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Subject: [OMPI users] openmpi-1.3: segmentation fault using Cygwin-1.5 and gcc-3.4.4
From: Siegmar Gross (Siegmar.Gross_at_[hidden])
Date: 2009-02-12 09:09:23


Hi,

I have installed openmpi-1.3 using Cygwin 1.5 on top of Windows
XP Pro with gcc-3.4.4 with the following commands.

At first I added "#define NOMINMAX" before the line
"#include MCA_timer_IMPLEMENTATION_HEADER" and "#undef NOMINMAX"
after that line in file "ompi/tools/ompi_info/param.cc" as described
in the mail archives.

configure --prefix=/usr/local/openmpi-1.3 \
  CFLAGS="" CXXFLAGS="" FFLAGS="" FCFLAGS="" \
  CPPFLAGS="" C_INCL_PATH="" C_INCLUDE_PATH="" CPLUS_INCLUDE_PATH="" \
  OBJC_INCLUDE_PATH="" \
  --without-udapl \
  --enable-cxx-exceptions --enable-mpi-threads \
  --enable-progress-threads --with-threads=posix \
  --enable-static --without-cs-fs \
  --enable-heterogeneous --with-mpi-param_check=always \
  --enable-contrib-no-build=vt \
  --enable-mca-no-build=memory_mallopt,paffinity \
  |& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV

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

I get the following output when I run some commands.

eiger Admin 5 set MPI = openmpi-1.3
eiger Admin 6 source .mpi.csh

eiger hello1 9 make
mpicc -m32 -Wall -Wstrict-prototypes -Wmissing-prototypes -pedantic -std=c99
-DCygwin -Dx86 -c -o hello1_mpi.o \
        hello1_mpi.c
mpicc -m32 -o /home/Admin/Cygwin/x86/bin/hello1_mpi.exe hello1_mpi.o
/usr/lib/gcc/i686-pc-cygwin/3.4.4/../../../../i686-pc-cygwin/bin/ld: cannot find
-lmpi
collect2: ld returned 1 exit status
make: *** [/home/Admin/Cygwin/x86/bin/hello1_mpi.exe] Error 1
eiger hello1 10 ls -l /usr/local/openmpi-1.3/lib/
total 5432
-rwxr-xr-x 1 Admin Kein 969 Feb 8 14:17 libmpi.la
-rw-r--r-- 1 Admin Kein 2852212 Feb 8 14:17 libmpi.lib
-rwxr-xr-x 1 Admin Kein 1018 Feb 8 14:22 libmpi_cxx.la
-rw-r--r-- 1 Admin Kein 591668 Feb 8 14:22 libmpi_cxx.lib
-rwxr-xr-x 1 Admin Kein 1018 Feb 8 14:22 libmpi_f77.la
-rw-r--r-- 1 Admin Kein 858986 Feb 8 14:22 libmpi_f77.lib
-rwxr-xr-x 1 Admin Kein 900 Feb 8 14:13 libopen-pal.la
-rw-r--r-- 1 Admin Kein 468364 Feb 8 14:13 libopen-pal.lib
-rwxr-xr-x 1 Admin Kein 942 Feb 8 14:14 libopen-rte.la
-rw-r--r-- 1 Admin Kein 758034 Feb 8 14:14 libopen-rte.lib
drwxr-xr-x+ 2 Admin Kein 0 Feb 8 14:15 openmpi
eiger hello1 11

Indeed the library isn't available. When I search the log-files I
can find the following problems.

wi23 openmpi-1.3-gcc 3 grep -i warning log.configure.Cygwin.x86
configure: WARNING: -fno-strict-aliasing has been added to CFLAGS
configure: WARNING: -finline-functions has been added to CXXFLAGS
configure: WARNING: MPI_REAL16 and MPI_COMPLEX32 support have been disabled
configure: WARNING: *** Fortran 90/95 bindings disabled (could not find
compiler)
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
configure: WARNING: unrecognized options: --without-udapl,
--enable-cxx-exceptions, --enable-mpi-threads, --enable-progress-threads,
--with-threads, --without-cs-fs, --enable-heterogeneous, --with-mpi-param_check,
--enable-contrib-no-build, --enable-mca-no-build, --enable-ltdl-convenience
configure: WARNING: unrecognized options: --without-udapl,
--enable-cxx-exceptions, --enable-mpi-threads, --enable-progress-threads,
--with-threads, --without-cs-fs, --enable-heterogeneous, --with-mpi-param_check,
--enable-contrib-no-build, --enable-mca-no-build, --enable-ltdl-convenience
wi23 openmpi-1.3-gcc 4

wi23 openmpi-1.3-gcc 4 grep -i warning log.make.Cygwin.x86
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
base/plm_base_launch_support.c:334: warning: passing arg 3 of pointer to
function from incompatible pointer type
base/plm_base_launch_support.c:360: warning: passing arg 3 of pointer to
function from incompatible pointer type
runtime/orte_mca_params.c:159: warning: passing arg 7 of
`mca_base_param_reg_int_name' from incompatible pointer type
util/nidmap.c:370: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:394: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:401: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:409: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:416: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:423: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:430: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:437: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:479: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:485: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:508: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:519: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:546: warning: passing arg 3 of pointer to function from
incompatible pointer type
util/nidmap.c:560: warning: passing arg 3 of pointer to function from
incompatible pointer type
*** Warning: This system can not link to static lib archive
/home/Admin/MPI/OpenMpi/openmpi-1.3/opal/libopen-pal.la.
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
orte-ps.c:802: warning: passing arg 3 of `orte_util_comm_query_job_info' from
incompatible pointer type
orte-ps.c:813: warning: passing arg 3 of `orte_util_comm_query_node_info' from
incompatible pointer type
../../ompi/datatype/datatype_pack.h:41: warning: passing arg 5 of
`opal_bcopy_uicsum_partial' from incompatible pointer type
../../ompi/datatype/datatype_pack.h:51: warning: passing arg 5 of
`opal_bcopy_uicsum_partial' from incompatible pointer type
../../ompi/datatype/datatype_pack.h:82: warning: passing arg 5 of
`opal_bcopy_uicsum_partial' from incompatible pointer type
datatype_pack.c:75: warning: passing arg 3 of `opal_uicsum_partial' from
incompatible pointer type
datatype_pack.c:80: warning: passing arg 5 of `opal_bcopy_uicsum_partial' from
incompatible pointer type
datatype_pack.c:143: warning: passing arg 3 of `opal_uicsum_partial' from
incompatible pointer type
datatype_pack.c:162: warning: passing arg 3 of `opal_uicsum_partial' from
incompatible pointer type
datatype_pack.c:168: warning: passing arg 3 of `opal_uicsum_partial' from
incompatible pointer type
datatype_pack.c:193: warning: passing arg 5 of `opal_bcopy_uicsum_partial' from
incompatible pointer type
datatype_pack.c:203: warning: passing arg 5 of `opal_bcopy_uicsum_partial' from
incompatible pointer type
datatype_pack.c:214: warning: passing arg 5 of `opal_bcopy_uicsum_partial' from
incompatible pointer type
../../ompi/datatype/datatype_unpack.h:41: warning: passing arg 5 of
`opal_bcopy_uicsum_partial' from incompatible pointer type
../../ompi/datatype/datatype_unpack.h:51: warning: passing arg 5 of
`opal_bcopy_uicsum_partial' from incompatible pointer type
../../ompi/datatype/datatype_unpack.h:82: warning: passing arg 5 of
`opal_bcopy_uicsum_partial' from incompatible pointer type
datatype_unpack.c:221: warning: passing arg 5 of `opal_bcopy_uicsum_partial'
from incompatible pointer type
datatype_unpack.c:239: warning: passing arg 5 of `opal_bcopy_uicsum_partial'
from incompatible pointer type
datatype_unpack.c:250: warning: passing arg 5 of `opal_bcopy_uicsum_partial'
from incompatible pointer type
datatype_unpack.c:263: warning: passing arg 5 of `opal_bcopy_uicsum_partial'
from incompatible pointer type
datatype_unpack.c:400: warning: passing arg 3 of `opal_uicsum_partial' from
incompatible pointer type
datatype_unpack.c:434: warning: passing arg 3 of `opal_uicsum_partial' from
incompatible pointer type
dt_args.c:605: warning: passing arg 1 of `__ompi_ddt_create_from_args' from
incompatible pointer type
dt_args.c:642: warning: passing arg 2 of `ompi_ddt_create_indexed' from
incompatible pointer type
dt_args.c:642: warning: passing arg 3 of `ompi_ddt_create_indexed' from
incompatible pointer type
dt_args.c:647: warning: passing arg 2 of `ompi_ddt_create_hindexed' from
incompatible pointer type
dt_args.c:651: warning: passing arg 3 of `ompi_ddt_create_indexed_block' from
incompatible pointer type
dt_args.c:656: warning: passing arg 2 of `ompi_ddt_create_struct' from
incompatible pointer type
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
pcomm_get_errhandler.c:65: warning: cast from pointer to integer of different
size
pcomm_get_errhandler.c:65: warning: cast from pointer to integer of different
size
pcomm_set_errhandler.c:67: warning: cast from pointer to integer of different
size
pcomm_set_errhandler.c:67: warning: cast from pointer to integer of different
size
pcomm_set_errhandler.c:74: warning: cast from pointer to integer of different
size
pcomm_set_errhandler.c:74: warning: cast from pointer to integer of different
size
ppack_external.c:93: warning: passing arg 3 of `ompi_convertor_pack' from
incompatible pointer type
ppack.c:91: warning: passing arg 3 of `ompi_convertor_pack' from incompatible
pointer type
ptype_contiguous.c:66: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
ptype_create_darray.c:226: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
ptype_create_f90_complex.c:101: warning: passing arg 3 of `ompi_ddt_set_args'
from incompatible pointer type
ptype_create_f90_integer.c:100: warning: passing arg 3 of `ompi_ddt_set_args'
from incompatible pointer type
ptype_create_f90_real.c:102: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
ptype_create_hindexed.c:84: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
ptype_create_hvector.c:77: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
ptype_create_indexed_block.c:76: warning: passing arg 3 of `ompi_ddt_set_args'
from incompatible pointer type
ptype_create_struct.c:92: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
ptype_create_subarray.c:147: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
ptype_get_contents.c:68: warning: passing arg 3 of `ompi_ddt_get_args' from
incompatible pointer type
ptype_get_contents.c:68: warning: passing arg 4 of `ompi_ddt_get_args' from
incompatible pointer type
ptype_get_contents.c:68: warning: passing arg 5 of `ompi_ddt_get_args' from
incompatible pointer type
ptype_get_contents.c:68: warning: passing arg 7 of `ompi_ddt_get_args' from
incompatible pointer type
ptype_get_envelope.c:63: warning: passing arg 3 of `ompi_ddt_get_args' from
incompatible pointer type
ptype_get_envelope.c:63: warning: passing arg 5 of `ompi_ddt_get_args' from
incompatible pointer type
ptype_get_envelope.c:63: warning: passing arg 7 of `ompi_ddt_get_args' from
incompatible pointer type
ptype_get_envelope.c:63: warning: passing arg 9 of `ompi_ddt_get_args' from
incompatible pointer type
ptype_indexed.c:88: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
ptype_vector.c:73: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
punpack_external.c:85: warning: passing arg 3 of `ompi_convertor_unpack' from
incompatible pointer type
punpack.c:96: warning: passing arg 3 of `ompi_convertor_unpack' from
incompatible pointer type
pwin_get_errhandler.c:57: warning: cast from pointer to integer of different
size
pwin_get_errhandler.c:57: warning: cast from pointer to integer of different
size
pwin_set_errhandler.c:60: warning: cast from pointer to integer of different
size
pwin_set_errhandler.c:60: warning: cast from pointer to integer of different
size
pwin_set_errhandler.c:66: warning: cast from pointer to integer of different
size
pwin_set_errhandler.c:66: warning: cast from pointer to integer of different
size
pfile_get_errhandler.c:64: warning: cast from pointer to integer of different
size
pfile_get_errhandler.c:64: warning: cast from pointer to integer of different
size
pfile_set_errhandler.c:67: warning: cast from pointer to integer of different
size
pfile_set_errhandler.c:67: warning: cast from pointer to integer of different
size
pfile_set_errhandler.c:73: warning: cast from pointer to integer of different
size
pfile_set_errhandler.c:73: warning: cast from pointer to integer of different
size
comm_get_errhandler.c:65: warning: cast from pointer to integer of different
size
comm_get_errhandler.c:65: warning: cast from pointer to integer of different
size
comm_set_errhandler.c:67: warning: cast from pointer to integer of different
size
comm_set_errhandler.c:67: warning: cast from pointer to integer of different
size
comm_set_errhandler.c:74: warning: cast from pointer to integer of different
size
comm_set_errhandler.c:74: warning: cast from pointer to integer of different
size
pack_external.c:93: warning: passing arg 3 of `ompi_convertor_pack' from
incompatible pointer type
pack.c:91: warning: passing arg 3 of `ompi_convertor_pack' from incompatible
pointer type
type_contiguous.c:66: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
type_create_darray.c:226: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
type_create_f90_complex.c:101: warning: passing arg 3 of `ompi_ddt_set_args'
from incompatible pointer type
type_create_f90_integer.c:100: warning: passing arg 3 of `ompi_ddt_set_args'
from incompatible pointer type
type_create_f90_real.c:102: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
type_create_hindexed.c:84: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
type_create_hvector.c:77: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
type_create_indexed_block.c:76: warning: passing arg 3 of `ompi_ddt_set_args'
from incompatible pointer type
type_create_struct.c:92: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
type_create_subarray.c:147: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
type_get_contents.c:68: warning: passing arg 3 of `ompi_ddt_get_args' from
incompatible pointer type
type_get_contents.c:68: warning: passing arg 4 of `ompi_ddt_get_args' from
incompatible pointer type
type_get_contents.c:68: warning: passing arg 5 of `ompi_ddt_get_args' from
incompatible pointer type
type_get_contents.c:68: warning: passing arg 7 of `ompi_ddt_get_args' from
incompatible pointer type
type_get_envelope.c:63: warning: passing arg 3 of `ompi_ddt_get_args' from
incompatible pointer type
type_get_envelope.c:63: warning: passing arg 5 of `ompi_ddt_get_args' from
incompatible pointer type
type_get_envelope.c:63: warning: passing arg 7 of `ompi_ddt_get_args' from
incompatible pointer type
type_get_envelope.c:63: warning: passing arg 9 of `ompi_ddt_get_args' from
incompatible pointer type
type_indexed.c:88: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
type_vector.c:73: warning: passing arg 3 of `ompi_ddt_set_args' from
incompatible pointer type
unpack_external.c:85: warning: passing arg 3 of `ompi_convertor_unpack' from
incompatible pointer type
unpack.c:96: warning: passing arg 3 of `ompi_convertor_unpack' from incompatible
pointer type
win_get_errhandler.c:57: warning: cast from pointer to integer of different size
win_get_errhandler.c:57: warning: cast from pointer to integer of different size
win_set_errhandler.c:60: warning: cast from pointer to integer of different size
win_set_errhandler.c:60: warning: cast from pointer to integer of different size
win_set_errhandler.c:66: warning: cast from pointer to integer of different size
win_set_errhandler.c:66: warning: cast from pointer to integer of different size
file_get_errhandler.c:64: warning: cast from pointer to integer of different
size
file_get_errhandler.c:64: warning: cast from pointer to integer of different
size
file_set_errhandler.c:67: warning: cast from pointer to integer of different
size
file_set_errhandler.c:67: warning: cast from pointer to integer of different
size
file_set_errhandler.c:73: warning: cast from pointer to integer of different
size
file_set_errhandler.c:73: warning: cast from pointer to integer of different
size
base/pml_base_bsend.c:258: warning: passing arg 3 of `ompi_convertor_pack' from
incompatible pointer type
pml_cm_send.c:79: warning: passing arg 3 of `ompi_convertor_pack' from
incompatible pointer type
pml_cm_send.c:144: warning: passing arg 3 of `ompi_convertor_pack' from
incompatible pointer type
pml_cm_start.c:116: warning: passing arg 3 of `ompi_convertor_pack' from
incompatible pointer type
pml_ob1_sendreq.c:388: warning: passing arg 3 of `ompi_convertor_pack' from
incompatible pointer type
pml_ob1_sendreq.c:427: warning: passing arg 3 of `ompi_convertor_pack' from
incompatible pointer type
pml_ob1_sendreq.c:534: warning: passing arg 3 of `ompi_convertor_pack' from
incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_start.c:29: warning: passing arg 1 of
`vprotocol_pessimist_matching_replay' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
vprotocol_pessimist_sender_based.h:55: warning: passing arg 3 of
`ompi_convertor_pack' from incompatible pointer type
attribute/attribute.c:681: warning: passing arg 1 of pointer to function from
incompatible pointer type
attribute/attribute.c:681: warning: passing arg 1 of pointer to function from
incompatible pointer type
attribute/attribute.c:897: warning: passing arg 1 of pointer to function from
incompatible pointer type
attribute/attribute.c:897: warning: passing arg 1 of pointer to function from
incompatible pointer type
attribute/attribute.c:1067: warning: passing arg 1 of pointer to function from
incompatible pointer type
attribute/attribute.c:1067: warning: passing arg 1 of pointer to function from
incompatible pointer type
*** Warning: This system can not link to static lib archive
/home/Admin/MPI/OpenMpi/openmpi-1.3/orte/libopen-rte.la.
*** Warning: This system can not link to static lib archive
/home/Admin/MPI/OpenMpi/openmpi-1.3/opal/libopen-pal.la.
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
*** Warning: This system can not link to static lib archive
../../../ompi/libmpi.la.
*** Warning: This system can not link to static lib archive
/home/Admin/MPI/OpenMpi/openmpi-1.3/orte/libopen-rte.la.
*** Warning: This system can not link to static lib archive
/home/Admin/MPI/OpenMpi/openmpi-1.3/opal/libopen-pal.la.
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
*** Warning: This system can not link to static lib archive
../../../ompi/libmpi.la.
*** Warning: This system can not link to static lib archive
/home/Admin/MPI/OpenMpi/openmpi-1.3/orte/libopen-rte.la.
*** Warning: This system can not link to static lib archive
/home/Admin/MPI/OpenMpi/openmpi-1.3/opal/libopen-pal.la.
libtool: link: warning: undefined symbols not allowed in i686-pc-cygwin shared
libraries
wi23 openmpi-1.3-gcc 5

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