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Subject: [OMPI users] openmpi-1.2.8: segmentation fault using Cygwin-1.5 and gcc-4.3.2
From: Siegmar Gross (Siegmar.Gross_at_[hidden])
Date: 2009-02-12 09:09:03


Hi,

I have installed openmpi-1.2.8 using Cygwin 1.5 on top of Windows
XP Pro with gcc-4.3.2 with the following commands.

configure --prefix=/usr/local/openmpi-1.2.8-gcc-4 \
  CFLAGS="" CXXFLAGS="" FFLAGS="" FCFLAGS="" \
  CPPFLAGS="" C_INCL_PATH="" C_INCLUDE_PATH="" CPLUS_INCLUDE_PATH="" \
  OBJC_INCLUDE_PATH="" \
  CC="gcc-4" CPP="cpp-4" CXX="g++-4" CXXCPP="cpp-4" F77="gfortran-4" \
  FC="gfortran-4" \
  --enable-cxx-exceptions --enable-mpi-threads \
  --enable-progress-threads --with-threads=posix \
  --enable-static --without-cs-fs \
  |& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV.gcc-4

cp -p opal/mca/timer/windows/timer_windows.h \
  opal/mca/timer/windows/timer_windows_component.h

make |& tee log.make.$SYSTEM_ENV.$MACHINE_ENV.gcc-4
make install |& tee log.make-install.$SYSTEM_ENV.$MACHINE_ENV.gcc-4

I get the following output when I run some commands.

eiger Admin 4 set MPI = openmpi-1.2.8-gcc-4
eiger Admin 5 source .mpi.csh

eiger hello1 8 mpicc -show
[eiger:02344] *** Process received signal ***
[eiger:02344] Signal: Segmentation fault (11)
[eiger:02344] Signal code: (23)
[eiger:02344] Failing at address: 0x401b0e
[eiger:02344] *** End of error message ***
Segmentation fault (core dumped)
eiger hello1 9

I can run "--help" with orted, orterun, and ompi_info, but
"ompi_info" displays a strange result.

eiger hello1 12 ompi_info
                Open MPI: 1.2.8
   Open MPI SVN revision: r19718
                Open RTE: 1.2.8
   Open RTE SVN revision: r19718
                    OPAL: 1.2.8
       OPAL SVN revision: r19718
                  Prefix: /usr/local/openmpi-1.2.8-gcc-4
 Configured architecture: i686-pc-cygwin
           Configured by: fd1026
           Configured on: Tue Jan 6 19:55:41 2009
          Configure host: eiger
                Built by: fd1026
                Built on: Tue Jan 6 22:44:29 2009
              Built host: eiger
              C bindings: yes
            C++ bindings: yes
      Fortran77 bindings: yes (single underscore)
      Fortran90 bindings: yes
 Fortran90 bindings size: small
              C compiler: gcc-4
     C compiler absolute: /usr/bin/gcc-4
            C++ compiler: g++-4
   C++ compiler absolute: /usr/bin/g++-4
      Fortran77 compiler: gfortran-4
  Fortran77 compiler abs: /usr/bin/gfortran-4
      Fortran90 compiler: gfortran-4
  Fortran90 compiler abs: /usr/bin/gfortran-4
             C profiling: yes
           C++ profiling: yes
     Fortran77 profiling: yes
     Fortran90 profiling: yes
          C++ exceptions: no
          Thread support: posix (mpi: no, progress: no)
  Internal debug support: no
     MPI parameter check: runtime
Memory profiling support: no
Memory debugging support: no
         libltdl support: yes
   Heterogeneous support: yes

 mpirun default --prefix: no
[eiger:00716] mca: base: component_find: unable to open paffinity windows: can't
open the module (ignored)
[eiger:00716] mca: base: component_find: unable to open maffinity first_use:
can't open the module (ignored)
[eiger:00716] mca: base: component_find: unable to open oob tcp: can't open the
module (ignored)
[eiger:00716] mca: base: component_find: unable to open errmgr hnp: can't open
the module (ignored)
[eiger:00716] mca: base: component_find: unable to open errmgr orted: can't open
the module (ignored)
[eiger:00716] mca: base: component_find: unable to open errmgr proxy: can't open
the module (ignored)
[eiger:00716] mca: base: component_find: unable to open gpr null: can't open the
module (ignored)
[eiger:00716] mca: base: component_find: unable to open gpr proxy: can't open
the module (ignored)
[eiger:00716] mca: base: component_find: unable to open gpr replica: can't open
the module (ignored)
...
[eiger:00716] mca: base: component_find: unable to open btl tcp: can't open the
module (ignored)
[eiger:00716] mca: base: component_find: unable to open topo unity: can't open
the module (ignored)
           MCA backtrace: none (MCA v1.0, API v1.0, Component v1.2.8)
               MCA timer: windows (MCA v1.0, API v1.0, Component v1.2.8)
         MCA installdirs: env (MCA v1.0, API v1.0, Component v1.2.8)
         MCA installdirs: config (MCA v1.0, API v1.0, Component v1.2.8)
eiger hello1 13

When I search the log-files I can find the following problems.

openmpi-1.2.8-gcc-4:
--------------------

wi23 openmpi-1.2.8-gcc-4 31 grep -i warning log.configure.Cygwin.x86.gcc-4
configure: WARNING: -fno-strict-aliasing has been added to CFLAGS
configure: WARNING: -finline-functions has been added to CXXFLAGS
configure: WARNING: *** Shared libraries have been disabled (--disable-shared)
configure: WARNING: *** Building MCA components as DSOs automatically disabled
configure: WARNING: Unknown architecture ... proceeding anyway
configure: WARNING: File locks may not work with NFS. See the Installation and
wi23 openmpi-1.2.8-gcc-4 32

wi23 openmpi-1.2.8-gcc-4 32 grep -i warning log.make.Cygwin.x86.gcc-4
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
*** Warning: This system can not link to static lib archive
/home/Admin/MPI/OpenMpi/openmpi-1.2.8-gcc-4/opal/libopen-pal.la.
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
../../ompi/datatype/datatype_pack.h:41: warning: passing argument 5 of
'opal_bcopy_uicsum_partial' from incompatible pointer type
../../ompi/datatype/datatype_pack.h:51: warning: passing argument 5 of
'opal_bcopy_uicsum_partial' from incompatible pointer type
../../ompi/datatype/datatype_pack.h:82: warning: passing argument 5 of
'opal_bcopy_uicsum_partial' from incompatible pointer type
datatype_pack.c:75: warning: passing argument 3 of 'opal_uicsum_partial' from
incompatible pointer type
datatype_pack.c:80: warning: passing argument 5 of 'opal_bcopy_uicsum_partial'
from incompatible pointer type
datatype_pack.c:143: warning: passing argument 3 of 'opal_uicsum_partial' from
incompatible pointer type
datatype_pack.c:162: warning: passing argument 3 of 'opal_uicsum_partial' from
incompatible pointer type
datatype_pack.c:168: warning: passing argument 3 of 'opal_uicsum_partial' from
incompatible pointer type
datatype_pack.c:193: warning: passing argument 5 of 'opal_bcopy_uicsum_partial'
from incompatible pointer type
datatype_pack.c:203: warning: passing argument 5 of 'opal_bcopy_uicsum_partial'
from incompatible pointer type
datatype_pack.c:214: warning: passing argument 5 of 'opal_bcopy_uicsum_partial'
from incompatible pointer type
../../ompi/datatype/datatype_unpack.h:41: warning: passing argument 5 of
'opal_bcopy_uicsum_partial' from incompatible pointer type
../../ompi/datatype/datatype_unpack.h:51: warning: passing argument 5 of
'opal_bcopy_uicsum_partial' from incompatible pointer type
../../ompi/datatype/datatype_unpack.h:82: warning: passing argument 5 of
'opal_bcopy_uicsum_partial' from incompatible pointer type
datatype_unpack.c:216: warning: passing argument 5 of
'opal_bcopy_uicsum_partial' from incompatible pointer type
datatype_unpack.c:234: warning: passing argument 5 of
'opal_bcopy_uicsum_partial' from incompatible pointer type
datatype_unpack.c:245: warning: passing argument 5 of
'opal_bcopy_uicsum_partial' from incompatible pointer type
datatype_unpack.c:258: warning: passing argument 5 of
'opal_bcopy_uicsum_partial' from incompatible pointer type
datatype_unpack.c:395: warning: passing argument 3 of 'opal_uicsum_partial' from
incompatible pointer type
datatype_unpack.c:429: warning: passing argument 3 of 'opal_uicsum_partial' from
incompatible pointer type
dt_args.c:611: warning: passing argument 1 of '__ompi_ddt_create_from_args' from
incompatible pointer type
dt_args.c:649: warning: passing argument 2 of 'ompi_ddt_create_indexed' from
incompatible pointer type
dt_args.c:649: warning: passing argument 3 of 'ompi_ddt_create_indexed' from
incompatible pointer type
dt_args.c:654: warning: passing argument 2 of 'ompi_ddt_create_hindexed' from
incompatible pointer type
dt_args.c:658: warning: passing argument 3 of 'ompi_ddt_create_indexed_block'
from incompatible pointer type
dt_args.c:663: warning: passing argument 2 of 'ompi_ddt_create_struct' from
incompatible pointer type
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
ppack_external.c:78: warning: passing argument 3 of 'ompi_convertor_pack' from
incompatible pointer type
ppack.c:80: warning: passing argument 3 of 'ompi_convertor_pack' from
incompatible pointer type
ptype_contiguous.c:58: warning: passing argument 3 of 'ompi_ddt_set_args' from
incompatible pointer type
ptype_create_darray.c:218: warning: passing argument 3 of 'ompi_ddt_set_args'
from incompatible pointer type
ptype_create_hindexed.c:77: warning: passing argument 3 of 'ompi_ddt_set_args'
from incompatible pointer type
ptype_create_hvector.c:70: warning: passing argument 3 of 'ompi_ddt_set_args'
from incompatible pointer type
ptype_create_indexed_block.c:68: warning: passing argument 3 of
'ompi_ddt_set_args' from incompatible pointer type
ptype_create_struct.c:81: warning: passing argument 3 of 'ompi_ddt_set_args'
from incompatible pointer type
ptype_create_subarray.c:143: warning: passing argument 3 of 'ompi_ddt_set_args'
from incompatible pointer type
ptype_get_contents.c:61: warning: passing argument 3 of 'ompi_ddt_get_args' from
incompatible pointer type
ptype_get_contents.c:61: warning: passing argument 4 of 'ompi_ddt_get_args' from
incompatible pointer type
ptype_get_contents.c:61: warning: passing argument 5 of 'ompi_ddt_get_args' from
incompatible pointer type
ptype_get_contents.c:61: warning: passing argument 7 of 'ompi_ddt_get_args' from
incompatible pointer type
ptype_get_envelope.c:56: warning: passing argument 3 of 'ompi_ddt_get_args' from
incompatible pointer type
ptype_get_envelope.c:56: warning: passing argument 5 of 'ompi_ddt_get_args' from
incompatible pointer type
ptype_get_envelope.c:56: warning: passing argument 7 of 'ompi_ddt_get_args' from
incompatible pointer type
ptype_get_envelope.c:56: warning: passing argument 9 of 'ompi_ddt_get_args' from
incompatible pointer type
ptype_indexed.c:81: warning: passing argument 3 of 'ompi_ddt_set_args' from
incompatible pointer type
ptype_vector.c:66: warning: passing argument 3 of 'ompi_ddt_set_args' from
incompatible pointer type
punpack_external.c:75: warning: passing argument 3 of 'ompi_convertor_unpack'
from incompatible pointer type
punpack.c:84: warning: passing argument 3 of 'ompi_convertor_unpack' from
incompatible pointer type
pack_external.c:78: warning: passing argument 3 of 'ompi_convertor_pack' from
incompatible pointer type
pack.c:80: warning: passing argument 3 of 'ompi_convertor_pack' from
incompatible pointer type
type_contiguous.c:58: warning: passing argument 3 of 'ompi_ddt_set_args' from
incompatible pointer type
type_create_darray.c:218: warning: passing argument 3 of 'ompi_ddt_set_args'
from incompatible pointer type
type_create_hindexed.c:77: warning: passing argument 3 of 'ompi_ddt_set_args'
from incompatible pointer type
type_create_hvector.c:70: warning: passing argument 3 of 'ompi_ddt_set_args'
from incompatible pointer type
type_create_indexed_block.c:68: warning: passing argument 3 of
'ompi_ddt_set_args' from incompatible pointer type
type_create_struct.c:81: warning: passing argument 3 of 'ompi_ddt_set_args' from
incompatible pointer type
type_create_subarray.c:143: warning: passing argument 3 of 'ompi_ddt_set_args'
from incompatible pointer type
type_get_contents.c:61: warning: passing argument 3 of 'ompi_ddt_get_args' from
incompatible pointer type
type_get_contents.c:61: warning: passing argument 4 of 'ompi_ddt_get_args' from
incompatible pointer type
type_get_contents.c:61: warning: passing argument 5 of 'ompi_ddt_get_args' from
incompatible pointer type
type_get_contents.c:61: warning: passing argument 7 of 'ompi_ddt_get_args' from
incompatible pointer type
type_get_envelope.c:56: warning: passing argument 3 of 'ompi_ddt_get_args' from
incompatible pointer type
type_get_envelope.c:56: warning: passing argument 5 of 'ompi_ddt_get_args' from
incompatible pointer type
type_get_envelope.c:56: warning: passing argument 7 of 'ompi_ddt_get_args' from
incompatible pointer type
type_get_envelope.c:56: warning: passing argument 9 of 'ompi_ddt_get_args' from
incompatible pointer type
type_indexed.c:81: warning: passing argument 3 of 'ompi_ddt_set_args' from
incompatible pointer type
type_vector.c:66: warning: passing argument 3 of 'ompi_ddt_set_args' from
incompatible pointer type
unpack_external.c:75: warning: passing argument 3 of 'ompi_convertor_unpack'
from incompatible pointer type
unpack.c:84: warning: passing argument 3 of 'ompi_convertor_unpack' from
incompatible pointer type
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
base/pml_base_bsend.c:255: warning: passing argument 3 of 'ompi_convertor_pack'
from incompatible pointer type
pml_cm_send.c:77: warning: passing argument 3 of 'ompi_convertor_pack' from
incompatible pointer type
pml_cm_send.c:142: warning: passing argument 3 of 'ompi_convertor_pack' from
incompatible pointer type
pml_cm_start.c:124: warning: passing argument 3 of 'ompi_convertor_pack' from
incompatible pointer type
pml_ob1_sendreq.c:417: warning: passing argument 3 of 'ompi_convertor_pack' from
incompatible pointer type
pml_ob1_sendreq.c:468: warning: passing argument 3 of 'ompi_convertor_pack' from
incompatible pointer type
pml_ob1_sendreq.c:533: warning: passing argument 3 of 'ompi_convertor_pack' from
incompatible pointer type
attribute/attribute.c:685: warning: passing argument 1 of
'keyval->delete_attr_fn.attr_mpi1_fortran_delete_fn' from incompatible pointer
type
attribute/attribute.c:685: warning: passing argument 1 of
'keyval->delete_attr_fn.attr_mpi2_fortran_delete_fn' from incompatible pointer
type
attribute/attribute.c:901: warning: passing argument 1 of
'hash_value->copy_attr_fn.attr_mpi1_fortran_copy_fn' from incompatible pointer
type
attribute/attribute.c:901: warning: passing argument 1 of
'hash_value->copy_attr_fn.attr_mpi2_fortran_copy_fn' from incompatible pointer
type
attribute/attribute.c:1071: warning: passing argument 1 of
'keyval->delete_attr_fn.attr_mpi1_fortran_delete_fn' from incompatible pointer
type
attribute/attribute.c:1071: warning: passing argument 1 of
'keyval->delete_attr_fn.attr_mpi2_fortran_delete_fn' from incompatible pointer
type
*** Warning: This system can not link to static lib archive
/home/Admin/MPI/OpenMpi/openmpi-1.2.8-gcc-4/orte/libopen-rte.la.
*** Warning: This system can not link to static lib archive
/home/Admin/MPI/OpenMpi/openmpi-1.2.8-gcc-4/opal/libopen-pal.la.
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
wi23 openmpi-1.2.8-gcc-4 33

The log-files contain no errors. Does anybody know what's wrong with
the installation? Does anybody have a working installation? Thank
you very much for any help in advance.

Kind regads

Siegmar