No :-(
I need some extra work to stop declaring orte_process_name_t and
ompi_process_name_t variables.
#249 will make things much easier.
One option is to use opal_process_name_t everywhere or typedef orte and ompi
types to the opal one.
An other (lightweight but error prone imho) is to change variable declaration
only.
Any thought ?
Ralph Castain <r...@open-mpi.org> wrote:
>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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>>>>>>>> Link to this post:
>>>>>>>> http://www.open-mpi.org/community/lists/users/2014/10/25581.php
>>>>>>>
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>>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>
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>>>
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