Hello Gilley, Howard,
I configured without disable dlopen - same error.
I test these classes on another cluster and: IT WORKS!
So it is a problem of the cluster configuration. Thank you all very much
for all your help! When the admin can solve the problem, i will let you
know, what he had changed.
Cheers Gundram
On 07/08/2016 04:19 PM, Howard Pritchard wrote:
Hi Gundram
Could you configure without the disable dlopen option and retry?
Howard
Am Freitag, 8. Juli 2016 schrieb Gilles Gouaillardet :
the JVM sets its own signal handlers, and it is important openmpi
dones not override them.
this is what previously happened with PSM (infinipath) but this
has been solved since.
you might be linking with a third party library that hijacks
signal handlers and cause the crash
(which would explain why I cannot reproduce the issue)
the master branch has a revamped memory patcher (compared to v2.x
or v1.10), and that could have some bad interactions with the JVM,
so you might also give v2.x a try
Cheers,
Gilles
On Friday, July 8, 2016, Gundram Leifert
<gundram.leif...@uni-rostock.de
<javascript:_e(%7B%7D,'cvml','gundram.leif...@uni-rostock.de');>>
wrote:
You made the best of it... thanks a lot!
Whithout MPI it runs.
Just adding MPI.init() causes the crash!
maybe I installed something wrong...
install newest automake, autoconf, m4, libtoolize in right
order and same prefix
check out ompi,
autogen
configure with same prefix, pointing to the same jdk, I later use
make
make install
I will test some different configurations of ./configure...
On 07/08/2016 01:40 PM, Gilles Gouaillardet wrote:
I am running out of ideas ...
what if you do not run within slurm ?
what if you do not use '-cp executor.jar'
or what if you configure without --disable-dlopen
--disable-mca-dso ?
if you
mpirun -np 1 ...
then MPI_Bcast and MPI_Barrier are basically no-op, so it is
really weird your program is still crashing. an other test is
to comment out MPI_Bcast and MPI_Barrier and try again with -np 1
Cheers,
Gilles
On Friday, July 8, 2016, Gundram Leifert
<gundram.leif...@uni-rostock.de> wrote:
In any cases the same error.
this is my code:
salloc -n 3
export IPATH_NO_BACKTRACE
ulimit -s 10240
mpirun -np 3 java -cp executor.jar
de.uros.citlab.executor.test.TestSendBigFiles2
also for 1 or two cores, the process crashes.
On 07/08/2016 12:32 PM, Gilles Gouaillardet wrote:
you can try
export IPATH_NO_BACKTRACE
before invoking mpirun (that should not be needed though)
an other test is to
ulimit -s 10240
before invoking mpirun.
btw, do you use mpirun or srun ?
can you reproduce the crash with 1 or 2 tasks ?
Cheers,
Gilles
On Friday, July 8, 2016, Gundram Leifert
<gundram.leif...@uni-rostock.de> wrote:
Hello,
configure:
./configure --enable-mpi-java
--with-jdk-dir=/home/gl069/bin/jdk1.7.0_25
--disable-dlopen --disable-mca-dso
1 node with 3 cores. I use SLURM to allocate one
node. I changed --mem, but it has no effect.
salloc -n 3
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 256564
max locked memory (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
open files (-n) 100000
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) unlimited
cpu time (seconds, -t) unlimited
max user processes (-u) 4096
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
uname -a
Linux titan01.service 3.10.0-327.13.1.el7.x86_64 #1
SMP Thu Mar 31 16:04:38 UTC 2016 x86_64 x86_64
x86_64 GNU/Linux
cat /etc/system-release
CentOS Linux release 7.2.1511 (Core)
what else do you need?
Cheers, Gundram
On 07/07/2016 10:05 AM, Gilles Gouaillardet wrote:
Gundram,
can you please provide more information on your
environment :
- configure command line
- OS
- memory available
- ulimit -a
- number of nodes
- number of tasks used
- interconnect used (if any)
- batch manager (if any)
Cheers,
Gilles
On 7/7/2016 4:17 PM, Gundram Leifert wrote:
Hello Gilles,
I tried you code and it crashes after 3-15
iterations (see (1)). It is always the same error
(only the "94" varies).
Meanwhile I think Java and MPI use the same memory
because when I delete the hash-call, the program
runs sometimes more than 9k iterations.
When it crashes, there are different lines (see
(2) and (3)). The crashes also occurs on rank 0.
##### (1)#####
# Problematic frame:
# J 94 C2
de.uros.citlab.executor.test.TestSendBigFiles2.hashcode([BI)I
(42 bytes) @ 0x00002b03242dc9c4
[0x00002b03242dc860+0x164]
#####(2)#####
# Problematic frame:
# V [libjvm.so+0x68d0f6]
JavaCallWrapper::JavaCallWrapper(methodHandle,
Handle, JavaValue*, Thread*)+0xb6
#####(3)#####
# Problematic frame:
# V [libjvm.so+0x4183bf]
ThreadInVMfromNative::ThreadInVMfromNative(JavaThread*)+0x4f
Any more idea?
On 07/07/2016 03:00 AM, Gilles Gouaillardet wrote:
Gundram,
fwiw, i cannot reproduce the issue on my box
- centos 7
- java version "1.8.0_71"
Java(TM) SE Runtime Environment (build
1.8.0_71-b15)
Java HotSpot(TM) 64-Bit Server VM (build
25.71-b15, mixed mode)
i noticed on non zero rank saveMem is allocated
at each iteration.
ideally, the garbage collector can take care of
that and this should not be an issue.
would you mind giving the attached file a try ?
Cheers,
Gilles
On 7/7/2016 7:41 AM, Gilles Gouaillardet wrote:
I will have a look at it today
how did you configure OpenMPI ?
Cheers,
Gilles
On Thursday, July 7, 2016, Gundram Leifert
<gundram.leif...@uni-rostock.de> wrote:
Hello Giles,
thank you for your hints! I did 3 changes,
unfortunately the same error occures:
update ompi:
commit ae8444682f0a7aa158caea08800542ce9874455e
Author: Ralph Castain <r...@open-mpi.org>
Date: Tue Jul 5 20:07:16 2016 -0700
update java:
java version "1.8.0_92"
Java(TM) SE Runtime Environment (build
1.8.0_92-b14)
Java HotSpot(TM) Server VM (build 25.92-b14,
mixed mode)
delete hashcode-lines.
Now I get this error message - to 100%,
after different number of iterations (15-300):
0/ 3:length = 100000000
0/ 3:bcast length done (length = 100000000)
1/ 3:bcast length done (length = 100000000)
2/ 3:bcast length done (length = 100000000)
#
# A fatal error has been detected by the
Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00002b3d022fcd24,
pid=16578, tid=0x00002b3d29716700
#
# JRE version: Java(TM) SE Runtime
Environment (8.0_92-b14) (build 1.8.0_92-b14)
# Java VM: Java HotSpot(TM) 64-Bit Server VM
(25.92-b14 mixed mode linux-amd64 compressed
oops)
# Problematic frame:
# V [libjvm.so+0x414d24]
ciEnv::get_field_by_index(ciInstanceKlass*,
int)+0x94
#
# Failed to write core dump. Core dumps have
been disabled. To enable core dumping, try
"ulimit -c unlimited" before starting Java again
#
# An error report file with more information
is saved as:
#
/home/gl069/ompi/bin/executor/hs_err_pid16578.log
#
# Compiler replay data is saved as:
#
/home/gl069/ompi/bin/executor/replay_pid16578.log
#
# If you would like to submit a bug report,
please visit:
# http://bugreport.java.com/bugreport/crash.jsp
#
[titan01:16578] *** Process received signal ***
[titan01:16578] Signal: Aborted (6)
[titan01:16578] Signal code: (-6)
[titan01:16578] [ 0]
/usr/lib64/libpthread.so.0(+0xf100)[0x2b3d01500100]
[titan01:16578] [ 1]
/usr/lib64/libc.so.6(gsignal+0x37)[0x2b3d01b5c5f7]
[titan01:16578] [ 2]
/usr/lib64/libc.so.6(abort+0x148)[0x2b3d01b5dce8]
[titan01:16578] [ 3]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x91e605)[0x2b3d02806605]
[titan01:16578] [ 4]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0xabda63)[0x2b3d029a5a63]
[titan01:16578] [ 5]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(JVM_handle_linux_signal+0x14f)[0x2b3d0280be2f]
[titan01:16578] [ 6]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x91a5c3)[0x2b3d028025c3]
[titan01:16578] [ 7]
/usr/lib64/libc.so.6(+0x35670)[0x2b3d01b5c670]
[titan01:16578] [ 8]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x414d24)[0x2b3d022fcd24]
[titan01:16578] [ 9]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x43c5ae)[0x2b3d023245ae]
[titan01:16578] [10]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x369ade)[0x2b3d02251ade]
[titan01:16578] [11]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x36eda0)[0x2b3d02256da0]
[titan01:16578] [12]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x37091b)[0x2b3d0225891b]
[titan01:16578] [13]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x3712b6)[0x2b3d022592b6]
[titan01:16578] [14]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x36d2cf)[0x2b3d022552cf]
[titan01:16578] [15]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x36e412)[0x2b3d02256412]
[titan01:16578] [16]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x36ed8d)[0x2b3d02256d8d]
[titan01:16578] [17]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x37091b)[0x2b3d0225891b]
[titan01:16578] [18]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x3712b6)[0x2b3d022592b6]
[titan01:16578] [19]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x36d2cf)[0x2b3d022552cf]
[titan01:16578] [20]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x36e412)[0x2b3d02256412]
[titan01:16578] [21]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x36ed8d)[0x2b3d02256d8d]
[titan01:16578] [22]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x3708c2)[0x2b3d022588c2]
[titan01:16578] [23]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x3724e7)[0x2b3d0225a4e7]
[titan01:16578] [24]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x37a817)[0x2b3d02262817]
[titan01:16578] [25]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x37a92f)[0x2b3d0226292f]
[titan01:16578] [26]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x358edb)[0x2b3d02240edb]
[titan01:16578] [27]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x35929e)[0x2b3d0224129e]
[titan01:16578] [28]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x3593ce)[0x2b3d022413ce]
[titan01:16578] [29]
/home/gl069/bin/jdk1.8.0_92/jre/lib/amd64/server/libjvm.so(+0x35973e)[0x2b3d0224173e]
[titan01:16578] *** End of error message ***
-------------------------------------------------------
Primary job terminated normally, but 1
process returned
a non-zero exit code. Per user-direction,
the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID
0 on node titan01 exited on signal 6 (Aborted).
--------------------------------------------------------------------------
I don't know if it is a problem of java or
ompi - but the last years, java worked with
no problems on my machine...
Thank you for your tips in advance!
Gundram
On 07/06/2016 03:10 PM, Gilles Gouaillardet
wrote:
Note a race condition in MPI_Init has been
fixed yesterday in the master.
can you please update your OpenMPI and try
again ?
hopefully the hang will disappear.
Can you reproduce the crash with a simpler
(and ideally deterministic) version of your
program.
the crash occurs in hashcode, and this
makes little sense to me. can you also
update your jdk ?
Cheers,
Gilles
On Wednesday, July 6, 2016, Gundram Leifert
<gundram.leif...@uni-rostock.de> wrote:
Hello Jason,
thanks for your response! I thing it is
another problem. I try to send 100MB
bytes. So there are not many tries
(between 10 and 30). I realized that
the execution of this code can result 3
different errors:
1. most often the posted error message
occures.
2. in <10% the cases i have a live
lock. I can see 3 java-processes, one
with 200% and two with 100% processor
utilization. After ~15 minutes without
new system outputs this error occurs.
[thread 47499823949568 also had an error]
# A fatal error has been detected by
the Java Runtime Environment:
#
# Internal Error (safepoint.cpp:317),
pid=24256, tid=47500347131648
# guarantee(PageArmed == 0) failed:
invariant
#
# JRE version: 7.0_25-b15
# Java VM: Java HotSpot(TM) 64-Bit
Server VM (23.25-b01 mixed mode
linux-amd64 compressed oops)
# Failed to write core dump. Core dumps
have been disabled. To enable core
dumping, try "ulimit -c unlimited"
before starting Java again
#
# An error report file with more
information is saved as:
#
/home/gl069/ompi/bin/executor/hs_err_pid24256.log
#
# If you would like to submit a bug
report, please visit:
#
http://bugreport.sun.com/bugreport/crash.jsp
#
[titan01:24256] *** Process received
signal ***
[titan01:24256] Signal: Aborted (6)
[titan01:24256] Signal code: (-6)
[titan01:24256] [ 0]
/usr/lib64/libpthread.so.0(+0xf100)[0x2b336a324100]
[titan01:24256] [ 1]
/usr/lib64/libc.so.6(gsignal+0x37)[0x2b336a9815f7]
[titan01:24256] [ 2]
/usr/lib64/libc.so.6(abort+0x148)[0x2b336a982ce8]
[titan01:24256] [ 3]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x742ac5)[0x2b336b44fac5]
[titan01:24256] [ 4]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x8a2137)[0x2b336b5af137]
[titan01:24256] [ 5]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x407262)[0x2b336b114262]
[titan01:24256] [ 6]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x7c6c34)[0x2b336b4d3c34]
[titan01:24256] [ 7]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x8a9c17)[0x2b336b5b6c17]
[titan01:24256] [ 8]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x8aa2c0)[0x2b336b5b72c0]
[titan01:24256] [ 9]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x744270)[0x2b336b451270]
[titan01:24256] [10]
/usr/lib64/libpthread.so.0(+0x7dc5)[0x2b336a31cdc5]
[titan01:24256] [11]
/usr/lib64/libc.so.6(clone+0x6d)[0x2b336aa4228d]
[titan01:24256] *** End of error
message ***
-------------------------------------------------------
Primary job terminated normally, but 1
process returned
a non-zero exit code. Per
user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with
PID 0 on node titan01 exited on signal
6 (Aborted).
--------------------------------------------------------------------------
3. in <10% the cases i have a dead lock
while MPI.init. This stays for more
than 15 minutes without returning with
an error message...
Can I enable some debug-flags to see
what happens on C / OpenMPI side?
Thanks in advance for your help!
Gundram Leifert
On 07/05/2016 06:05 PM, Jason Maldonis
wrote:
After reading your thread looks like
it may be related to an issue I had a
few weeks ago (I'm a novice though).
Maybe my thread will be of help:
https://www.open-mpi.org/community/lists/users/2016/06/29425.php
When you say "After a specific number
of repetitions the process either
hangs up or returns with a SIGSEGV."
does you mean that a single call
hangs, or that at some point during
the for loop a call hangs? If you mean
the latter, then it might relate to my
issue. Otherwise my thread probably
won't be helpful.
Jason Maldonis
Research Assistant of Professor Paul
Voyles
Materials Science Grad Student
University of Wisconsin, Madison
1509 University Ave, Rm M142
Madison, WI 53706
maldo...@wisc.edu
608-295-5532
On Tue, Jul 5, 2016 at 9:58 AM,
Gundram Leifert
<gundram.leif...@uni-rostock.de> wrote:
Hello,
I try to send many byte-arrays via
broadcast. After a specific number
of repetitions the process either
hangs up or returns with a
SIGSEGV. Does any one can help me
solving the problem:
########## The code:
import java.util.Random;
import mpi.*;
public class TestSendBigFiles {
public static void log(String
msg) {
try {
System.err.println(String.format("%2d/%2d:%s",
MPI.COMM_WORLD.getRank(),
MPI.COMM_WORLD.getSize(), msg));
} catch (MPIException ex) {
System.err.println(String.format("%2s/%2s:%s",
"?", "?", msg));
}
}
private static int
hashcode(byte[] bytearray) {
if (bytearray == null) {
return 0;
}
int hash = 39;
for (int i = 0; i <
bytearray.length; i++) {
byte b = bytearray[i];
hash = hash * 7 + (int) b;
}
return hash;
}
public static void main(String
args[]) throws MPIException {
log("start main");
MPI.Init(args);
try {
log("initialized done");
byte[] saveMem = new byte[100000000];
MPI.COMM_WORLD.barrier();
Random r = new Random();
r.nextBytes(saveMem);
if
(MPI.COMM_WORLD.getRank() == 0) {
for (int i = 0; i < 1000; i++) {
saveMem[r.nextInt(saveMem.length)]++;
log("i = " + i);
int[] lengthData = new
int[]{saveMem.length};
log("object hash = " +
hashcode(saveMem));
log("length = " + lengthData[0]);
MPI.COMM_WORLD.bcast(lengthData,
1, MPI.INT <http://MPI.INT>, 0);
log("bcast length done (length = "
+ lengthData[0] + ")");
MPI.COMM_WORLD.barrier();
MPI.COMM_WORLD.bcast(saveMem,
lengthData[0], MPI.BYTE, 0);
log("bcast data done");
MPI.COMM_WORLD.barrier();
}
MPI.COMM_WORLD.bcast(new int[]{0},
1, MPI.INT <http://MPI.INT>, 0);
} else {
while (true) {
int[] lengthData = new int[1];
MPI.COMM_WORLD.bcast(lengthData,
1, MPI.INT <http://MPI.INT>, 0);
log("bcast length done (length = "
+ lengthData[0] + ")");
if (lengthData[0] == 0) {
break;
}
MPI.COMM_WORLD.barrier();
saveMem = new
byte[lengthData[0]];
MPI.COMM_WORLD.bcast(saveMem,
saveMem.length, MPI.BYTE, 0);
log("bcast data done");
MPI.COMM_WORLD.barrier();
log("object hash = " +
hashcode(saveMem));
}
}
MPI.COMM_WORLD.barrier();
} catch (MPIException ex) {
System.out.println("caugth error."
+ ex);
log(ex.getMessage());
} catch (RuntimeException
ex) {
System.out.println("caugth error."
+ ex);
log(ex.getMessage());
} finally {
MPI.Finalize();
}
}
}
############ The Error (if it does
not just hang up):
#
# A fatal error has been detected
by the Java Runtime Environment:
#
# SIGSEGV (0xb) at
pc=0x00002b7e9c86e3a1, pid=1172,
tid=47822674495232
#
#
# A fatal error has been detected
by the Java Runtime Environment:
# JRE version: 7.0_25-b15
# Java VM: Java HotSpot(TM) 64-Bit
Server VM (23.25-b01 mixed mode
linux-amd64 compressed oops)
# Problematic frame:
# #
# SIGSEGV (0xb) at
pc=0x00002af69c0693a1, pid=1173,
tid=47238546896640
#
# JRE version: 7.0_25-b15
J
de.uros.citlab.executor.test.TestSendBigFiles.hashcode([B)I
#
# Failed to write core dump. Core
dumps have been disabled. To
enable core dumping, try "ulimit
-c unlimited" before starting Java
again
#
# Java VM: Java HotSpot(TM) 64-Bit
Server VM (23.25-b01 mixed mode
linux-amd64 compressed oops)
# Problematic frame:
# J
de.uros.citlab.executor.test.TestSendBigFiles.hashcode([B)I
#
# Failed to write core dump. Core
dumps have been disabled. To
enable core dumping, try "ulimit
-c unlimited" before starting Java
again
#
# An error report file with more
information is saved as:
#
/home/gl069/ompi/bin/executor/hs_err_pid1172.log
# An error report file with more
information is saved as:
#
/home/gl069/ompi/bin/executor/hs_err_pid1173.log
#
# If you would like to submit a
bug report, please visit:
#
http://bugreport.sun.com/bugreport/crash.jsp
#
#
# If you would like to submit a
bug report, please visit:
#
http://bugreport.sun.com/bugreport/crash.jsp
#
[titan01:01172] *** Process
received signal ***
[titan01:01172] Signal: Aborted (6)
[titan01:01172] Signal code: (-6)
[titan01:01173] *** Process
received signal ***
[titan01:01173] Signal: Aborted (6)
[titan01:01173] Signal code: (-6)
[titan01:01172] [ 0]
/usr/lib64/libpthread.so.0(+0xf100)[0x2b7e9596a100]
[titan01:01172] [ 1]
/usr/lib64/libc.so.6(gsignal+0x37)[0x2b7e95fc75f7]
[titan01:01172] [ 2]
/usr/lib64/libc.so.6(abort+0x148)[0x2b7e95fc8ce8]
[titan01:01172] [ 3]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x742ac5)[0x2b7e96a95ac5]
[titan01:01172] [ 4]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x8a2137)[0x2b7e96bf5137]
[titan01:01172] [ 5]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(JVM_handle_linux_signal+0x140)[0x2b7e96a995e0]
[titan01:01172] [ 6]
[titan01:01173] [ 0]
/usr/lib64/libpthread.so.0(+0xf100)[0x2af694ded100]
[titan01:01173] [ 1]
/usr/lib64/libc.so.6(+0x35670)[0x2b7e95fc7670]
[titan01:01172] [ 7] [0x2b7e9c86e3a1]
[titan01:01172] *** End of error
message ***
/usr/lib64/libc.so.6(gsignal+0x37)[0x2af69544a5f7]
[titan01:01173] [ 2]
/usr/lib64/libc.so.6(abort+0x148)[0x2af69544bce8]
[titan01:01173] [ 3]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x742ac5)[0x2af695f18ac5]
[titan01:01173] [ 4]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x8a2137)[0x2af696078137]
[titan01:01173] [ 5]
/home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(JVM_handle_linux_signal+0x140)[0x2af695f1c5e0]
[titan01:01173] [ 6]
/usr/lib64/libc.so.6(+0x35670)[0x2af69544a670]
[titan01:01173] [ 7] [0x2af69c0693a1]
[titan01:01173] *** End of error
message ***
-------------------------------------------------------
Primary job terminated normally,
but 1 process returned
a non-zero exit code. Per
user-direction, the job has been
aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 1
with PID 0 on node titan01 exited
on signal 6 (Aborted).
########CONFIGURATION:
I used the ompi master sources
from github:
commit
267821f0dd405b5f4370017a287d9a49f92e734a
Author: Gilles Gouaillardet
<gil...@rist.or.jp>
Date: Tue Jul 5 13:47:50 2016 +0900
./configure --enable-mpi-java
--with-jdk-dir=/home/gl069/bin/jdk1.7.0_25
--disable-dlopen --disable-mca-dso
Thanks a lot for your help!
Gundram
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