[mvapich-discuss] failing to configure mvapich2 on debian amd64 -
umad.h not found
Jonathan Perkins
perkinjo at cse.ohio-state.edu
Tue Aug 17 18:38:33 EDT 2010
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
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