[mvapich-discuss] Configure error confdefs.h

Hoot Thompson hoot at ptpnow.com
Mon Jun 6 17:46:13 EDT 2011 

Actually, I just tried the first suggestion and got the same basic error so
I'm moving on to building mvapich2 with the --with option.


On 6/6/11 5:39 PM, "Jonathan Perkins" <perkinjo at cse.ohio-state.edu> wrote:

> No problem, let us know if you encounter any more issues.
> 
> On Mon, Jun 6, 2011 at 5:34 PM, Hoot Thompson <hoot at ptpnow.com> wrote:
>> Good stuff, thanks! I'm actually using the new Intel NICs that support
>> SR-IOV. My goal is to test base metal versus VMs.
>> 
>> Hoot
>> 
>> 
>> On 6/6/11 5:27 PM, "Jonathan Perkins" <perkinjo at cse.ohio-state.edu> wrote:
>> 
>>> 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.htm
>>> l#
>>> x1-140004.5
>>> http://mvapich.cse.ohio-state.edu/support/user_guide_mvapich2-1.7_alpha2.htm
>>> l#
>>> 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/
>>>>>> lt
>>>>>> o-
>>>>>> 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
>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 
>> 
>> 
> 
>

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