Kawashima-san,
thanks a lot for the detailled explanation.
FWIW, i was previously testing on Solaris 11 that behaves like Linux :
printf("%s", NULL) outputs '(null)'
vs a SIGSEGV on Solaris 10
i commited a16c1e44189366fbc8e967769e050f517a40f3f8 in order to fix this
issue
(i moved the call to mca_base_var_register *after* MPI_Init)
regarding the BUS error reported by Siegmar, i also commited
62bde1fcb554079143030bb305512c236672386f
in order to fix it (this is based on code review only, i have no sparc64
hardware to test it is enough)
Siegmar, --enable-heterogeneous is known to be broken on the trunk, and
there are discussions on how to fix it.
in the mean time, you can either apply the attached minimal
heterogeneous.diff patch or avoid the --enable-heterogeneous option
/* the attached patch "fixes" --enable-heterogeneous on homogeneous
clusters *only* */
about attaching a process with gdb, i usually run
gdb none <pid>
on Linux and everything is fine
on Solaris, i had to do
gdb /usr/bin/java <pid>
in order to get the symbols loaded by gdb
and then
thread 11
f 3
set _dbg=0
/* but this is likely environment specific */
Cheers,
Gilles
On 2014/10/27 10:58, Ralph Castain wrote:
> Oh yeah - that would indeed be very bad :-(
>
>
>> On Oct 26, 2014, at 6:06 PM, Kawashima, Takahiro
>> <t-kawash...@jp.fujitsu.com> wrote:
>>
>> Siegmar, Oscar,
>>
>> I suspect that the problem is calling mca_base_var_register
>> without initializing OPAL in JNI_OnLoad.
>>
>> ompi/mpi/java/c/mpi_MPI.c:
>> ----------------------------------------------------------------
>> jint JNI_OnLoad(JavaVM *vm, void *reserved)
>> {
>> libmpi = dlopen("libmpi." OPAL_DYN_LIB_SUFFIX, RTLD_NOW | RTLD_GLOBAL);
>>
>> if(libmpi == NULL)
>> {
>> fprintf(stderr, "Java bindings failed to load liboshmem.\n");
>> exit(1);
>> }
>>
>> mca_base_var_register("ompi", "mpi", "java", "eager",
>> "Java buffers eager size",
>> MCA_BASE_VAR_TYPE_INT, NULL, 0, 0,
>> OPAL_INFO_LVL_5,
>> MCA_BASE_VAR_SCOPE_READONLY,
>> &ompi_mpi_java_eager);
>>
>> return JNI_VERSION_1_6;
>> }
>> ----------------------------------------------------------------
>>
>> I suppose JNI_OnLoad is the first function in the libmpi_java.so
>> which is called by JVM. So OPAL is not initialized yet.
>> As shown in Siegmar's JRE log, SEGV occurred in asprintf called
>> by mca_base_var_cache_files.
>>
>> Siegmar's hs_err_pid13080.log:
>> ----------------------------------------------------------------
>> siginfo:si_signo=SIGSEGV: si_errno=0, si_code=1 (SEGV_MAPERR),
>> si_addr=0x0000000000000000
>>
>> Stack: [0xffffffff7b400000,0xffffffff7b500000], sp=0xffffffff7b4fc730,
>> free space=1009k
>> Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native
>> code)
>> C [libc.so.1+0x3c7f0] strlen+0x50
>> C [libc.so.1+0xaf640] vsnprintf+0x84
>> C [libc.so.1+0xaadb4] vasprintf+0x20
>> C [libc.so.1+0xaaf04] asprintf+0x28
>> C [libopen-pal.so.0.0.0+0xaf3cc] mca_base_var_cache_files+0x160
>> C [libopen-pal.so.0.0.0+0xaed90] mca_base_var_init+0x4e8
>> C [libopen-pal.so.0.0.0+0xb260c] register_variable+0x214
>> C [libopen-pal.so.0.0.0+0xb36a0] mca_base_var_register+0x104
>> C [libmpi_java.so.0.0.0+0x221e8] JNI_OnLoad+0x128
>> C [libjava.so+0x10860]
>> Java_java_lang_ClassLoader_00024NativeLibrary_load+0xb8
>> j java.lang.ClassLoader$NativeLibrary.load(Ljava/lang/String;Z)V+-665819
>> j java.lang.ClassLoader$NativeLibrary.load(Ljava/lang/String;Z)V+0
>> j java.lang.ClassLoader.loadLibrary0(Ljava/lang/Class;Ljava/io/File;)Z+328
>> j
>> java.lang.ClassLoader.loadLibrary(Ljava/lang/Class;Ljava/lang/String;Z)V+290
>> j java.lang.Runtime.loadLibrary0(Ljava/lang/Class;Ljava/lang/String;)V+54
>> j java.lang.System.loadLibrary(Ljava/lang/String;)V+7
>> j mpi.MPI.<clinit>()V+28
>> ----------------------------------------------------------------
>>
>> mca_base_var_cache_files passes opal_install_dirs.sysconfdir to
>> asprintf.
>>
>> opal/mca/base/mca_base_var.c:
>> ----------------------------------------------------------------
>> asprintf(&mca_base_var_files, "%s"OPAL_PATH_SEP".openmpi" OPAL_PATH_SEP
>> "mca-params.conf%c%s" OPAL_PATH_SEP "openmpi-mca-params.conf",
>> home, OPAL_ENV_SEP, opal_install_dirs.sysconfdir);
>> ----------------------------------------------------------------
>>
>> In this situation, opal_install_dirs.sysconfdir is still NULL.
>>
>> I run a MPI Java program that only calls MPI.Init() and
>> MPI.Finalize() with MCA variable mpi_show_mca_params=1 on
>> Linux to confirm this. mca_base_param_files contains "(null)".
>>
>> mpi_show_mca_params=1:
>> ----------------------------------------------------------------
>> [ppc:12232]
>> mca_base_param_files=/home/rivis/.openmpi/mca-params.conf:(null)/openmpi-mca-params.conf
>> (default)
>> [ppc:12232]
>> mca_param_files=/home/rivis/.openmpi/mca-params.conf:(null)/openmpi-mca-params.conf
>> (default)
>> [ppc:12232]
>> mca_base_override_param_file=(null)/openmpi-mca-params-override.conf
>> (default)
>> [ppc:12232] mca_base_suppress_override_warning=false (default)
>> [ppc:12232] mca_base_param_file_prefix= (default)
>> [ppc:12232]
>> mca_base_param_file_path=(null)/amca-param-sets:/home/rivis/src/mpisample
>> (default)
>> [ppc:12232] mca_base_param_file_path_force= (default)
>> [ppc:12232] mca_base_env_list= (default)
>> [ppc:12232] mca_base_env_list_delimiter=; (default)
>> [ppc:12232] mpi_java_eager=65536 (default)
>> (snip)
>> ----------------------------------------------------------------
>>
>> GNU libc sets "(null)" for asprintf(buf, "%s", NULL) but
>> Solaris libc raises SEGV for it. I think this is the difference
>> of Siegmar's runs on Linux and Solaris.
>>
>> I think this mca_base_var_register should be moved to another
>> place or opal_init_util or something should be called before
>> this mca_base_var_register.
>>
>> Thanks,
>> Takahiro
>>
>>> Hi Gilles,
>>>
>>> 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/2014/10/25590.php
>> <http://www.open-mpi.org/community/lists/users/2014/10/25590.php>
>
>
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commit c9c5d4011bf6ea1ade1a5bd9b6a77f02157dc774
Author: Gilles Gouaillardet <gilles.gouaillar...@iferc.org>
List-Post: users@lists.open-mpi.org
Date: Wed Oct 15 17:19:13 2014 +0900
Fix heterogeneous support
* correctly send OPAL_DSTORE_ARCH key
diff --git a/ompi/proc/proc.c b/ompi/proc/proc.c
index d30182f..12b781e 100644
--- a/ompi/proc/proc.c
+++ b/ompi/proc/proc.c
@@ -107,6 +107,7 @@ int ompi_proc_init(void)
OMPI_CAST_RTE_NAME(&proc->super.proc_name)->vpid = i;
if (i == OMPI_PROC_MY_NAME->vpid) {
+ opal_value_t kv;
ompi_proc_local_proc = proc;
proc->super.proc_flags = OPAL_PROC_ALL_LOCAL;
proc->super.proc_hostname = strdup(ompi_process_info.nodename);
@@ -115,8 +116,13 @@ int ompi_proc_init(void)
opal_proc_local_set(&proc->super);
#if OPAL_ENABLE_HETEROGENEOUS_SUPPORT
/* add our arch to the modex */
- OPAL_MODEX_SEND_STRING(ret, PMIX_SYNC_REQD, PMIX_REMOTE,
OPAL_DSTORE_ARCH,
- &proc->super.proc_arch, OPAL_UINT32);
+ OBJ_CONSTRUCT(&kv, opal_value_t);
+ kv.key = strdup(OPAL_DSTORE_ARCH);
+ kv.type = OPAL_UINT32;
+ kv.data.uint32 = opal_local_arch;
+ ret = opal_pmix.put(PMIX_REMOTE, &kv);
+ OBJ_DESTRUCT(&kv);
+
if (OPAL_SUCCESS != ret) {
return ret;
}
