Hi Siegmar,
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
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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>
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