starbeast2 on CIPRES

[Brian D.]

Hi all,
Trying to run starbeast2 on CIPRES and received the errors below. Does anyone know if the starbeast2 template is available on the CIPRES cluster? I can't find any information on installed packages on the site. The stderr says the starbeast2 package is not available, among other errors, but I'm not sure if this is the root problem or if its one of the other errors.

Thanks for any help!
Brian



Unloading compiler-dependent module mvapich2_ib/2.1
Unloading compiler-dependent module openmpi_ib/1.8.4
intel/2015.2.164(64):ERROR:105: Unable to locate a modulefile for 'openmpi_ib'
cmdModule.c(567):ERROR:50: Cannot open file '/opt/modulefiles/applications/gateway-usage-reporting/1.0' for 'reading'
Warning: at xsl:stylesheet on line 3 column 80 of xsl.2.4.x:
  Running an XSLT 10 stylesheet with an XSLT 20 processor
NOTICE : Your input file may have been altered to activate multi-threading.
File: infile_altered.xml seed: 1486413749395 threads: 6
Loading package STACEY v1.2.2
Library expoTree not found in Phylodynamics lib directory...
Trying java.library.path (set command line argument or copy to run directory
java.lang.UnsatisfiedLinkError: no expoTree in java.library.path
    at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1865)
    at java.lang.Runtime.loadLibrary0(Runtime.java:870)
    at java.lang.System.loadLibrary(System.java:1122)
    at beast.phylodynamics.ExactBDSIS.<clinit>(Unknown Source)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:264)
    at beast.util.AddOnManager.find(Unknown Source)
    at beast.util.AddOnManager.find(Unknown Source)
    at beast.util.XMLParserUtils.<clinit>(Unknown Source)
    at beast.util.XMLParser.parseFile(Unknown Source)
    at beast.app.BeastMCMC.parseArgs(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)
java.lang.NoClassDefFoundError: no/uib/cipr/matrix/Vector
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:264)
    at beast.util.AddOnManager.find(Unknown Source)
    at beast.util.AddOnManager.find(Unknown Source)
    at beast.util.XMLParserUtils.<clinit>(Unknown Source)
    at beast.util.XMLParser.parseFile(Unknown Source)
    at beast.app.BeastMCMC.parseArgs(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)
Caused by: java.lang.ClassNotFoundException: no.uib.cipr.matrix.Vector
    at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 8 more
java.lang.NoClassDefFoundError: no/uib/cipr/matrix/Matrix
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:264)
    at beast.util.AddOnManager.find(Unknown Source)
    at beast.util.AddOnManager.find(Unknown Source)
    at beast.util.XMLParserUtils.<clinit>(Unknown Source)
    at beast.util.XMLParser.parseFile(Unknown Source)
    at beast.app.BeastMCMC.parseArgs(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)
Caused by: java.lang.ClassNotFoundException: no.uib.cipr.matrix.Matrix
    at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 8 more
The following package is required, but is not available: starbeast2 v0.13.1
See http://beast2.org/managing-packages/ for details on how to install packages.
Exception in thread "main" java.lang.NoClassDefFoundError: com/google/common/collect/Multimap
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:264)
    at beast.util.XMLParser.createObject(Unknown Source)
    at beast.util.XMLParser.parseInputs(Unknown Source)
    at beast.util.XMLParser.createObject(Unknown Source)
    at beast.util.XMLParser.parseInputs(Unknown Source)
    at beast.util.XMLParser.createObject(Unknown Source)
    at beast.util.XMLParser.parseRunElement(Unknown Source)
    at beast.util.XMLParser.parse(Unknown Source)
    at beast.util.XMLParser.parseFile(Unknown Source)
    at beast.app.BeastMCMC.parseArgs(Unknown Source)
    at beast.app.beastapp.BeastMain.main(Unknown Source)
Caused by: java.lang.ClassNotFoundException: com.google.common.collect.Multimap
    at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 12 more
srun: error: comet-10-25: task 0: Exited with exit code 1

[Miller, Mark]

Hi Brian,

We are struggling to get starbeast working, sad to say.

We have been swept away from the task by other priorities this week.

We had trouble getting the package installer to see that package, and haven’t figured out the issue yet.

We hope to have this done in the next week.

 

Mark

 

From: beast...@googlegroups.com [mailto:beast...@googlegroups.com] On Behalf Of Brian D.
Sent: Wednesday, February 08, 2017 10:15 AM
To: beast-users <beast...@googlegroups.com>
Subject: starbeast2 on CIPRES

 

Hi all,
Trying to run starbeast2 on CIPRES and received the errors below. Does anyone know if the starbeast2 template is available on the CIPRES cluster? I can't find any information on installed packages on the site. The stderr says the starbeast2 package is not available, among other errors, but I'm not sure if this is the root problem or if its one of the other errors.

Thanks for any help

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To post to this group, send email to beast...@googlegroups.com.
Visit this group at https://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.

[Brian D.]

Thanks for the very quick reply Mark. If you do get starbeast installed and the starbeast2 template, could we get an update on the CIPRES website or maybe here?

Thanks very much and good luck!

Brian

[Miller, Mark]

Yes indeed. I will post it when we get it done.

Thanks for your patience.

[Miller, Mark]

OK, It looks like StarBeast is working now. Sorry for the wait. It was an issue on my side.

[Brian D.]

Thanks Mark! Just saw this. Quicker than I expected.

Cheers
Brian