[mvapich-discuss] failing to configure mvapich2 on debian amd64 -
umad.h not found
Denis
denismpa at gmail.com
Tue Aug 17 18:55:31 EDT 2010
Head-Shot!!!
Thanks Jonathan! That was exactly the problem. I ll report the dependency
bug to the package maintainer.
Thank you a lot!
Denis.
2010/8/17 Jonathan Perkins <perkinjo at cse.ohio-state.edu>
> That's fine, you've captured the portion that I was concerned with.
> It looks like this infiniband/common.h file is missing. Can you
> check to see if you have this installed. If not, it appears that some
> dependency wasn't captured by the ibumad package that was installed.
>
> On Tue, Aug 17, 2010 at 5:58 PM, Denis <denismpa at gmail.com> wrote:
> > Tring to avoid the post of the whole file ( 590 lines ) I am sending the
> > lines that seems to be related to umad.h's checking.
> > If there is any missing information, just let me know and I ll post the
> > rest.
> > configure:4423: gcc -E
> -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src conftest.c
> > configure:4430: $? = 0
> > configure:4444: result: yes
> > configure:4472: checking for hwloc.h
> > configure:4479: result: yes
> > configure:4605: checking for the InfiniBand includes path
> > configure:4612: result: default
> > configure:4616: checking for the InfiniBand library path
> > configure:4643: result: default
> > configure:4646: checking for library containing umad_init
> > configure:4687: gcc -o conftest -g -O2 -DNDEBUG -O2
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src conftest.c -lhwloc
> > -lhwloc -lpthread >&5
> > /tmp/ccpaMZS6.o: In function `main':
> >
> /root/src/mvapich2-1.5-2010-08-12/src/mpid/ch3/channels/mrail/conftest.c:35:
> > undefined reference to `umad_init'
> > collect2: ld returned 1 exit status
> > configure:4694: $? = 1
> > configure: failed program was:
> > | /* confdefs.h. */
> > | #define PACKAGE_NAME ""
> > | #define PACKAGE_TARNAME ""
> > | #define PACKAGE_VERSION ""
> > | #define PACKAGE_STRING ""
> > | #define PACKAGE_BUGREPORT ""
> > | #define STDC_HEADERS 1
> > | #define HAVE_SYS_TYPES_H 1
> > | #define HAVE_SYS_STAT_H 1
> > | #define HAVE_STDLIB_H 1
> > | #define HAVE_STRING_H 1
> > | #define HAVE_MEMORY_H 1
> > | #define HAVE_STRINGS_H 1
> > | #define HAVE_INTTYPES_H 1
> > | #define HAVE_STDINT_H 1
> > | #define HAVE_UNISTD_H 1
> > | #define HAVE_ERRNO_H 1
> > | #define HAVE_STDLIB_H 1
> > | #define HAVE_UNISTD_H 1
> > | #define HAVE_PTHREAD_H 1
> > | #define HAVE_LIBHWLOC /**/
> > | #define _EM64T_ 1
> > | /* end confdefs.h. */
> > |
> > | /* Override any GCC internal prototype to avoid an error.
> > | Use char because int might match the return type of a GCC
> > | builtin and then its argument prototype would still apply. */
> > | #ifdef __cplusplus
> > | extern "C"
> > | #endif
> > | char umad_init ();
> > | int
> > | main ()
> > | {
> > | return umad_init ();
> > | ;
> > | return 0;
> > | }
> > configure:4687: gcc -o conftest -g -O2 -DNDEBUG -O2
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src conftest.c -libumad
> > -lhwloc -lhwloc -lpthread >&5
> > configure:4694: $? = 0
> > configure:4725: result: -libumad
> > configure:4737: checking for library containing ibv_open_device
> > configure:4778: gcc -o conftest -g -O2 -DNDEBUG -O2
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src conftest.c -libumad
> > -lhwloc -lhwloc -lpthread >&5
> > /tmp/ccgpFcr5.o: In function `main':
> >
> /root/src/mvapich2-1.5-2010-08-12/src/mpid/ch3/channels/mrail/conftest.c:35:
> > undefined reference to `ibv_open_device'
> > collect2: ld returned 1 exit status
> > configure:4785: $? = 1
> > configure: failed program was:
> > | /* confdefs.h. */
> > | #define PACKAGE_NAME ""
> > | #define PACKAGE_TARNAME ""
> > | #define PACKAGE_VERSION ""
> > | #define PACKAGE_STRING ""
> > | #define PACKAGE_BUGREPORT ""
> > | #define STDC_HEADERS 1
> > | #define HAVE_SYS_TYPES_H 1
> > | #define HAVE_SYS_STAT_H 1
> > | #define HAVE_STDLIB_H 1
> > | #define HAVE_STRING_H 1
> > | #define HAVE_MEMORY_H 1
> > | #define HAVE_STRINGS_H 1
> > | #define HAVE_INTTYPES_H 1
> > | #define HAVE_STDINT_H 1
> > | #define HAVE_UNISTD_H 1
> > | #define HAVE_ERRNO_H 1
> > | #define HAVE_STDLIB_H 1
> > | #define HAVE_UNISTD_H 1
> > | #define HAVE_PTHREAD_H 1
> > | #define HAVE_LIBHWLOC /**/
> > | #define _EM64T_ 1
> > | /* end confdefs.h. */
> > |
> > | /* Override any GCC internal prototype to avoid an error.
> > | Use char because int might match the return type of a GCC
> > | builtin and then its argument prototype would still apply. */
> > | #ifdef __cplusplus
> > | extern "C"
> > | #endif
> > | char ibv_open_device ();
> > | int
> > | main ()
> > | {
> > | return ibv_open_device ();
> > | ;
> > | return 0;
> > | }
> > configure:4778: gcc -o conftest -g -O2 -DNDEBUG -O2
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src conftest.c -libverbs
> > -libumad -lhwloc -lhwloc -lpthread >&5
> > configure:4785: $? = 0
> > configure:4816: result: -libverbs
> > configure:4838: checking infiniband/umad.h usability
> > configure:4855: gcc -c -g -O2 -DNDEBUG -O2
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src conftest.c >&5
> > In file included from conftest.c:57:
> > /usr/include/infiniband/umad.h:37:31: error: infiniband/common.h: No such
> > file or directory
> > configure:4862: $? = 1
> > configure: failed program was:
> > | /* confdefs.h. */
> > | #define PACKAGE_NAME ""
> > | #define PACKAGE_TARNAME ""
> > | #define PACKAGE_VERSION ""
> > | #define PACKAGE_STRING ""
> > | #define PACKAGE_BUGREPORT ""
> > | #define STDC_HEADERS 1
> > | #define HAVE_SYS_TYPES_H 1
> > | #define HAVE_SYS_STAT_H 1
> > | #define HAVE_STDLIB_H 1
> > | #define HAVE_STRING_H 1
> > | #define HAVE_MEMORY_H 1
> > | #define HAVE_STRINGS_H 1
> > | #define HAVE_INTTYPES_H 1
> > | #define HAVE_STDINT_H 1
> > | #define HAVE_UNISTD_H 1
> > | #define HAVE_ERRNO_H 1
> > | #define HAVE_STDLIB_H 1
> > | #define HAVE_UNISTD_H 1
> > | #define HAVE_PTHREAD_H 1
> > | #define HAVE_LIBHWLOC /**/
> > | #define _EM64T_ 1
> > | /* end confdefs.h. */
> > | #include <stdio.h>
> > | #ifdef HAVE_SYS_TYPES_H
> > | # include <sys/types.h>
> > | #endif
> > | #ifdef HAVE_SYS_STAT_H
> > | # include <sys/stat.h>
> > | #endif
> > | #ifdef STDC_HEADERS
> > | # include <stdlib.h>
> > | # include <stddef.h>
> > | #else
> > | # ifdef HAVE_STDLIB_H
> > | # include <stdlib.h>
> > | # endif
> > | #endif
> > | #ifdef HAVE_STRING_H
> > | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
> > | # include <memory.h>
> > | # endif
> > | # include <string.h>
> > | #endif
> > | #ifdef HAVE_STRINGS_H
> > | # include <strings.h>
> > | #endif
> > | #ifdef HAVE_INTTYPES_H
> > | # include <inttypes.h>
> > | #endif
> > | #ifdef HAVE_STDINT_H
> > | # include <stdint.h>
> > | #endif
> > | #ifdef HAVE_UNISTD_H
> > | # include <unistd.h>
> > | #endif
> > | #include <infiniband/umad.h>
> > configure:4876: result: no
> > configure:4880: checking infiniband/umad.h presence
> > configure:4895: gcc -E
> -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src conftest.c
> > In file included from conftest.c:24:
> > /usr/include/infiniband/umad.h:37:31: error: infiniband/common.h: No such
> > file or directory
> > configure:4902: $? = 1
> > configure: failed program was:
> > | /* confdefs.h. */
> > | #define PACKAGE_NAME ""
> > | #define PACKAGE_TARNAME ""
> > | #define PACKAGE_VERSION ""
> > | #define PACKAGE_STRING ""
> > | #define PACKAGE_BUGREPORT ""
> > | #define STDC_HEADERS 1
> > | #define HAVE_SYS_TYPES_H 1
> > | #define HAVE_SYS_STAT_H 1
> > | #define HAVE_STDLIB_H 1
> > | #define HAVE_STRING_H 1
> > | #define HAVE_MEMORY_H 1
> > | #define HAVE_STRINGS_H 1
> > | #define HAVE_INTTYPES_H 1
> > | #define HAVE_STDINT_H 1
> > | #define HAVE_UNISTD_H 1
> > | #define HAVE_ERRNO_H 1
> > | #define HAVE_STDLIB_H 1
> > | #define HAVE_UNISTD_H 1
> > | #define HAVE_PTHREAD_H 1
> > | #define HAVE_LIBHWLOC /**/
> > | #define _EM64T_ 1
> > | /* end confdefs.h. */
> > | #include <infiniband/umad.h>
> > configure:4916: result: no
> > configure:4944: checking for infiniband/umad.h
> > configure:4951: result: no
> > configure:4958: error: 'infiniband/umad.h not found. Did you specify
> > --with-ib-include=?'
> > ## ---------------- ##
> > ## Cache variables. ##
> > ## ---------------- ##
> > ac_cv_build=x86_64-unknown-linux-gnu
> > ac_cv_c_compiler_gnu=yes
> > ac_cv_env_CC_set=set
> > ac_cv_env_CC_value=gcc
> > ac_cv_env_CFLAGS_set=set
> > ac_cv_env_CFLAGS_value='-g -O2 -DNDEBUG -O2'
> > ac_cv_env_CPPFLAGS_set=set
> > ac_cv_env_CPPFLAGS_value='
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src'
> > 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=set
> > ac_cv_env_LIBS_value='-lhwloc -lpthread'
> > 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_header_errno_h=yes
> > ac_cv_header_hwloc_h=yes
> > ac_cv_header_infiniband_umad_h=no
> > ac_cv_header_inttypes_h=yes
> > ac_cv_header_memory_h=yes
> > ac_cv_header_pthread_h=yes
> > ac_cv_header_stdc=yes
> > ac_cv_header_stdint_h=yes
> > ac_cv_header_stdlib_h=yes
> > ac_cv_header_string_h=yes
> > ac_cv_header_strings_h=yes
> > ac_cv_header_sys_stat_h=yes
> > ac_cv_header_sys_types_h=yes
> > ac_cv_header_unistd_h=yes
> > ac_cv_lib_hwloc_hwloc_topology_set_pid=yes
> > ac_cv_objext=o
> > ac_cv_path_EGREP='/bin/grep -E'
> > ac_cv_path_GREP=/bin/grep
> > ac_cv_prog_CPP='gcc -E'
> > ac_cv_prog_MAKE=make
> > ac_cv_prog_ac_ct_CC=gcc
> > ac_cv_prog_cc_c89=
> > ac_cv_prog_cc_g=yes
> > ac_cv_search_ibv_open_device=-libverbs
> > ac_cv_search_umad_init=-libumad
> >
> pac_cv_my_conf_dir=/root/src/mvapich2-1.5-2010-08-12/src/mpid/ch3/channels/mrail
> > pac_cv_prog_make_allows_comments=yes
> > pac_cv_prog_make_found_clock_skew=no
> > pac_cv_prog_make_include=yes
> > pac_cv_prog_make_set_cflags=yes
> > pac_cv_prog_make_vpath=VPATH
> > ## ----------------- ##
> > ## Output variables. ##
> > ## ----------------- ##
> > AR='ar'
> > CC='gcc'
> > CC_SHL='true'
> > CFLAGS='-g -O2 -DNDEBUG -O2'
> > CPP='gcc -E'
> > CPPFLAGS=' -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src
> > -I/root/src/mvapich2-1.5-2010-08-12/src/openpa/src'
> > C_LINK_SHL='true'
> > DEFS=''
> > ECHO_C=''
> > ECHO_N='-n'
> > ECHO_T=''
> > EGREP='/bin/grep -E'
> > ENABLE_SHLIB='none'
> > ETAGS=''
> > ETAGSADD=''
> > EXEEXT=''
> > GREP='/bin/grep'
> > LDFLAGS=''
> > LIBOBJS=''
> > LIBS='-libverbs -libumad -lhwloc -lhwloc -lpthread'
> > LIBTOOL=''
> > LTLIBOBJS=''
> > MAKE='make'
> > MAKE_DEPEND_C='gcc -MM'
> > MPILIBNAME='mpich'
> > OBJEXT='o'
> > PACKAGE_BUGREPORT=''
> > PACKAGE_NAME=''
> > PACKAGE_STRING=''
> > PACKAGE_TARNAME=''
> > PACKAGE_VERSION=''
> > PATH_SEPARATOR=':'
> > RANLIB='ranlib'
> > SET_CFLAGS='CFLAGS='
> > SET_MAKE='MAKE=make'
> > SHELL='/bin/bash'
> > SHLIB_EXT='so'
> > VPATH='VPATH=.:${srcdir}'
> > ac_ct_CC='gcc'
> > bindir='${exec_prefix}/bin'
> > build='x86_64-unknown-linux-gnu'
> > build_alias=''
> > build_cpu='x86_64'
> > build_os='linux-gnu'
> > build_vendor='unknown'
> > channel_name='mrail'
> > datadir='${datarootdir}'
> > datarootdir='${prefix}/share'
> > device_name='ch3'
> > docdir='${datarootdir}/doc/${PACKAGE}'
> > dvidir='${docdir}'
> > exec_prefix='NONE'
> > host_alias=''
> > htmldir='${docdir}'
> > includedir='${prefix}/include'
> > infodir='${datarootdir}/info'
> > libdir='${exec_prefix}/lib'
> > libexecdir='${exec_prefix}/libexec'
> > localedir='${datarootdir}/locale'
> > localstatedir='${prefix}/var'
> > mandir='${datarootdir}/man'
> > master_top_builddir='/root/src/mvapich2-1.5-2010-08-12'
> > master_top_srcdir='/root/src/mvapich2-1.5-2010-08-12'
> > mrail_fflags=''
> > mrail_ld_library_path=''
> > mrail_ldflags=''
> > mrail_libs=''
> > oldincludedir='/usr/include'
> > other_subdirs='gen2'
> > pdfdir='${docdir}'
> > prefix='/usr/local'
> > program_transform_name='s,x,x,'
> > psdir='${docdir}'
> > sbindir='${exec_prefix}/sbin'
> > sharedstatedir='${prefix}/com'
> > subdirs=''
> > sysconfdir='${prefix}/etc'
> > target_alias=''
> > use_internal_hwloc='no'
> > ## ----------- ##
> > ## confdefs.h. ##
> > ## ----------- ##
> > #define PACKAGE_NAME ""
> > #define PACKAGE_TARNAME ""
> > #define PACKAGE_VERSION ""
> > #define PACKAGE_STRING ""
> > #define PACKAGE_BUGREPORT ""
> > #define STDC_HEADERS 1
> > #define HAVE_SYS_TYPES_H 1
> > #define HAVE_SYS_STAT_H 1
> > #define HAVE_STDLIB_H 1
> > #define HAVE_STRING_H 1
> > #define HAVE_MEMORY_H 1
> > #define HAVE_STRINGS_H 1
> > #define HAVE_INTTYPES_H 1
> > #define HAVE_STDINT_H 1
> > #define HAVE_UNISTD_H 1
> > #define HAVE_ERRNO_H 1
> > #define HAVE_STDLIB_H 1
> > #define HAVE_UNISTD_H 1
> > #define HAVE_PTHREAD_H 1
> > #define HAVE_LIBHWLOC /**/
> > #define _EM64T_ 1
> > configure: exit 1
> >
> > thank you, Jonathan.
> >
> >
> > 2010/8/17 Jonathan Perkins <perkinjo at cse.ohio-state.edu>
> >>
> >> Can you post the config.log file from the src/mpid/ch3/channels/mrail
> >> directory? There could be something odd going on when its checking
> >> for umad.h's usability.
> >>
> >> On Tue, Aug 17, 2010 at 5:26 PM, Denis <denismpa at gmail.com> wrote:
> >> > Hi All,
> >> > I am trying to build mvapich2-1.5 on debian but it won't configure
> >> > complaining that the header file infiniband/umad.h cannot be found.
> >> > the last configure lines are below
> >> > checking pthread.h usability... yes
> >> > checking pthread.h presence... yes
> >> > checking for pthread.h... yes
> >> > ./configure: line 4137: enable_ftb-cr=no: command not found
> >> > configure: checking for any hwloc installation...
> >> > checking for hwloc_topology_set_pid in -lhwloc... yes
> >> > checking hwloc.h usability... yes
> >> > checking hwloc.h presence... yes
> >> > checking for hwloc.h... yes
> >> > checking for the InfiniBand includes path... /usr/include/infiniband
> >> > checking for the InfiniBand library path... default
> >> > checking for library containing umad_init... -libumad
> >> > checking for library containing ibv_open_device... -libverbs
> >> > checking infiniband/umad.h usability... no
> >> > checking infiniband/umad.h presence... no
> >> > checking for infiniband/umad.h... no
> >> > configure: error: 'infiniband/umad.h not found. Did you specify
> >> > --with-ib-include=?'
> >> > configure: error: ./configure failed for channels/mrail
> >> > configure: error: Configure of src/mpid/ch3 failed!
> >> >
> >> > I have tried the version 1.5 and the daily versions from 2010-08-11
> and
> >> > 2010-08-12. They all give me the same issue.
> >> >
> >> > However the header file is on the default place,
> >> > root at localhost:~/src/mvapich2-1.5-2010-08-12# ls
> >> > /usr/include/infiniband/umad.h
> >> > /usr/include/infiniband/umad.h
> >> >
> >> > as the configure is complaining, I have also tried to specify it with
> >> > the
> >> > --with-ib-include option.
> >> >
> >> >
> >> >
> >> > The library and header files were installed by packages and have the
> >> > following versions:
> >> >
> >> > root at localhost:~/src/mvapich2-1.5-2010-08-12# dpkg -S
> >> > /usr/include/infiniband/umad.h
> >> > libibumad-dev: /usr/include/infiniband/umad.h
> >> > root at localhost:~/src/mvapich2-1.5-2010-08-12# aptitude show
> >> > libibumad-dev
> >> > Package: libibumad-dev
> >> > New: yes
> >> > State: installed
> >> > Automatically installed: no
> >> > Version: 1.2.3-20090314-1
> >> >
> >> > root at localhost:~/src/mvapich2-1.5-2010-08-12# aptitude show
> libibumad1
> >> > Package: libibumad1
> >> > New: yes
> >> > State: installed
> >> > Automatically installed: yes
> >> > Version: 1.2.3-20090314-1
> >> >
> >> > The only way I found that mvapich will configure ( but not compile) is
> >> > if I
> >> > specify --with-devices=nemesis:ib .
> >> > The problem seems to lie on the ch3 channel and/or mrail. Whenever I
> >> > enable
> >> > ch3 or gen2, I fall on the same problem.
> >> >
> >> > Any suggestions?
> >> > Thanks!
> >> >
> >> > Denis
> >> > _______________________________________________
> >> > mvapich-discuss mailing list
> >> > mvapich-discuss at cse.ohio-state.edu
> >> > http://mail.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Jonathan Perkins
> >
> >
> >
> > --
> > Denis Anjos,
> > www.versatushpc.com.br
> >
> > _______________________________________________
> > mvapich-discuss mailing list
> > mvapich-discuss at cse.ohio-state.edu
> > http://mail.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
> >
> >
>
>
>
> --
> Jonathan Perkins
>
--
Denis Anjos,
www.versatushpc.com.br
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