes renamed --with-timer-includes
configure: * --with-papi-libs renamed --with-timer-libs
configure: * new option --with-trio-flavor is available
configure: * new option --with-trio-includes is available
configure: * new option --with-trio-libs is available
==============================================================================
=== Option consistency checking ===
==============================================================================
configure: checking consistency of library-related options
configure: |---> all OK
configure:
configure: checking consistency of plug-in options
configure: |---> all OK
configure:
configure: checking consistency of experimental options
configure: |---> all OK
configure:
configure: parsing command-line options
==============================================================================
=== Connector startup ===
==============================================================================
configure: Initializing MPI support
configure: looking for MPI in /homes/renyu/pkgs/lam-7.1.4
checking for a MPI C compiler... /homes/renyu/pkgs/lam-7.1.4/bin/mpicc
checking for a MPI C++ compiler... /homes/renyu/pkgs/lam-7.1.4/bin/mpic++
checking for a MPI Fortran compiler... none found
checking for a MPI runner... /homes/renyu/pkgs/lam-7.1.4/bin/mpirun
configure: GPU support disabled from command-line
==============================================================================
=== Utilities ===
==============================================================================
checking for sh... /bin/sh
checking for mv... /bin/mv
checking for perl... /usr/nikola/bin/perl
checking for rm... /bin/rm
checking for dvips... dvips
checking for dvipdf... dvipdf
checking for latex... latex
checking for markdown... no
checking for md5sum... md5sum
checking for patch... patch
checking for ps2pdf... ps2pdf
checking for tar... tar
checking for wget... wget
checking for curl... curl
configure: using internal version of MarkDown
==============================================================================
=== C support ===
==============================================================================
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking which type of compiler we have... gnu 4.2
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 for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking which type of C++ compiler we have... gnu 4.2
==============================================================================
=== Fortran support ===
==============================================================================
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking which type of Fortran compiler we have... gnu 4.2
checking fortran 90 modules extension... mod
checking for Fortran flag to compile .F90 files... none
configure: determining Fortran module case
checking whether Fortran modules are upper-case... no
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran... -L/afs/ee.washington.edu/nikola/.as40-amd64/pkgs/gcc/.4.2.1+32/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.1 -L/afs/ee.washington.edu/nikola/.as40-amd64/pkgs/gcc/.4.2.1+32/bin/../lib/gcc -L/usr/nikola/pkgs/gcc/.4.2.1+32/lib/gcc/x86_64-unknown-linux-gnu/4.2.1 -L/afs/ee.washington.edu/nikola/.as40-amd64/pkgs/gcc/.4.2.1+32/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.1/../../../../lib64 -L/usr/nikola/pkgs/gcc/.4.2.1+32/lib/gcc/x86_64-unknown-linux-gnu/4.2.1/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/afs/ee.washington.edu/nikola/.as40-amd64/pkgs/gcc/.4.2.1+32/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.1/../../.. -L/usr/nikola/pkgs/gcc/.4.2.1+32/lib/gcc/x86_64-unknown-linux-gnu/4.2.1/../../.. -lgfortranbegin -lgfortran -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
==============================================================================
=== Python support ===
==============================================================================
checking for python... python
checking for python-config... python-config
checking for Python CPPFLAGS... -I/afs/.ee.washington.edu/nikola/.as40-amd64/pkgs/python/.2.5.1/include/python2.5 -I/afs/.ee.washington.edu/nikola/.as40-amd64/pkgs/python/.2.5.1/include/python2.5
checking for bzr... no
checking for Python NumPy headers... not found
checking numarray/arrayobject.h usability... no
checking numarray/arrayobject.h presence... no
checking for numarray/arrayobject.h... no
==============================================================================
=== Libraries and linking ===
==============================================================================
checking for ar... ar
checking for ranlib... ranlib
==============================================================================
=== Hints ===
==============================================================================
checking for cpp... cpp
checking for a true C preprocessor... cpp
checking which cpp hints to apply... default/default/default
checking which cc hints to apply... gnu/default/default
checking which xpp hints to apply... none/none/none
checking which cxx hints to apply... gnu/default/default
checking which fpp hints to apply... default/default/default
checking which fc hints to apply... gnu/default/default
checking which ar hints to apply... none/none/none
checking which Fortran preprocessor to use...
checking which Fortran preprocessor flags to apply...
checking whether to wrap Fortran compiler calls... no
==============================================================================
=== Debugging ===
==============================================================================
checking debugging status... enabled (profile mode: basic)
configure: setting C debug flags to '-g'
configure: setting C++ debug flags to '-g'
configure: setting Fortran debug flags to '-g'
checking whether to activate debug mode in source files... no
checking which cc debug flags to apply... gnu/default/default
checking which cxx debug flags to apply... none/none/none
checking which fc debug flags to apply... gnu/default/default
checking whether to activate design-by-contract debugging... no
==============================================================================
=== Optimizations ===
==============================================================================
checking optimization status... enabled (profile mode: standard)
checking which cc optimizations to apply... gnu/4.2/intel_xeon
checking which cxx optimizations to apply... gnu/4.2/intel_xeon
checking which fc optimizations to apply... gnu/4.2/intel_xeon
checking whether to apply per-directory optimizations... yes
==============================================================================
=== 64-bit support ===
==============================================================================
checking for a 64-bit architecture... yes
checking whether to use 64-bit flags... no
checking for user-defined 64-bit flags...
==============================================================================
=== Build flags ===
==============================================================================
configure: static builds may be performed
==============================================================================
=== Advanced compiler features ===
==============================================================================
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking mcheck.h usability... yes
checking mcheck.h presence... yes
checking for mcheck.h... yes
checking for abort... yes
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of unsigned int... 4
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of size_t... 8
checking size of ptrdiff_t... 8
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether the Fortran compiler provides the iso_c_binding module... no
checking whether the Fortran compiler accepts exit()... yes
checking whether the Fortran compiler accepts flush()... yes
checking whether the Fortran compiler accepts flush_()... no
checking whether the Fortran compiler accepts gamma()... no
checking whether the Fortran compiler accepts getenv()... yes
checking whether the Fortran compiler accepts getpid()... no
checking whether the Fortran compiler accepts the null() intrinsic... yes
checking whether the Fortran compiler accepts quadruple integers... yes
checking whether the Fortran compiler accepts long lines... yes
checking whether the Fortran compiler accepts etime()... no
checking whether to use C clock for timings... no
==============================================================================
=== Connectors ===
==============================================================================
checking whether MPI is usable... no
configure: WARNING: MPI support is broken!
configure: enabling MPI I/O support
checking whether to build MPI code... yes
checking whether to build MPI I/O code... yes
checking whether to build MPI I/O untested features... no
checking whether to build MPI time tracing code... no
checking which level of MPI is supported by the Fortran compiler... none
checking whether to activate GPU support... no
checking whether to use transferable I/O libraries... no
checking whether to use optimized timer libraries... no
checking whether to use optimized linear algebra libraries... yes
checking whether to activate ScaLAPACK support... no
checking for the requested linear algebra support... netlib
checking for zgemm in -lblas... yes
checking for zhpev in -llapack... yes
checking for the actual linear algebra support... netlib
checking whether to use optimized math libraries... no
checking whether to use optimized FFT libraries... no
checking whether to use DFT libraries... no
==============================================================================
=== Plug-ins ===
==============================================================================
configure: using tarball repository /homes/renyu/.abinit/tarballs
checking whether to enable the FOX plug-in... no
checking whether to build the FOX plug-in... no
checking for a source tarball of NETCDF... yes
configure: tarball MD5 check succeeded
configure: applying NetCDF tricks (vendor: gnu, version: 4.2)
checking whether to enable the NETCDF plug-in... yes
checking whether to build the NETCDF plug-in... yes
checking for a source tarball of ETSF_IO... yes
configure: tarball MD5 check succeeded
configure: applying ETSF_IO tricks (vendor: gnu, version: 4.2)
checking whether to enable the ETSF_IO plug-in... yes
checking whether to build the ETSF_IO plug-in... yes
checking for a source tarball of LIBXC... yes
configure: tarball MD5 check succeeded
configure: applying LIBXC tricks
checking whether to enable the LIBXC plug-in... yes
checking whether to build the LIBXC plug-in... yes
checking for a source tarball of BIGDFT... yes
configure: tarball MD5 check succeeded
configure: applying BigDFT tricks (vendor: gnu, version: 4.2)
checking whether to enable the BIGDFT plug-in... yes
checking whether to build the BIGDFT plug-in... yes
checking for a source tarball of WANNIER90... yes
configure: tarball MD5 check succeeded
configure: applying Wannier90 tricks (vendor: gnu, version: 4.2)
checking whether to enable the WANNIER90 plug-in... yes
checking whether to build the WANNIER90 plug-in... yes
==============================================================================
=== Nightly builds ===
==============================================================================
checking whether to build test timeout code... no
checking timeout for automatic tests... none
==============================================================================
=== Experimental developments ===
==============================================================================
checking whether to enable bindings... no
checking whether to enable BSE unpacking... no
checking whether to enable CLib... no
checking whether to build exports... no
checking whether to accelerate 'make check'... no
checking whether to enable GW cut-off... no
checking whether to enable GW double-precision calculations... no
checking whether to enable optimal GW... no
checking whether to enable GW wrapper... no
checking whether to activate maintainer checks... no
checking whether to use macroave... yes
checking whether to read input from stdin... yes
checking whether to activate Symmetric Multi-Processing... no
checking whether to activate ZDOTC and ZDOTU workaround... no
==============================================================================
=== Output ===
==============================================================================
...
Configuration complete.
You may now type "make" to build ABINIT.
(or, on a SMP machine, "make mj4", or "make multi multi_nprocs=<n>")
