Hello Gilles and Oscar,
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.
