BEAST runs not terminating correctly on our cluster

[Kurt Wollenberg]

Hello:

I have recently been performing pretty standard BEAST analyses in a cluster environment and having some odd behavior. The runs finish pretty efficiently but it seems the processes do not terminate and occupy nodes until I stumble across them and manually kill them. The environment under which these runs are running is:

BEAST v 1.8.1 running on Centos 5, with beagle-lib 5 Feb 2015.
java version "1.7.0_05"
Java(TM) SE Runtime Environment (build 1.7.0_05-b06)
Java HotSpot(TM) 64-Bit Server VM (build 23.1-b03, mixed mode)

running on
8 x 2.67 GHz Intel X5550, 24 GB RAM, 8 MB secondary cache.

What we are seeing is

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
14564 XXXXXXXX  19   0 67964 1480 1208 S  0.0  0.0   0:00.01 bash
14589 XXXXXXXX  22   0 63808 1220 1032 S  0.0  0.0   0:00.00 8705183.biobos.
14592 XXXXXXXX  20   0 63812 1264 1076 S  0.0  0.0   0:01.75 beast
14593 XXXXXXXX  15   0 63808  576  388 S  0.0  0.0   0:00.00 8705183.biobos.
14594 XXXXXXXX  15   0 63808  576  388 S  0.0  0.0   0:00.00 8705183.biobos.
14595 XXXXXXXX  15   0 63808  576  388 S  0.0  0.0   0:00.00 8705183.biobos.
14596 XXXXXXXX  15   0 63808  576  388 S  0.0  0.0   0:00.00 8705183.biobos.
14597 XXXXXXXX  18   0 63808  576  388 S  0.0  0.0   0:00.00 8705183.biobos.
14606 XXXXXXXX  18   0 2585m 284m  11m S  0.0  1.2   0:11.12 java
14607 XXXXXXXX  18   0 63812 1264 1076 S  0.0  0.0   0:01.73 beast
14633 XXXXXXXX  19   0 2586m 125m  11m S  0.0  0.5 369:55.49 java
14656 XXXXXXXX  18   0 63812 1264 1076 S  0.0  0.0   0:01.65 beast
14666 XXXXXXXX  18   0 2592m 293m  11m S  0.0  1.2   0:09.39 java
 
I've been in contact with our cluster administrators and they believe this is a bug in BEAST when implemented in this type of environment.

[Andrew Rambaut]

Hi Kurt,

This bug was introduced in 1.8.1 and has been fixed. An update will be out in the next day or so. 

Andrew

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[Jorge Sebastião Soares]

Hi, Kurt, Andrew,

I'm seeing this as well on our LSF cluster running Ubuntu Precise 12.04 with

java version "1.6.0_32"
OpenJDK Runtime Environment (IcedTea6 1.13.4) (6b32-1.13.4-4ubuntu0.12.04.2)
OpenJDK 64-Bit Server VM (build 23.25-b01, mixed mode)

I ran BEAST 1.8.1 with strace and it seems to drop a wait4 call and never wakes up again. Last lines of strace after running beast/beagle on the benchmark1.xml file:

clone(child_stack=0, flags=CLONE_CHILD_CLEARTID|CLONE_CHILD_SETTID|SIGCHLD, child_tidptr=0x2ae1d9902e10) = 4981
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
rt_sigprocmask(SIG_BLOCK, [CHLD], [], 8) = 0
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
rt_sigprocmask(SIG_BLOCK, [CHLD], [], 8) = 0
rt_sigaction(SIGINT, {0x43f370, [], SA_RESTORER, 0x2ae1d9579150}, {SIG_DFL, [], SA_RESTORER, 0x2ae1d9579150}, 8) = 0
wait4(-1,

Has an update been released already?

Best,

Jorge

[Jorge Sebastião Soares]

This has been solved by Andrew already.

It took a while for the reply to be posted so I emailed Andrew directly.

All sorted with the 1.8.2 BEAST pre-release.

Thanks Andrew.

Regards,

Jorge

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