search

cBio / cbio-cluster

MSKCC cBio cluster documentation
12 stars 2 forks source link

Java is sometimes unhappy on the login node #3

Closed pgrinaway closed 10 years ago

pgrinaway commented 10 years ago

Attempting to get the version of Java with java -version yields

[pgrinaway@mskcc-ln1 ~]$ java -version
Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.

Additionally, I get a similar error trying to compile OpenMM on the login node:

[pgrinaway@mskcc-ln1 openmm]$ make
Scanning dependencies of target ApiWrappers
[  0%] Generating OpenMMApi.xml
[  0%] Generating OpenMMCWrapper.h
Error occurred during initialization of VM
Could not reserve enough space for object heap
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
make[2]: *** [wrappers/OpenMMCWrapper.h] Error 1
make[1]: *** [wrappers/CMakeFiles/ApiWrappers.dir/all] Error 2
make: *** [all] Error 2

I'm not sure if this is a Java configuration issue, though, since on the compute nodes it seems to work fine:

[pgrinaway@gpu-2-9 openmm]$ java -version
java version "1.6.0_24"
OpenJDK Runtime Environment (IcedTea6 1.11.11.90) (rhel-1.62.1.11.11.90.el6_4-    x86_64)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

Does everyone else have this problem?

kyleabeauchamp commented 10 years ago

I can confirm this issue:

-bash-4.1$ java -version
Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.
``
pgrinaway commented 10 years ago

@csirving Also could we get Oracle HotSpot JVM installed, perhaps as a module?

jchodera commented 10 years ago

@pgrinaway : Has this been resolved, or do we need @csirving to install?

tatarsky commented 10 years ago

I believe the limits on the head node (data or as) conflict with the default java heap size. A brief test confirms that is likely:

java -Xmx2000000 -version java version "1.6.0_24" OpenJDK Runtime Environment (IcedTea6 1.11.11.90) (rhel-1.62.1.11.11.90.el6_4-x86_64) OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

This will be reviewed post move.

I see no module for Oracle HotSpot JVM. Please re-open as a new issue. Do not chain issues.

csirving commented 10 years ago

Yes this is a problem do the limits on the login node and java's default max heap size.

[root@mskcc-ln1 profile.d]# /usr/java/latest/bin/java -XX:+PrintFlagsFinal -version |grep -i HeapSize uintx ErgoHeapSizeLimit = 0 {product} uintx HeapSizePerGCThread = 87241520 {product} uintx InitialHeapSize := 2147483648 {product} uintx LargePageHeapSizeThreshold = 134217728 {product} uintx MaxHeapSize := 32126271488 {product} java version "1.7.0_25" Java(TM) SE Runtime Environment (build 1.7.0_25-b15) Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

Also the Oracle jre which includes the "HotSpot JVM" has been installed on the cluster since it was initially setup. I didn't realize openJDK was causing a conflict. You could solve this with a module for the Oracle jre but unless someone is particularly fond of openJDK, I for one am not, you could just jettison it.

[root@mskcc-ln1 /]# /usr/java/latest/bin/java -version java version "1.7.0_25" Java(TM) SE Runtime Environment (build 1.7.0_25-b15) Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

From: tatarsky notifications@github.com<mailto:notifications@github.com> Reply-To: cBio/cbio-cluster reply@reply.github.com<mailto:reply@reply.github.com> Date: Thu, 3 Jul 2014 10:03:50 -0700 To: cBio/cbio-cluster cbio-cluster@noreply.github.com<mailto:cbio-cluster@noreply.github.com> Cc: csirving cirving@sdsc.edu<mailto:cirving@sdsc.edu> Subject: Re: [cbio-cluster] Java is sometimes unhappy on the login node (#3)

I believe the limits on the head node (data or as) conflict with the default java heap size. A brief test confirms that is likely:

java -Xmx2000000 -version java version "1.6.0_24" OpenJDK Runtime Environment (IcedTea6 1.11.11.90) (rhel-1.62.1.11.11.90.el6_4-x86_64) OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

This will be reviewed post move.

I see no module for Oracle HotSpot JVM. Please re-open as a new issue. Do not chain issues.

— Reply to this email directly or view it on GitHubhttps://github.com/cBio/cbio-cluster/issues/3#issuecomment-47956941.

tatarsky commented 10 years ago

We believe this is resolved or at least documented for workaround. If you agree, please close the issue.

tatarsky commented 10 years ago

Closing. Re-open if needed.