[mvapich-discuss] Configure error confdefs.h

Mon Jun 6 17:27:46 EDT 2011

If you just want to build and run the benchmarks against mpich2 you
should be able to grab the benchmarks from
http://mvapich.cse.ohio-state.edu/benchmarks/osu-micro-benchmarks-3.3.tar.gz
and build with the following steps.

./configure CC=/path/to/mpich2/mpicc
make

You can also build mvapich2 for TCP (10GE) by using
--with-device=ch3:nemesis:tcp.  Please note that you are able to use
the default build of mvapich2 via iWARP if you are using 10GE cards
that support RDMA (eg, Chelsio or NetEffect cards).

Please refer to the following links from our user guide for more
information on this.

http://mvapich.cse.ohio-state.edu/support/user_guide_mvapich2-1.7_alpha2.html#x1-140004.5
http://mvapich.cse.ohio-state.edu/support/user_guide_mvapich2-1.7_alpha2.html#x1-290005.2.6

On Mon, Jun 6, 2011 at 5:17 PM, Hoot Thompson <hoot at ptpnow.com> wrote:
> 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
>>>>
>>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>
>
>
>

-- 
Jonathan Perkins
http://www.cse.ohio-state.edu/~perkinjo