[mvapich-discuss] Configure error confdefs.h

Mon Jun 6 17:17:40 EDT 2011

My apologies for the confusion, yes am I just trying to compile the
benchmarks and run them using mpich2. I may be exposing my naivety but I'm
wanting to run the benchmarks over 10GE not IB. mpich2 is installed and
working. Is there a way to build mvapich2 without IB?

On 6/6/11 5:10 PM, "Jonathan Perkins" <perkinjo at cse.ohio-state.edu> wrote:

> This is the config.log for the osu micro benchmarks.  Did mvapich2
> configure and build successfully?  It looks like mvapich2 was built
> with checkpoint/restart support but ``libcr'' is not being found when
> trying to compile the benchmarks.
> 
> Please let me know what it is that you're compiling and the steps that
> you've used.  Thanks.
> 
> On Mon, Jun 6, 2011 at 5:05 PM, Hoot Thompson <hoot at ptpnow.com> wrote:
>> This file contains any messages produced by compilers while
>> running configure, to aid debugging if configure makes a mistake.
>> 
>> It was created by OSU-Micro-Benchmarks configure 3.3, which was
>> generated by GNU Autoconf 2.65.  Invocation command line was
>> 
>>   $ ./configure
>> 
>> ## --------- ##
>> ## Platform. ##
>> ## --------- ##
>> 
>> hostname = ubuntu-1
>> uname -m = x86_64
>> uname -r = 2.6.38-8-server
>> uname -s = Linux
>> uname -v = #42-Ubuntu SMP Mon Apr 11 03:49:04 UTC 2011
>> 
>> /usr/bin/uname -p = unknown
>> /bin/uname -X     = unknown
>> 
>> /bin/arch              = unknown
>> /usr/bin/arch -k       = unknown
>> /usr/convex/getsysinfo = unknown
>> /usr/bin/hostinfo      = unknown
>> /bin/machine           = unknown
>> /usr/bin/oslevel       = unknown
>> /bin/universe          = unknown
>> 
>> PATH: /usr/local/sbin
>> PATH: /usr/local/bin
>> PATH: /usr/sbin
>> PATH: /usr/bin
>> PATH: /sbin
>> PATH: /bin
>> PATH: /usr/games
>> 
>> 
>> ## ----------- ##
>> ## Core tests. ##
>> ## ----------- ##
>> 
>> configure:2154: checking for a BSD-compatible install
>> configure:2222: result: /usr/bin/install -c
>> configure:2233: checking whether build environment is sane
>> configure:2283: result: yes
>> configure:2424: checking for a thread-safe mkdir -p
>> configure:2463: result: /bin/mkdir -p
>> configure:2476: checking for gawk
>> configure:2506: result: no
>> configure:2476: checking for mawk
>> configure:2492: found /usr/bin/mawk
>> configure:2503: result: mawk
>> configure:2514: checking whether make sets $(MAKE)
>> configure:2536: result: yes
>> configure:2672: checking for mpicc
>> configure:2688: found /usr/bin/mpicc
>> configure:2699: result: mpicc
>> configure:2730: checking for C compiler version
>> configure:2739: mpicc --version >&5
>> gcc (Ubuntu/Linaro 4.5.2-8ubuntu4) 4.5.2
>> Copyright (C) 2010 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions.  There is NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>> 
>> configure:2750: $? = 0
>> configure:2739: mpicc -v >&5
>> mpicc for MPICH2 version 1.3.1
>> Using built-in specs.
>> COLLECT_GCC=gcc
>> COLLECT_LTO_WRAPPER=/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/lto-
>> wrapper
>> Target: x86_64-linux-gnu
>> Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro
>> 4.5.2-8ubuntu4' --with-bugurl=file:///usr/share/doc/gcc-4.5/README.Bugs
>> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
>> --program-suffix=-4.5 --enable-shared --enable-multiarch
>> --with-multiarch-defaults=x86_64-linux-gnu --enable-linker-build-id
>> --with-system-zlib --libexecdir=/usr/lib/x86_64-linux-gnu
>> --without-included-gettext --enable-threads=posix
>> --with-gxx-include-dir=/usr/include/c++/4.5
>> --libdir=/usr/lib/x86_64-linux-gnu --enable-nls --with-sysroot=/
>> --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes
>> --enable-plugin --enable-gold --enable-ld=default --with-plugin-ld=ld.gold
>> --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic
>> --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu
>> --target=x86_64-linux-gnu
>> Thread model: posix
>> gcc version 4.5.2 (Ubuntu/Linaro 4.5.2-8ubuntu4)
>> configure:2750: $? = 0
>> configure:2739: mpicc -V >&5
>> gcc: '-V' must come at the start of the command line
>> configure:2750: $? = 1
>> configure:2739: mpicc -qversion >&5
>> gcc: unrecognized option '-qversion'
>> /usr/bin/ld: cannot find -lcr
>> collect2: ld returned 1 exit status
>> configure:2750: $? = 1
>> configure:2770: checking whether the C compiler works
>> configure:2792: mpicc    conftest.c  >&5
>> /usr/bin/ld: cannot find -lcr
>> collect2: ld returned 1 exit status
>> configure:2796: $? = 1
>> configure:2834: result: no
>> configure: failed program was:
>> | /* confdefs.h */
>> | #define PACKAGE_NAME "OSU-Micro-Benchmarks"
>> | #define PACKAGE_TARNAME "osu-micro-benchmarks"
>> | #define PACKAGE_VERSION "3.3"
>> | #define PACKAGE_STRING "OSU-Micro-Benchmarks 3.3"
>> | #define PACKAGE_BUGREPORT "mvapich-discuss at cse.ohio-state.edu"
>> | #define PACKAGE_URL ""
>> | #define PACKAGE "osu-micro-benchmarks"
>> | #define VERSION "3.3"
>> | /* end confdefs.h.  */
>> |
>> | int
>> | main ()
>> | {
>> |
>> |   ;
>> |   return 0;
>> | }
>> configure:2839: error: in
>> `/home/hoot/mpistuff/osu/osu-micro-benchmarks-3.3':
>> configure:2843: error: C compiler cannot create executables
>> See `config.log' for more details.
>> 
>> ## ---------------- ##
>> ## Cache variables. ##
>> ## ---------------- ##
>> 
>> ac_cv_env_CC_set=
>> ac_cv_env_CC_value=
>> ac_cv_env_CFLAGS_set=
>> ac_cv_env_CFLAGS_value=
>> ac_cv_env_CPPFLAGS_set=
>> ac_cv_env_CPPFLAGS_value=
>> ac_cv_env_CPP_set=
>> ac_cv_env_CPP_value=
>> ac_cv_env_LDFLAGS_set=
>> ac_cv_env_LDFLAGS_value=
>> ac_cv_env_LIBS_set=
>> ac_cv_env_LIBS_value=
>> ac_cv_env_build_alias_set=
>> ac_cv_env_build_alias_value=
>> ac_cv_env_host_alias_set=
>> ac_cv_env_host_alias_value=
>> ac_cv_env_target_alias_set=
>> ac_cv_env_target_alias_value=
>> ac_cv_path_install='/usr/bin/install -c'
>> ac_cv_path_mkdir=/bin/mkdir
>> ac_cv_prog_AWK=mawk
>> ac_cv_prog_ac_ct_CC=mpicc
>> ac_cv_prog_make_make_set=yes
>> 
>> ## ----------------- ##
>> ## Output variables. ##
>> ## ----------------- ##
>> 
>> ACLOCAL='${SHELL} /home/hoot/mpistuff/osu/osu-micro-benchmarks-3.3/missing
>> --run aclocal-1.11'
>> AMDEPBACKSLASH=''
>> AMDEP_FALSE=''
>> AMDEP_TRUE=''
>> AMTAR='${SHELL} /home/hoot/mpistuff/osu/osu-micro-benchmarks-3.3/missing
>> --run tar'
>> AUTOCONF='${SHELL} /home/hoot/mpistuff/osu/osu-micro-benchmarks-3.3/missing
>> --run autoconf'
>> AUTOHEADER='${SHELL}
>> /home/hoot/mpistuff/osu/osu-micro-benchmarks-3.3/missing --run autoheader'
>> AUTOMAKE='${SHELL} /home/hoot/mpistuff/osu/osu-micro-benchmarks-3.3/missing
>> --run automake-1.11'
>> AWK='mawk'
>> CC='mpicc'
>> CCDEPMODE=''
>> CFLAGS=''
>> CPP=''
>> CPPFLAGS=''
>> CYGPATH_W='echo'
>> DEFS=''
>> DEPDIR=''
>> ECHO_C=''
>> ECHO_N='-n'
>> ECHO_T=''
>> EGREP=''
>> EXEEXT=''
>> GREP=''
>> INSTALL_DATA='${INSTALL} -m 644'
>> INSTALL_PROGRAM='${INSTALL}'
>> INSTALL_SCRIPT='${INSTALL}'
>> INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
>> LDFLAGS=''
>> LIBOBJS=''
>> LIBS=''
>> LTLIBOBJS=''
>> MAKEINFO='${SHELL} /home/hoot/mpistuff/osu/osu-micro-benchmarks-3.3/missing
>> --run makeinfo'
>> MKDIR_P='/bin/mkdir -p'
>> MPI2_LIBRARY_FALSE=''
>> MPI2_LIBRARY_TRUE=''
>> OBJEXT=''
>> PACKAGE='osu-micro-benchmarks'
>> PACKAGE_BUGREPORT='mvapich-discuss at cse.ohio-state.edu'
>> PACKAGE_NAME='OSU-Micro-Benchmarks'
>> PACKAGE_STRING='OSU-Micro-Benchmarks 3.3'
>> PACKAGE_TARNAME='osu-micro-benchmarks'
>> PACKAGE_URL=''
>> PACKAGE_VERSION='3.3'
>> PATH_SEPARATOR=':'
>> SET_MAKE=''
>> SHELL='/bin/bash'
>> STRIP=''
>> VERSION='3.3'
>> ac_ct_CC='mpicc'
>> am__EXEEXT_FALSE=''
>> am__EXEEXT_TRUE=''
>> am__fastdepCC_FALSE=''
>> am__fastdepCC_TRUE=''
>> am__include=''
>> am__isrc=''
>> am__leading_dot='.'
>> am__quote=''
>> am__tar='${AMTAR} chof - "$$tardir"'
>> am__untar='${AMTAR} xf -'
>> bindir='${exec_prefix}/bin'
>> build_alias=''
>> datadir='${datarootdir}'
>> datarootdir='${prefix}/share'
>> docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
>> dvidir='${docdir}'
>> exec_prefix='NONE'
>> host_alias=''
>> htmldir='${docdir}'
>> includedir='${prefix}/include'
>> infodir='${datarootdir}/info'
>> install_sh='${SHELL}
>> /home/hoot/mpistuff/osu/osu-micro-benchmarks-3.3/install-sh'
>> libdir='${exec_prefix}/lib'
>> libexecdir='${exec_prefix}/libexec'
>> localedir='${datarootdir}/locale'
>> localstatedir='${prefix}/var'
>> mandir='${datarootdir}/man'
>> mkdir_p='/bin/mkdir -p'
>> oldincludedir='/usr/include'
>> pdfdir='${docdir}'
>> prefix='NONE'
>> program_transform_name='s,x,x,'
>> psdir='${docdir}'
>> sbindir='${exec_prefix}/sbin'
>> sharedstatedir='${prefix}/com'
>> sysconfdir='${prefix}/etc'
>> target_alias=''
>> 
>> ## ----------- ##
>> ## confdefs.h. ##
>> ## ----------- ##
>> 
>> /* confdefs.h */
>> #define PACKAGE_NAME "OSU-Micro-Benchmarks"
>> #define PACKAGE_TARNAME "osu-micro-benchmarks"
>> #define PACKAGE_VERSION "3.3"
>> #define PACKAGE_STRING "OSU-Micro-Benchmarks 3.3"
>> #define PACKAGE_BUGREPORT "mvapich-discuss at cse.ohio-state.edu"
>> #define PACKAGE_URL ""
>> #define PACKAGE "osu-micro-benchmarks"
>> #define VERSION "3.3"
>> 
>> configure: exit 77
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> -----Original Message-----
>> From: Jonathan Perkins <perkinjo at cse.ohio-state.edu>
>> To: Hoot Thompson <hoot at ptpnow.com>
>> Cc: mvapich-discuss at cse.ohio-state.edu
>> Subject: Re: [mvapich-discuss] Configure error confdefs.h
>> Date: Mon, 6 Jun 2011 17:00:23 -0400
>> 
>> Can you send me the config.log?
>> 
>> On Mon, Jun 6, 2011 at 4:40 PM, Hoot Thompson <hoot at ptpnow.com> wrote:
>>> Running Ubuntu 11.04 and I can't get past the configure step. I'm missing
>>> confdefs.h it appears even with seemingly all relevant packages installed.
>>> What Ubuntu (apt-get install) package installs confdefs.h?
>>> 
>>> 
>>> Thanks in advance...
>>> 
>>> 
>>> _______________________________________________
>>> mvapich-discuss mailing list
>>> mvapich-discuss at cse.ohio-state.edu
>>> http://mail.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
>>> 
>>> 
>> 
>> 
>> 
>> 
>> 
> 
> 