Will PR#249 solve it? If so, we should just go with it as I suspect that is the
long-term solution.
> On Oct 26, 2014, at 4:25 PM, Gilles Gouaillardet
> <gilles.gouaillar...@gmail.com> wrote:
>
> It looks like we faced a similar issue :
> opal_process_name_t is 64 bits aligned wheteas orte_process_name_t is 32 bits
> aligned. If you run an alignment sensitive cpu such as sparc and you are not
> lucky (so to speak) you can run into this issue.
> i will make a patch for this shortly
>
> Ralph Castain <r...@open-mpi.org> wrote:
>> Afraid this must be something about the Sparc - just ran on a Solaris 11 x86
>> box and everything works fine.
>>
>>
>>> On Oct 26, 2014, at 8:22 AM, Siegmar Gross
>>> <siegmar.gr...@informatik.hs-fulda.de> wrote:
>>>
>>> Hi Gilles,
>>>
>>> I wanted to explore which function is called, when I call MPI_Init
>>> in a C program, because this function should be called from a Java
>>> program as well. Unfortunately C programs break with a Bus Error
>>> once more for openmpi-dev-124-g91e9686 on Solaris. I assume that's
>>> the reason why I get no useful backtrace for my Java program.
>>>
>>> tyr small_prog 117 mpicc -o init_finalize init_finalize.c
>>> tyr small_prog 118 /usr/local/gdb-7.6.1_64_gcc/bin/gdb mpiexec
>>> ...
>>> (gdb) run -np 1 init_finalize
>>> Starting program: /usr/local/openmpi-1.9.0_64_gcc/bin/mpiexec -np 1
>>> init_finalize
>>> [Thread debugging using libthread_db enabled]
>>> [New Thread 1 (LWP 1)]
>>> [New LWP 2 ]
>>> [tyr:19240] *** Process received signal ***
>>> [tyr:19240] Signal: Bus Error (10)
>>> [tyr:19240] Signal code: Invalid address alignment (1)
>>> [tyr:19240] Failing at address: ffffffff7bd1c10c
>>> /export2/prog/SunOS_sparc/openmpi-1.9.0_64_gcc/lib64/libopen-pal.so.0.0.0:opal_backtrace_print+0x2c
>>> /export2/prog/SunOS_sparc/openmpi-1.9.0_64_gcc/lib64/libopen-pal.so.0.0.0:0xdcc04
>>> /lib/sparcv9/libc.so.1:0xd8b98
>>> /lib/sparcv9/libc.so.1:0xcc70c
>>> /lib/sparcv9/libc.so.1:0xcc918
>>> /export2/prog/SunOS_sparc/openmpi-1.9.0_64_gcc/lib64/libopen-pal.so.0.0.0:opal_proc_set_name+0x1c
>>> [ Signal 10 (BUS)]
>>> /export2/prog/SunOS_sparc/openmpi-1.9.0_64_gcc/lib64/openmpi/mca_pmix_native.so:0x103e8
>>> /export2/prog/SunOS_sparc/openmpi-1.9.0_64_gcc/lib64/openmpi/mca_ess_pmi.so:0x33dc
>>> /export2/prog/SunOS_sparc/openmpi-1.9.0_64_gcc/lib64/libopen-rte.so.0.0.0:orte_init+0x67c
>>> /export2/prog/SunOS_sparc/openmpi-1.9.0_64_gcc/lib64/libmpi.so.0.0.0:ompi_mpi_init+0x374
>>> /export2/prog/SunOS_sparc/openmpi-1.9.0_64_gcc/lib64/libmpi.so.0.0.0:PMPI_Init+0x2a8
>>> /home/fd1026/work/skripte/master/parallel/prog/mpi/small_prog/init_finalize:main+0x20
>>> /home/fd1026/work/skripte/master/parallel/prog/mpi/small_prog/init_finalize:_start+0x7c
>>> [tyr:19240] *** End of error message ***
>>> --------------------------------------------------------------------------
>>> mpiexec noticed that process rank 0 with PID 0 on node tyr exited on signal
>>> 10 (Bus Error).
>>> --------------------------------------------------------------------------
>>> [LWP 2 exited]
>>> [New Thread 2 ]
>>> [Switching to Thread 1 (LWP 1)]
>>> sol_thread_fetch_registers: td_ta_map_id2thr: no thread can be found to
>>> satisfy query
>>> (gdb) bt
>>> #0 0xffffffff7f6173d0 in rtld_db_dlactivity () from
>>> /usr/lib/sparcv9/ld.so.1
>>> #1 0xffffffff7f6175a8 in rd_event () from /usr/lib/sparcv9/ld.so.1
>>> #2 0xffffffff7f618950 in lm_delete () from /usr/lib/sparcv9/ld.so.1
>>> #3 0xffffffff7f6226bc in remove_so () from /usr/lib/sparcv9/ld.so.1
>>> #4 0xffffffff7f624574 in remove_hdl () from /usr/lib/sparcv9/ld.so.1
>>> #5 0xffffffff7f61d97c in dlclose_core () from /usr/lib/sparcv9/ld.so.1
>>> #6 0xffffffff7f61d9d4 in dlclose_intn () from /usr/lib/sparcv9/ld.so.1
>>> #7 0xffffffff7f61db0c in dlclose () from /usr/lib/sparcv9/ld.so.1
>>> #8 0xffffffff7ec87f60 in vm_close (loader_data=0x0,
>>> module=0xffffffff7c901fe0)
>>> at ../../../openmpi-dev-124-g91e9686/opal/libltdl/loaders/dlopen.c:212
>>> #9 0xffffffff7ec85534 in lt_dlclose (handle=0x100189b50)
>>> at ../../../openmpi-dev-124-g91e9686/opal/libltdl/ltdl.c:1982
>>> #10 0xffffffff7ecaabd4 in ri_destructor (obj=0x1001893a0)
>>> at
>>> ../../../../openmpi-dev-124-g91e9686/opal/mca/base/mca_base_component_repository.c:382
>>> #11 0xffffffff7eca9504 in opal_obj_run_destructors (object=0x1001893a0)
>>> at ../../../../openmpi-dev-124-g91e9686/opal/class/opal_object.h:446
>>> #12 0xffffffff7ecaa474 in mca_base_component_repository_release (
>>> component=0xffffffff7b1236f0 <mca_oob_tcp_component>)
>>> at
>>> ../../../../openmpi-dev-124-g91e9686/opal/mca/base/mca_base_component_repository.c:240
>>> #13 0xffffffff7ecac774 in mca_base_component_unload (
>>> component=0xffffffff7b1236f0 <mca_oob_tcp_component>, output_id=-1)
>>> at
>>> ../../../../openmpi-dev-124-g91e9686/opal/mca/base/mca_base_components_close.c:47
>>> #14 0xffffffff7ecac808 in mca_base_component_close (
>>> component=0xffffffff7b1236f0 <mca_oob_tcp_component>, output_id=-1)
>>> at
>>> ../../../../openmpi-dev-124-g91e9686/opal/mca/base/mca_base_components_close.c:60
>>> #15 0xffffffff7ecac8dc in mca_base_components_close (output_id=-1,
>>> components=0xffffffff7f14ba58 <orte_oob_base_framework+80>, skip=0x0)
>>> at
>>> ../../../../openmpi-dev-124-g91e9686/opal/mca/base/mca_base_components_close.c:86
>>> #16 0xffffffff7ecac844 in mca_base_framework_components_close (
>>> framework=0xffffffff7f14ba08 <orte_oob_base_framework>, skip=0x0)
>>> at
>>> ../../../../openmpi-dev-124-g91e9686/opal/mca/base/mca_base_components_close.c:66
>>> #17 0xffffffff7efcaf58 in orte_oob_base_close ()
>>> at
>>> ../../../../openmpi-dev-124-g91e9686/orte/mca/oob/base/oob_base_frame.c:112
>>> #18 0xffffffff7ecc136c in mca_base_framework_close (
>>> framework=0xffffffff7f14ba08 <orte_oob_base_framework>)
>>> at
>>> ../../../../openmpi-dev-124-g91e9686/opal/mca/base/mca_base_framework.c:187
>>> #19 0xffffffff7be07858 in rte_finalize ()
>>> at
>>> ../../../../../openmpi-dev-124-g91e9686/orte/mca/ess/hnp/ess_hnp_module.c:857
>>> #20 0xffffffff7ef338a4 in orte_finalize ()
>>> at ../../openmpi-dev-124-g91e9686/orte/runtime/orte_finalize.c:66
>>> #21 0x000000010000723c in orterun (argc=4, argv=0xffffffff7fffe0b8)
>>> at ../../../../openmpi-dev-124-g91e9686/orte/tools/orterun/orterun.c:1103
>>> #22 0x0000000100003e80 in main (argc=4, argv=0xffffffff7fffe0b8)
>>> at ../../../../openmpi-dev-124-g91e9686/orte/tools/orterun/main.c:13
>>> (gdb)
>>>
>>> Kind regards
>>>
>>> Siegmar
>>>
>>>
>>>
>>>> thank you very much for the quick tutorial. Unfortunately I still
>>>> can't get a backtrace.
>>>>
>>>>> You might need to configure with --enable-debug and add -g -O0
>>>>> to your CFLAGS and LDFLAGS
>>>>>
>>>>> Then once you attach with gdb, you have to find the thread that is
>>>>> polling :
>>>>> thread 1
>>>>> bt
>>>>> thread 2
>>>>> bt
>>>>> and so on until you find the good thread
>>>>> If _dbg is a local variable, you need to select the right frame
>>>>> before you can change the value :
>>>>> get the frame number from bt (generally 1 under linux)
>>>>> f <frame number>
>>>>> set _dbg=0
>>>>>
>>>>> I hope this helps
>>>>
>>>> "--enable-debug" is one of my default options. Now I used the
>>>> following command to configure Open MPI. I always start the
>>>> build process in an empty directory and I always remove
>>>> /usr/local/openmpi-1.9.0_64_gcc, before I install a new version.
>>>>
>>>> tyr openmpi-dev-124-g91e9686-SunOS.sparc.64_gcc 112 head config.log \
>>>> | grep openmpi
>>>> $ ../openmpi-dev-124-g91e9686/configure
>>>> --prefix=/usr/local/openmpi-1.9.0_64_gcc
>>>> --libdir=/usr/local/openmpi-1.9.0_64_gcc/lib64
>>>> --with-jdk-bindir=/usr/local/jdk1.8.0/bin
>>>> --with-jdk-headers=/usr/local/jdk1.8.0/include
>>>> JAVA_HOME=/usr/local/jdk1.8.0
>>>> LDFLAGS=-m64 -g -O0 CC=gcc CXX=g++ FC=gfortran
>>>> CFLAGS=-m64 -D_REENTRANT -g -O0
>>>> CXXFLAGS=-m64 FCFLAGS=-m64 CPP=cpp CXXCPP=cpp
>>>> CPPFLAGS=-D_REENTRANT CXXCPPFLAGS=
>>>> --enable-mpi-cxx --enable-cxx-exceptions --enable-mpi-java
>>>> --enable-heterogeneous --enable-mpi-thread-multiple
>>>> --with-threads=posix --with-hwloc=internal --without-verbs
>>>> --with-wrapper-cflags=-std=c11 -m64 --enable-debug
>>>> tyr openmpi-dev-124-g91e9686-SunOS.sparc.64_gcc 113
>>>>
>>>>
>>>> "gbd" doesn't allow any backtrace for any thread.
>>>>
>>>> tyr java 124 /usr/local/gdb-7.6.1_64_gcc/bin/gdb
>>>> GNU gdb (GDB) 7.6.1
>>>> ...
>>>> (gdb) attach 18876
>>>> Attaching to process 18876
>>>> [New process 18876]
>>>> Retry #1:
>>>> Retry #2:
>>>> Retry #3:
>>>> Retry #4:
>>>> 0x7eadcb04 in ?? ()
>>>> (gdb) info threads
>>>> [New LWP 12]
>>>> [New LWP 11]
>>>> [New LWP 10]
>>>> [New LWP 9]
>>>> [New LWP 8]
>>>> [New LWP 7]
>>>> [New LWP 6]
>>>> [New LWP 5]
>>>> [New LWP 4]
>>>> [New LWP 3]
>>>> [New LWP 2]
>>>> Id Target Id Frame
>>>> 12 LWP 2 0x7eadc6b0 in ?? ()
>>>> 11 LWP 3 0x7eadcbb8 in ?? ()
>>>> 10 LWP 4 0x7eadcbb8 in ?? ()
>>>> 9 LWP 5 0x7eadcbb8 in ?? ()
>>>> 8 LWP 6 0x7eadcbb8 in ?? ()
>>>> 7 LWP 7 0x7eadcbb8 in ?? ()
>>>> 6 LWP 8 0x7ead8b0c in ?? ()
>>>> 5 LWP 9 0x7eadcbb8 in ?? ()
>>>> 4 LWP 10 0x7eadcbb8 in ?? ()
>>>> 3 LWP 11 0x7eadcbb8 in ?? ()
>>>> 2 LWP 12 0x7eadcbb8 in ?? ()
>>>> * 1 LWP 1 0x7eadcb04 in ?? ()
>>>> (gdb) thread 1
>>>> [Switching to thread 1 (LWP 1)]
>>>> #0 0x7eadcb04 in ?? ()
>>>> (gdb) bt
>>>> #0 0x7eadcb04 in ?? ()
>>>> #1 0x7eaca12c in ?? ()
>>>> Backtrace stopped: previous frame identical to this frame (corrupt stack?)
>>>> (gdb) thread 2
>>>> [Switching to thread 2 (LWP 12)]
>>>> #0 0x7eadcbb8 in ?? ()
>>>> (gdb) bt
>>>> #0 0x7eadcbb8 in ?? ()
>>>> #1 0x7eac2638 in ?? ()
>>>> Backtrace stopped: previous frame identical to this frame (corrupt stack?)
>>>> (gdb) thread 3
>>>> [Switching to thread 3 (LWP 11)]
>>>> #0 0x7eadcbb8 in ?? ()
>>>> (gdb) bt
>>>> #0 0x7eadcbb8 in ?? ()
>>>> #1 0x7eac25a8 in ?? ()
>>>> Backtrace stopped: previous frame identical to this frame (corrupt stack?)
>>>> (gdb) thread 4
>>>> [Switching to thread 4 (LWP 10)]
>>>> #0 0x7eadcbb8 in ?? ()
>>>> (gdb) bt
>>>> #0 0x7eadcbb8 in ?? ()
>>>> #1 0x7eac2638 in ?? ()
>>>> Backtrace stopped: previous frame identical to this frame (corrupt stack?)
>>>> (gdb) thread 5
>>>> [Switching to thread 5 (LWP 9)]
>>>> #0 0x7eadcbb8 in ?? ()
>>>> (gdb) bt
>>>> #0 0x7eadcbb8 in ?? ()
>>>> #1 0x7eac2638 in ?? ()
>>>> Backtrace stopped: previous frame identical to this frame (corrupt stack?)
>>>> (gdb) thread 6
>>>> [Switching to thread 6 (LWP 8)]
>>>> #0 0x7ead8b0c in ?? ()
>>>> (gdb) bt
>>>> #0 0x7ead8b0c in ?? ()
>>>> #1 0x7eacbcb0 in ?? ()
>>>> Backtrace stopped: previous frame identical to this frame (corrupt stack?)
>>>> (gdb) thread 7
>>>> [Switching to thread 7 (LWP 7)]
>>>> #0 0x7eadcbb8 in ?? ()
>>>> (gdb) bt
>>>> #0 0x7eadcbb8 in ?? ()
>>>> #1 0x7eac25a8 in ?? ()
>>>> Backtrace stopped: previous frame identical to this frame (corrupt stack?)
>>>> (gdb) thread 8
>>>> [Switching to thread 8 (LWP 6)]
>>>> #0 0x7eadcbb8 in ?? ()
>>>> (gdb) bt
>>>> #0 0x7eadcbb8 in ?? ()
>>>> #1 0x7eac25a8 in ?? ()
>>>> Backtrace stopped: previous frame identical to this frame (corrupt stack?)
>>>> (gdb) thread 9
>>>> [Switching to thread 9 (LWP 5)]
>>>> #0 0x7eadcbb8 in ?? ()
>>>> (gdb) bt
>>>> #0 0x7eadcbb8 in ?? ()
>>>> #1 0x7eac2638 in ?? ()
>>>> Backtrace stopped: previous frame identical to this frame (corrupt stack?)
>>>> (gdb) thread 10
>>>> [Switching to thread 10 (LWP 4)]
>>>> #0 0x7eadcbb8 in ?? ()
>>>> (gdb) bt
>>>> #0 0x7eadcbb8 in ?? ()
>>>> #1 0x7eac25a8 in ?? ()
>>>> Backtrace stopped: previous frame identical to this frame (corrupt stack?)
>>>> (gdb) thread 11
>>>> [Switching to thread 11 (LWP 3)]
>>>> #0 0x7eadcbb8 in ?? ()
>>>> (gdb) bt
>>>> #0 0x7eadcbb8 in ?? ()
>>>> #1 0x7eac25a8 in ?? ()
>>>> Backtrace stopped: previous frame identical to this frame (corrupt stack?)
>>>> (gdb) thread 12
>>>> [Switching to thread 12 (LWP 2)]
>>>> #0 0x7eadc6b0 in ?? ()
>>>> (gdb)
>>>>
>>>>
>>>>
>>>> I also tried to set _dbg in all available frames without success.
>>>>
>>>> (gdb) f 1
>>>> #1 0x7eacb46c in ?? ()
>>>> (gdb) set _dbg=0
>>>> No symbol table is loaded. Use the "file" command.
>>>> (gdb) symbol-file /usr/local/openmpi-1.9.0_64_gcc/lib64/libmpi_java.so
>>>> Reading symbols from
>>>> /export2/prog/SunOS_sparc/openmpi-1.9.0_64_gcc/lib64/libmpi_java.so.0.0.0...done.
>>>> (gdb) f 1
>>>> #1 0x7eacb46c in ?? ()
>>>> (gdb) set _dbg=0
>>>> No symbol "_dbg" in current context.
>>>> (gdb) f 2
>>>> #0 0x00000000 in ?? ()
>>>> (gdb) set _dbg=0
>>>> No symbol "_dbg" in current context.
>>>> (gdb)
>>>> ...
>>>>
>>>>
>>>> With "list" I get source code from mpi_CartComm.c and not from mpi_MPI.c.
>>>> If a switch threads, "list" continues in the old file.
>>>>
>>>> (gdb) thread 1
>>>> [Switching to thread 1 (LWP 1)]
>>>> #0 0x7eadcb04 in ?? ()
>>>> (gdb) list 36
>>>> 31 distributed under the License is distributed on an "AS IS"
>>>> BASIS,
>>>> 32 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
>>>> or implied.
>>>> 33 See the License for the specific language governing
>>>> permissions and
>>>> 34 limitations under the License.
>>>> 35 */
>>>> 36 /*
>>>> 37 * File : mpi_CartComm.c
>>>> 38 * Headerfile : mpi_CartComm.h
>>>> 39 * Author : Sung-Hoon Ko, Xinying Li
>>>> 40 * Created : Thu Apr 9 12:22:15 1998
>>>> (gdb) thread 2
>>>> [Switching to thread 2 (LWP 12)]
>>>> #0 0x7eadcbb8 in ?? ()
>>>> (gdb) list
>>>> 41 * Revision : $Revision: 1.6 $
>>>> 42 * Updated : $Date: 2003/01/16 16:39:34 $
>>>> 43 * Copyright: Northeast Parallel Architectures Center
>>>> 44 * at Syracuse University 1998
>>>> 45 */
>>>> 46 #include "ompi_config.h"
>>>> 47
>>>> 48 #include <stdlib.h>
>>>> 49 #ifdef HAVE_TARGETCONDITIONALS_H
>>>> 50 #include <TargetConditionals.h>
>>>> (gdb)
>>>>
>>>>
>>>> Do you have any ideas, what's going wrong or if I must use a different
>>>> symbol table?
>>>>
>>>>
>>>> Kind regards
>>>>
>>>> Siegmar
>>>>
>>>>
>>>>
>>>>
>>>>>
>>>>> Gilles
>>>>>
>>>>>
>>>>> Siegmar Gross <siegmar.gr...@informatik.hs-fulda.de> wrote:
>>>>>> Hi Gilles,
>>>>>>
>>>>>> I changed _dbg to a static variable, so that it is visible in the
>>>>>> library, but unfortunately still not in the symbol table.
>>>>>>
>>>>>>
>>>>>> tyr java 419 nm /usr/local/openmpi-1.9.0_64_gcc/lib64/libmpi_java.so |
>>>>>> grep -i _dbg
>>>>>> [271] | 1249644| 4|OBJT |LOCL |0 |18 |_dbg.14258
>>>>>> tyr java 420 /usr/local/gdb-7.6.1_64_gcc/bin/gdb
>>>>>> GNU gdb (GDB) 7.6.1
>>>>>> ...
>>>>>> (gdb) attach 13019
>>>>>> Attaching to process 13019
>>>>>> [New process 13019]
>>>>>> Retry #1:
>>>>>> Retry #2:
>>>>>> Retry #3:
>>>>>> Retry #4:
>>>>>> 0x7eadcb04 in ?? ()
>>>>>> (gdb) symbol-file /usr/local/openmpi-1.9.0_64_gcc/lib64/libmpi_java.so
>>>>>> Reading symbols from
>>>> /export2/prog/SunOS_sparc/openmpi-1.9.0_64_gcc/lib64/libmpi_java.so.0.0.0...done.
>>>>>> (gdb) set var _dbg.14258=0
>>>>>> No symbol "_dbg" in current context.
>>>>>> (gdb)
>>>>>>
>>>>>>
>>>>>> Kind regards
>>>>>>
>>>>>> Siegmar
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> unfortunately I didn't get anything useful. It's probably my fault,
>>>>>>> because I'm still not very familiar with gdb or any other debugger.
>>>>>>> I did the following things.
>>>>>>>
>>>>>>>
>>>>>>> 1st window:
>>>>>>> -----------
>>>>>>>
>>>>>>> tyr java 174 setenv OMPI_ATTACH 1
>>>>>>> tyr java 175 mpijavac InitFinalizeMain.java
>>>>>>> warning: [path] bad path element
>>>>>>> "/usr/local/openmpi-1.9.0_64_gcc/lib64/shmem.jar":
>>>>>>> no such file or directory
>>>>>>> 1 warning
>>>>>>> tyr java 176 mpiexec -np 1 java InitFinalizeMain
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 2nd window:
>>>>>>> -----------
>>>>>>>
>>>>>>> tyr java 379 ps -aef | grep java
>>>>>>> noaccess 1345 1 0 May 22 ? 113:23 /usr/java/bin/java
>>>>>>> -server -Xmx128m
>>>> -XX:+UseParallelGC
>>>>>> -XX:ParallelGCThreads=4
>>>>>>> fd1026 3661 10753 0 14:09:12 pts/14 0:00 mpiexec -np 1 java
>>>>>>> InitFinalizeMain
>>>>>>> fd1026 3677 13371 0 14:16:55 pts/2 0:00 grep java
>>>>>>> fd1026 3663 3661 0 14:09:12 pts/14 0:01 java -cp
>>>>>> /home/fd1026/work/skripte/master/parallel/prog/mpi/java:/usr/local/jun
>>>>>>> tyr java 380 /usr/local/gdb-7.6.1_64_gcc/bin/gdb
>>>>>>> GNU gdb (GDB) 7.6.1
>>>>>>> ...
>>>>>>> (gdb) attach 3663
>>>>>>> Attaching to process 3663
>>>>>>> [New process 3663]
>>>>>>> Retry #1:
>>>>>>> Retry #2:
>>>>>>> Retry #3:
>>>>>>> Retry #4:
>>>>>>> 0x7eadcb04 in ?? ()
>>>>>>> (gdb) symbol-file /usr/local/openmpi-1.9.0_64_gcc/lib64/libmpi_java.so
>>>>>>> Reading symbols from
>>>> /export2/prog/SunOS_sparc/openmpi-1.9.0_64_gcc/lib64/libmpi_java.so.0.0.0...done.
>>>>>>> (gdb) set var _dbg=0
>>>>>>> No symbol "_dbg" in current context.
>>>>>>> (gdb) set var JNI_OnLoad::_dbg=0
>>>>>>> No symbol "_dbg" in specified context.
>>>>>>> (gdb) set JNI_OnLoad::_dbg=0
>>>>>>> No symbol "_dbg" in specified context.
>>>>>>> (gdb) info threads
>>>>>>> [New LWP 12]
>>>>>>> [New LWP 11]
>>>>>>> [New LWP 10]
>>>>>>> [New LWP 9]
>>>>>>> [New LWP 8]
>>>>>>> [New LWP 7]
>>>>>>> [New LWP 6]
>>>>>>> [New LWP 5]
>>>>>>> [New LWP 4]
>>>>>>> [New LWP 3]
>>>>>>> [New LWP 2]
>>>>>>> Id Target Id Frame
>>>>>>> 12 LWP 2 0x7eadc6b0 in ?? ()
>>>>>>> 11 LWP 3 0x7eadcbb8 in ?? ()
>>>>>>> 10 LWP 4 0x7eadcbb8 in ?? ()
>>>>>>> 9 LWP 5 0x7eadcbb8 in ?? ()
>>>>>>> 8 LWP 6 0x7eadcbb8 in ?? ()
>>>>>>> 7 LWP 7 0x7eadcbb8 in ?? ()
>>>>>>> 6 LWP 8 0x7ead8b0c in ?? ()
>>>>>>> 5 LWP 9 0x7eadcbb8 in ?? ()
>>>>>>> 4 LWP 10 0x7eadcbb8 in ?? ()
>>>>>>> 3 LWP 11 0x7eadcbb8 in ?? ()
>>>>>>> 2 LWP 12 0x7eadcbb8 in ?? ()
>>>>>>> * 1 LWP 1 0x7eadcb04 in ?? ()
>>>>>>> (gdb)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> It seems that "_dbg" is unknown and unavailable.
>>>>>>>
>>>>>>> tyr java 399 grep _dbg
>>>>>>> /export2/src/openmpi-1.9/openmpi-dev-124-g91e9686/ompi/mpi/java/c/*
>>>>>>> /export2/src/openmpi-1.9/openmpi-dev-124-g91e9686/ompi/mpi/java/c/mpi_MPI.c:
>>>>>>> volatile
>>>> int _dbg = 1;
>>>>>>> /export2/src/openmpi-1.9/openmpi-dev-124-g91e9686/ompi/mpi/java/c/mpi_MPI.c:
>>>>>>> while
>>>> (_dbg) poll(NULL, 0, 1);
>>>>>>> tyr java 400 nm /usr/local/openmpi-1.9.0_64_gcc/lib64/*.so | grep -i
>>>>>>> _dbg
>>>>>>> tyr java 401 nm /usr/local/openmpi-1.9.0_64_gcc/lib64/*.so | grep -i
>>>>>>> JNI_OnLoad
>>>>>>> [1057] | 139688| 444|FUNC |GLOB |0 |11
>>>>>>> |JNI_OnLoad
>>>>>>> tyr java 402
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> How can I set _dbg to zero to continue mpiexec? I also tried to
>>>>>>> set a breakpoint for function JNI_OnLoad, but it seems, that the
>>>>>>> function isn't called before SIGSEGV.
>>>>>>>
>>>>>>>
>>>>>>> tyr java 177 unsetenv OMPI_ATTACH
>>>>>>> tyr java 178 /usr/local/gdb-7.6.1_64_gcc/bin/gdb mpiexec
>>>>>>> GNU gdb (GDB) 7.6.1
>>>>>>> ...
>>>>>>> (gdb) b mpi_MPI.c:JNI_OnLoad
>>>>>>> No source file named mpi_MPI.c.
>>>>>>> Make breakpoint pending on future shared library load? (y or [n]) y
>>>>>>>
>>>>>>> Breakpoint 1 (mpi_MPI.c:JNI_OnLoad) pending.
>>>>>>> (gdb) run -np 1 java InitFinalizeMain
>>>>>>> Starting program: /usr/local/openmpi-1.9.0_64_gcc/bin/mpiexec -np 1
>>>>>>> java InitFinalizeMain
>>>>>>> [Thread debugging using libthread_db enabled]
>>>>>>> [New Thread 1 (LWP 1)]
>>>>>>> [New LWP 2 ]
>>>>>>> #
>>>>>>> # A fatal error has been detected by the Java Runtime Environment:
>>>>>>> #
>>>>>>> # SIGSEGV (0xb) at pc=0xffffffff7ea3c7f0, pid=3518, tid=2
>>>>>>> ...
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> tyr java 381 cat InitFinalizeMain.java
>>>>>>> import mpi.*;
>>>>>>>
>>>>>>> public class InitFinalizeMain
>>>>>>> {
>>>>>>> public static void main (String args[]) throws MPIException
>>>>>>> {
>>>>>>> MPI.Init (args);
>>>>>>> System.out.print ("Hello!\n");
>>>>>>> MPI.Finalize ();
>>>>>>> }
>>>>>>> }
>>>>>>>
>>>>>>>
>>>>>>> SIGSEGV happens in MPI.Init(args), because I can print a message
>>>>>>> before I call the method.
>>>>>>>
>>>>>>> tyr java 192 unsetenv OMPI_ATTACH
>>>>>>> tyr java 193 mpijavac InitFinalizeMain.java
>>>>>>> tyr java 194 mpiexec -np 1 java InitFinalizeMain
>>>>>>> Before MPI.Init()
>>>>>>> #
>>>>>>> # A fatal error has been detected by the Java Runtime Environment:
>>>>>>> #
>>>>>>> # SIGSEGV (0xb) at pc=0xffffffff7ea3c7f0, pid=3697, tid=2
>>>>>>> ...
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Any ideas, how I can continue? I couldn't find a C function for
>>>>>>> MPI.Init() in a C file. Do you know, which function is called first,
>>>>>>> so that I can set a breakpoint? By the way, I get the same error
>>>>>>> for Solaris 10 x86_64.
>>>>>>>
>>>>>>> tyr java 388 ssh sunpc1
>>>>>>> ...
>>>>>>> sunpc1 java 106 mpijavac InitFinalizeMain.java
>>>>>>> sunpc1 java 107 uname -a
>>>>>>> SunOS sunpc1 5.10 Generic_147441-21 i86pc i386 i86pc Solaris
>>>>>>> sunpc1 java 108 isainfo -k
>>>>>>> amd64
>>>>>>> sunpc1 java 109 mpiexec -np 1 java InitFinalizeMain
>>>>>>> #
>>>>>>> # A fatal error has been detected by the Java Runtime Environment:
>>>>>>> #
>>>>>>> # SIGSEGV (0xb) at pc=0xfffffd7fff1d77f0, pid=20256, tid=2
>>>>>>>
>>>>>>>
>>>>>>> Thank you very much for any help in advance.
>>>>>>>
>>>>>>> Kind regards
>>>>>>>
>>>>>>> Siegmar
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> thank you very much for your help.
>>>>>>>>
>>>>>>>>> how did you configure openmpi ? which java version did you use ?
>>>>>>>>>
>>>>>>>>> i just found a regression and you currently have to explicitly add
>>>>>>>>> CFLAGS=-D_REENTRANT CPPFLAGS=-D_REENTRANT
>>>>>>>>> to your configure command line
>>>>>>>>
>>>>>>>> I added "-D_REENTRANT" to my command.
>>>>>>>>
>>>>>>>> ../openmpi-dev-124-g91e9686/configure
>>>>>>>> --prefix=/usr/local/openmpi-1.9.0_64_gcc \
>>>>>>>> --libdir=/usr/local/openmpi-1.9.0_64_gcc/lib64 \
>>>>>>>> --with-jdk-bindir=/usr/local/jdk1.8.0/bin \
>>>>>>>> --with-jdk-headers=/usr/local/jdk1.8.0/include \
>>>>>>>> JAVA_HOME=/usr/local/jdk1.8.0 \
>>>>>>>> LDFLAGS="-m64" CC="gcc" CXX="g++" FC="gfortran" \
>>>>>>>> CFLAGS="-m64 -D_REENTRANT" CXXFLAGS="-m64" FCFLAGS="-m64" \
>>>>>>>> CPP="cpp" CXXCPP="cpp" \
>>>>>>>> CPPFLAGS="-D_REENTRANT" CXXCPPFLAGS="" \
>>>>>>>> --enable-mpi-cxx \
>>>>>>>> --enable-cxx-exceptions \
>>>>>>>> --enable-mpi-java \
>>>>>>>> --enable-heterogeneous \
>>>>>>>> --enable-mpi-thread-multiple \
>>>>>>>> --with-threads=posix \
>>>>>>>> --with-hwloc=internal \
>>>>>>>> --without-verbs \
>>>>>>>> --with-wrapper-cflags="-std=c11 -m64" \
>>>>>>>> --enable-debug \
>>>>>>>> |& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV.64_gcc
>>>>>>>>
>>>>>>>> I use Java 8.
>>>>>>>>
>>>>>>>> tyr openmpi-1.9 112 java -version
>>>>>>>> java version "1.8.0"
>>>>>>>> Java(TM) SE Runtime Environment (build 1.8.0-b132)
>>>>>>>> Java HotSpot(TM) 64-Bit Server VM (build 25.0-b70, mixed mode)
>>>>>>>> tyr openmpi-1.9 113
>>>>>>>>
>>>>>>>> Unfortunately I still get a SIGSEGV with openmpi-dev-124-g91e9686.
>>>>>>>> I have applied your patch and will try to debug my small Java
>>>>>>>> program tomorrow or next week and then let you know the result.
>>>>>>>
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>>>>>>
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>>>>>
>>>>
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>>>
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>>
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