possible missing java version issue on our server

[Stephane Plaisance]

Hi

After some updates on the server side, GP seems to not be avail anymore although a process is running.

genepat+ 24840  2.0  0.1 8722812 505736 pts/12 Sl   12:06   0:46 /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64/jre/bin/java -Xmx1024m -Xms256m com.zerog.lax.LAX /opt/genepattern/./StartGenePatternServer.lax /tmp/env.properties.24840

Could it be because of the differences below

cat /opt/genepattern/./StartGenePatternServer.lax | grep java
java.endorsed.dirs=./common/endorsed
java.io.tmpdir=./temp
lax.nl.current.vm=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.144-0.b01.el7_4.x86_64/jre/bin/java
#   main class of LaunchAnywhere's java launcher -- do not adjust
lax.nl.java.launcher.main.class=com.zerog.lax.LAX
#   main method of LaunchAnywhere's java launcher -- do not adjust
lax.nl.java.launcher.main.method=main
lax.nl.java.option.java.heap.size.initial=256m
lax.nl.java.option.java.heap.size.max=1024m

 

it seems GP looks for java-1.8.0-openjdk-1.8.0.144

which is not present below

[u0002316@gbw-s-nuc03 ~]$ ll /usr/lib/jvm/
total 16K
drwxr-xr-x. 11 root root 4.0K Jul 17 07:41 .
dr-xr-xr-x. 53 root root 8.0K Jul 17 07:41 ..
lrwxrwxrwx   1 root root   26 Jul 17 07:41 java -> /etc/alternatives/java_sdk
drwxr-xr-x.  3 root root   17 Mar  9 13:55 java-1.7.0-openjdk-1.7.0.161-2.6.12.0.el7_4.x86_64
drwxr-xr-x   3 root root   17 May 11 11:33 java-1.7.0-openjdk-1.7.0.171-2.6.13.0.el7_4.x86_64
drwxr-xr-x   3 root root   17 Jul 17 07:41 java-1.7.0-openjdk-1.7.0.181-2.6.14.5.el7.x86_64
drwxr-xr-x   4 root root  100 Jul 17 07:37 java-1.7.0-openjdk-1.7.0.181-2.6.14.8.el7_5.x86_64
lrwxrwxrwx   1 root root   32 Jul 17 07:41 java-1.8.0 -> /etc/alternatives/java_sdk_1.8.0
lrwxrwxrwx   1 root root   40 Jul 17 07:41 java-1.8.0-openjdk -> /etc/alternatives/java_sdk_1.8.0_openjdk
drwxr-xr-x.  3 root root   17 Jan  9  2018 java-1.8.0-openjdk-1.8.0.151-1.b12.el7_4.x86_64
drwxr-xr-x.  3 root root   17 Jan 23  2018 java-1.8.0-openjdk-1.8.0.151-5.b12.el7_4.x86_64
drwxr-xr-x.  3 root root   17 May 11 11:33 java-1.8.0-openjdk-1.8.0.161-0.b14.el7_4.x86_64
drwxr-xr-x   3 root root   17 Jul 17 07:41 java-1.8.0-openjdk-1.8.0.171-7.b10.el7.x86_64
drwxr-xr-x   7 root root   68 Jul 17 07:38 java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64
lrwxrwxrwx   1 root root   34 Jul 17 07:41 java-openjdk -> /etc/alternatives/java_sdk_openjdk
lrwxrwxrwx   1 root root   21 Jul 17 07:41 jre -> /etc/alternatives/jre
lrwxrwxrwx   1 root root   27 Jul 17 07:41 jre-1.7.0 -> /etc/alternatives/jre_1.7.0
lrwxrwxrwx   1 root root   35 Jul 17 07:41 jre-1.7.0-openjdk -> /etc/alternatives/jre_1.7.0_openjdk
lrwxrwxrwx   1 root root   54 Jul 17 07:37 jre-1.7.0-openjdk-1.7.0.181-2.6.14.8.el7_5.x86_64 -> java-1.7.0-openjdk-1.7.0.181-2.6.14.8.el7_5.x86_64/jre
lrwxrwxrwx   1 root root   27 Jul 17 07:41 jre-1.8.0 -> /etc/alternatives/jre_1.8.0
lrwxrwxrwx   1 root root   35 Jul 17 07:41 jre-1.8.0-openjdk -> /etc/alternatives/jre_1.8.0_openjdk
lrwxrwxrwx   1 root root   51 Jul 17 07:38 jre-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64 -> java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64/jre
lrwxrwxrwx   1 root root   29 Jul 17 07:41 jre-openjdk -> /etc/alternatives/jre_openjdk

if Yes, should I simply stop the server and edit the lax.nl.current to reflect the current java location?

[u0002316@gbw-s-nuc03 genepattern]$ java -version
openjdk version "1.8.0_171"
OpenJDK Runtime Environment (build 1.8.0_171-b10)
OpenJDK 64-Bit Server VM (build 25.171-b10, mixed mode) 

thanks

Stephane 

PS: after stopping the server (twice) and restarting it it came back to life but the question about the apparent java version mismatch still applies - this is weird and seems not to affect the server at all???)

[Peter Carr]

Hi Stephane,

At first glance, yes. Stop the server and set the java location.

I am away on vacation this week. I will look into this in more detail when I get back.

Regards,

Peter

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[Barbara Hill]

Hi Stephane, 

Did Peter's hints help get things back up and running for you?

Best

-Barbara

[Stephane Plaisance]

Hi Barbara

The java mismatch was apparently not involved and we only eeded to fully kill all gp jobs and restart it. I lso edited the conf file to match the actual java but this setting seems to be quite neutral.

Thanks for your concern

Best

Stephane

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[Barbara Hill]

Hi Stephane, 

Good news! I just wanted to be sure we hadn't left you hanging.

All the best

-Barbara