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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>>>>> Link to this post:
>>>>> http://www.open-mpi.org/community/lists/users/2014/10/25581.php
>>>>
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>>>
>>
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