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.
> >>
> >> _______________________________________________
> >> users mailing list
> >> us...@open-mpi.org
> >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users
> >> Link to this post:
> >> http://www.open-mpi.org/community/lists/users/2014/10/25581.php
> >
> >_______________________________________________
> >users mailing list
> >us...@open-mpi.org
> >Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users
> >Link to this post:
> >http://www.open-mpi.org/community/lists/users/2014/10/25582.php
>
