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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