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>
<javascript:_e(%7B%7D,'cvml','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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