These are chat archives for nextflow-io/nextflow

5th
May 2015
Paolo Di Tommaso
@pditommaso
May 05 2015 06:20
even easier, the provide a dashboard by using which you set a queue in which you define your ami to use, mem, storage, etc
then you can submit jobs in a very similar way you do with SGE qsub
Andrew Stewart
@andrewcstewart
May 05 2015 16:42
they host the dashboard?
Paolo Di Tommaso
@pditommaso
May 05 2015 16:43
yes
Andrew Stewart
@andrewcstewart
May 05 2015 16:43
it looks like this is a MapReduce platform though?
can you use it to just create a cluster?
Paolo Di Tommaso
@pditommaso
May 05 2015 16:44
it is not M/R, it's more similar to a batch scheduler
and they setup a cluster using spot instances on demand
Andrew Stewart
@andrewcstewart
May 05 2015 16:49
so its basically StarCluster
Paolo Di Tommaso
@pditommaso
May 05 2015 16:50
in principle, but better because it is designed to work in that environment
I remember that SC had huge scalability problems
Andrew Stewart
@andrewcstewart
May 05 2015 20:33
Any idea what this means?
Exception in thread "main" java.lang.UnsupportedClassVersionError: CapsuleLoader : Unsupported major.minor version 51.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:643)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:277)
    at java.net.URLClassLoader.access$000(URLClassLoader.java:73)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:212)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
Could not find the main class: CapsuleLoader. Program will exit.
Paolo Di Tommaso
@pditommaso
May 05 2015 20:33
uh
are you using Java 8?
umh, it looks you are using an old JVM
Andrew Stewart
@andrewcstewart
May 05 2015 20:36
yeah thats what im figuring
looking at two hosts (shared home directory, etc)
both java 7
but this would seem to be the source of why I can’t run nextflow at the moment
Paolo Di Tommaso
@pditommaso
May 05 2015 20:37
umh check the variable $JAVA_HOME
(mac or linux?)
Andrew Stewart
@andrewcstewart
May 05 2015 20:37
both linux
centos 6
aha
Paolo Di Tommaso
@pditommaso
May 05 2015 20:38
found ?
Andrew Stewart
@andrewcstewart
May 05 2015 20:38
the misbehaving host has JAVA_HOME -> 1.6
weird
Paolo Di Tommaso
@pditommaso
May 05 2015 20:39
that's the problem
Andrew Stewart
@andrewcstewart
May 05 2015 20:41
hopefully this runs then w/o me needing to update nextflow
Paolo Di Tommaso
@pditommaso
May 05 2015 20:42
um, what do you mean ?
Andrew Stewart
@andrewcstewart
May 05 2015 20:44
bc of our nextwork trouble with s3
Paolo Di Tommaso
@pditommaso
May 05 2015 20:45
um, any version of nextflow requires at least Java 1.7
Andrew Stewart
@andrewcstewart
May 05 2015 20:48
in other words, I hope that the jre mismatch was the only problem and that I dont have to repair my nextflow install
yesssss.. it worked
Paolo Di Tommaso
@pditommaso
May 05 2015 20:48
:+1:
Andrew Stewart
@andrewcstewart
May 05 2015 20:49
uggg.. the things I was trying yesterday to circumvent this problem
lets put it this way: I tried to setup a 2nd SGE submit host where nextflow was working on
:D
thanks for the advice
Paolo Di Tommaso
@pditommaso
May 05 2015 20:50
welcome
Andrew Stewart
@andrewcstewart
May 05 2015 22:47
Hey @pditommaso it might be a good idea to add -v to docker rm in the .command.run scripts
considering the # of volumes typically mounted by a container
(maybe this was added in a recent version of nfx, Im looking at output from 0.11.2 right now and I see "docker rm nxf-813b0f35 &>/dev/null &”)