> Can you also see if it happens in
> other Taverna versions say 1.7.1 or 2.1?
I have tried using taverna-2.1; Before opening the workflow I wanted to
apply recent updates but it became a bit tricky because of bimoby server
not working at that moment (i think) as I was getting 'too many open
files' problems with some biomoby signatures. After I removed biomoby
services from my workbench it looked like I was able to apply the
updates. I restarted the workbench and have tried opening the same
workflow (which includes some biomoby processors). It unfortunately
caused a JVM crash with the report copied below.
I don't know the exact reason but I started to feel guilty after I
reported my second bug yesterday. I thought I shouldn't SPAM such a
crowded email list with problems not relevant to all people on the list.
Before writing this email I attempted to login into taverna JIRA using a
username I had sometime ago, I was able to login but it looked like I'm
not able to submit new bug reports. So I'm sending another message to
the list. I would appreciate it if you let me know if there is another
way of submitting bug reports. Actually I can contact you directly, I
think I will follow that way next time.
I also have one question not relevant to above. In the workflow I tried
we have lists of ensembl ids with some null entries. We use these lists
as inputs to biomart queries to get relevant sequences. In
taverna-1.7.2, biomart queries returns with lists of reduced size, i.e
if an input list has 10 ids with 2 empty/null entries it returns a list
of size 8, rather than 10. This causes problems as in different lists we
have null entries in different places and we don't want to loose the
orders. In summary what we would like to see is an output list with 8
sequences and 2 empty elements, for the above example. I don't know how
to program such things in taverna, if anybody on the list thinks they
can help us we can provide more information and the workflow.
Mahmut
org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Too many open files
Fault code:
{http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
at
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.init(BiomobyActivity.java:774)
at
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.configure(BiomobyActivity.java:86)
at
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.configure(BiomobyActivity.java:60)
at
net.sf.taverna.t2.compatibility.activity.AbstractActivityTranslator.doTranslation(AbstractActivityTranslator.java:80)
at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.createActivity(WorkflowModelTranslator.java:424)
at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.createProcessor(WorkflowModelTranslator.java:388)
at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.createProcessors(WorkflowModelTranslator.java:362)
at
net.sf.taverna.t2.compatibility.WorkflowModelTranslator.doTranslation(WorkflowModelTranslator.java:164)
... 6 more
#
# A fatal error has been detected by the Java Runtime Environment:
#
# Internal Error (exceptions.cpp:364), pid=14385, tid=140034179036944
# Error: ExceptionMark destructor expects no pending exceptions
#
# JRE version: 6.0_18-b07
# Java VM: Java HotSpot(TM) 64-Bit Server VM (16.0-b13 mixed mode
linux-amd64 )
# Can not save log file, dump to screen..
#
# A fatal error has been detected by the Java Runtime Environment:
#
# Internal Error (exceptions.cpp:364), pid=14385, tid=140034179036944
# Error: ExceptionMark destructor expects no pending exceptions
#
# JRE version: 6.0_18-b07
# Java VM: Java HotSpot(TM) 64-Bit Server VM (16.0-b13 mixed mode
linux-amd64 )
# If you would like to submit a bug report, please visit:
# http://java.sun.com/webapps/bugreport/crash.jsp
#
--------------- T H R E A D ---------------
Current thread (0x00007f5c40049800): JavaThread "BioMOBY
GetOntologyThread" daemon [_thread_in_vm, id=14560,
stack(0x00007f5c3f6f7000,0x00007f5c3f7f8000)]
Stack: [0x00007f5c3f6f7000,0x00007f5c3f7f8000], sp=0x00007f5c3f7f39b0,
free space=3f20000000000000018k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code,
C=native code)
V [libjvm.so+0x70e5f0]
V [libjvm.so+0x2e3e26]
V [libjvm.so+0x332a6d]
V [libjvm.so+0x27e8a8]
V [libjvm.so+0x27def2]
V [libjvm.so+0x27df76]
V [libjvm.so+0x27f986]
V [libjvm.so+0x69feef]
V [libjvm.so+0x69e03b]
V [libjvm.so+0x69ced1]
V [libjvm.so+0x69cb43]
V [libjvm.so+0x45d439]
V [libjvm.so+0x4420bc]
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j
java.lang.Class.forName0(Ljava/lang/String;ZLjava/lang/ClassLoader;)Ljava/lang/Class;+0
j java.lang.Class.forName(Ljava/lang/String;)Ljava/lang/Class;+5
j java.nio.charset.Charset$3.run()Ljava/lang/Object;+2
v ~StubRoutines::call_stub
J
java.security.AccessController.doPrivileged(Ljava/security/PrivilegedAction;)Ljava/lang/Object;
j java.nio.charset.Charset.probeExtendedProvider()V+7
j
java.nio.charset.Charset.lookupExtendedCharset(Ljava/lang/String;)Ljava/nio/charset/Charset;+14
j
java.nio.charset.Charset.lookup2(Ljava/lang/String;)Ljava/nio/charset/Charset;+48
j
java.nio.charset.Charset.lookup(Ljava/lang/String;)Ljava/nio/charset/Charset;+40
j java.nio.charset.Charset.isSupported(Ljava/lang/String;)Z+1
j
com.hp.hpl.jena.util.CharEncoding.create(Ljava/lang/String;)Lcom/hp/hpl/jena/util/CharEncoding;+1
j
com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.setEncoding(Ljava/lang/String;)V+1
j com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser
$MySAXParser.xmlDecl(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/apache/xerces/xni/Augmentations;)V+14
j
org.apache.xerces.impl.XMLNamespaceBinder.xmlDecl(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/apache/xerces/xni/Augmentations;)V+23
j
org.apache.xerces.impl.dtd.XMLDTDValidator.xmlDecl(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Lorg/apache/xerces/xni/Augmentations;)V+41
j
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanXMLDeclOrTextDecl(Z)V+119
j org.apache.xerces.impl.XMLDocumentScannerImpl
$XMLDeclDispatcher.dispatch(Z)Z+242
j
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Z)Z
+24
j org.apache.xerces.parsers.DTDConfiguration.parse(Z)Z+60
j
org.apache.xerces.parsers.DTDConfiguration.parse(Lorg/apache/xerces/xni/parser/XMLInputSource;)V+29
j
org.apache.xerces.parsers.XMLParser.parse(Lorg/apache/xerces/xni/parser/XMLInputSource;)V+9
j
org.apache.xerces.parsers.AbstractSAXParser.parse(Lorg/xml/sax/InputSource;)V+43
j
com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(Lorg/xml/sax/InputSource;Ljava/lang/String;)V+32
j
com.hp.hpl.jena.rdf.arp.JenaReader.read(Lcom/hp/hpl/jena/graph/Graph;Lorg/xml/sax/InputSource;Ljava/lang/String;Lcom/hp/hpl/jena/rdf/model/Model;)V+58
j
com.hp.hpl.jena.rdf.arp.JenaReader.read(Lcom/hp/hpl/jena/rdf/model/Model;Lorg/xml/sax/InputSource;Ljava/lang/String;)V+21
j
com.hp.hpl.jena.rdf.arp.JenaReader.read(Lcom/hp/hpl/jena/rdf/model/Model;Ljava/io/InputStream;Ljava/lang/String;)V+11
j
org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF()[Lorg/biomoby/shared/MobyDataType;+66
j org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache()Z+31
j
org.biomoby.client.CentralDigestCachedSimpleImpl.updateCache(Ljava/lang/String;)V+46
j
net.sf.taverna.t2.activities.biomoby.BiomobyCache.cacheForRegistry(Lorg/biomoby/registry/meta/Registry;)V+61
j
net.sf.taverna.t2.activities.biomoby.BiomobyCache.cacheForRegistryEndpoint(Ljava/lang/String;)V+13
j net.sf.taverna.t2.activities.biomoby.GetOntologyThread.run()V+4
v ~StubRoutines::call_stub
--------------- P R O C E S S ---------------
Java Threads: ( => current thread )
=>0x00007f5c40049800 JavaThread "BioMOBY GetOntologyThread" daemon
[_thread_in_vm, id=14560, stack(0x00007f5c3f6f7000,0x00007f5c3f7f8000)]
0x00007f5c4003b800 JavaThread "Retry timer" daemon [_thread_blocked,
id=14554, stack(0x00007f5cc1bed000,0x00007f5cc1cee000)]
0x00007f5c40045800 JavaThread "Dispatch stack state cleanup" daemon
[_thread_blocked, id=14553,
stack(0x00007f5c9d8c6000,0x00007f5c9d9c7000)]
0x00007f5c703d7000 JavaThread "Timer-3" daemon [_thread_blocked,
id=14460, stack(0x00007f5c9d2ba000,0x00007f5c9d3bb000)]
0x00007f5c703bd000 JavaThread "RunnableQueue-0" daemon
[_thread_blocked, id=14459,
stack(0x00007f5c9ddcb000,0x00007f5c9decc000)]
0x00007f5c540ec800 JavaThread "Batik CleanerThread" daemon
[_thread_blocked, id=14458,
stack(0x00007f5c9dfcd000,0x00007f5c9e0ce000)]
0x00007f5c74044000 JavaThread "derby.rawStoreDaemon" daemon
[_thread_blocked, id=14449,
stack(0x00007f5cc01da000,0x00007f5cc02db000)]
0x00007f5c74271000 JavaThread "Timer-2" daemon [_thread_blocked,
id=14448, stack(0x00007f5c9d9c7000,0x00007f5c9dac8000)]
0x00007f5de4008800 JavaThread "DestroyJavaVM" [_thread_blocked,
id=14390, stack(0x00007f5de807c000,0x00007f5de817d000)]
0x00007f5c7426e000 JavaThread "Timer-1" daemon [_thread_blocked,
id=14447, stack(0x00007f5c9e0ce000,0x00007f5c9e1cf000)]
0x00007f5c70312000 JavaThread "pool-1-thread-1" [_thread_blocked,
id=14442, stack(0x00007f5c9d6c4000,0x00007f5c9d7c5000)]
0x00007f5c74053800 JavaThread "derby.antiGC" daemon [_thread_blocked,
id=14440, stack(0x00007f5c9dcca000,0x00007f5c9ddcb000)]
0x00007f5c702a1000 JavaThread "SVG Graph controller timer" daemon
[_thread_blocked, id=14435,
stack(0x00007f5c9d7c5000,0x00007f5c9d8c6000)]
0x00007f5c70320000 JavaThread "GraphAutoScrollTimer" daemon
[_thread_blocked, id=14434,
stack(0x00007f5c9dbc9000,0x00007f5c9dcca000)]
0x00007f5c70296000 JavaThread "Timer-0" daemon [_thread_blocked,
id=14429, stack(0x00007f5c9d5c3000,0x00007f5c9d6c4000)]
0x00007f5c58019000 JavaThread "Find service descriptions from Biomart
service http://www.biomart.org/biomart/martservice"; daemon
[_thread_in_native, id=14420,
stack(0x00007f5c9decc000,0x00007f5c9dfcd000)]
0x00007f5c70283000 JavaThread "TimerQueue" daemon [_thread_blocked,
id=14415, stack(0x00007f5cc02db000,0x00007f5cc03dc000)]
0x00007f5c70278800 JavaThread "Clear status line" daemon
[_thread_blocked, id=14413,
stack(0x00007f5cc04dd000,0x00007f5cc05de000)]
0x00007f5c7026a800 JavaThread "Search field timer" daemon
[_thread_blocked, id=14412,
stack(0x00007f5cc05de000,0x00007f5cc06df000)]
0x00007f5c7020c800 JavaThread "Check for updates thread" daemon
[_thread_blocked, id=14411,
stack(0x00007f5cc06df000,0x00007f5cc07e0000)]
0x00007f5c70208800 JavaThread "Deleting old workflow runs" daemon
[_thread_blocked, id=14410,
stack(0x00007f5cc07e0000,0x00007f5cc08e1000)]
0x00007f5de44b4800 JavaThread "AWT-EventQueue-0" [_thread_blocked,
id=14407, stack(0x00007f5cc19eb000,0x00007f5cc1aec000)]
0x00007f5de43a7800 JavaThread "AWT-Shutdown" [_thread_blocked,
id=14406, stack(0x00007f5cc1aec000,0x00007f5cc1bed000)]
0x00007f5de4471000 JavaThread "AWT-XAWT" daemon [_thread_in_native,
id=14404, stack(0x00007f5cc1cee000,0x00007f5cc1def000)]
0x00007f5de4408000 JavaThread "Java2D Disposer" daemon
[_thread_blocked, id=14403,
stack(0x00007f5cc200e000,0x00007f5cc210f000)]
0x00007f5de40cc000 JavaThread "Low Memory Detector" daemon
[_thread_blocked, id=14401,
stack(0x00007f5cc286e000,0x00007f5cc296f000)]
0x00007f5de40ca000 JavaThread "CompilerThread1" daemon
[_thread_blocked, id=14400,
stack(0x00007f5cc296f000,0x00007f5cc2a70000)]
0x00007f5de40c7800 JavaThread "CompilerThread0" daemon
[_thread_blocked, id=14399,
stack(0x00007f5cc2a70000,0x00007f5cc2b71000)]
0x00007f5de40c4800 JavaThread "Signal Dispatcher" daemon
[_thread_blocked, id=14398,
stack(0x00007f5cc2b71000,0x00007f5cc2c72000)]
0x00007f5de4091800 JavaThread "Finalizer" daemon [_thread_blocked,
id=14397, stack(0x00007f5cc2c72000,0x00007f5cc2d73000)]
0x00007f5de408f800 JavaThread "Reference Handler" daemon
[_thread_blocked, id=14396,
stack(0x00007f5cc2d73000,0x00007f5cc2e74000)]
Other Threads:
0x00007f5de408b000 VMThread [stack:
0x00007f5cc2e74000,0x00007f5cc2f75000] [id=14395]
0x00007f5de40ce800 WatcherThread [stack:
0x00007f5cc276d000,0x00007f5cc286e000] [id=14402]
VM state:not at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: None
Heap
PSYoungGen total 1107520K, used 337794K [0x00007f5d86b70000,
0x00007f5dd7dd0000, 0x00007f5de04c0000)
eden space 1039936K, 29% used
[0x00007f5d86b70000,0x00007f5d99bbc6b0,0x00007f5dc6300000)
from space 67584K, 38% used
[0x00007f5dc6300000,0x00007f5dc7c94498,0x00007f5dca500000)
to space 63680K, 0% used
[0x00007f5dd3fa0000,0x00007f5dd3fa0000,0x00007f5dd7dd0000)
PSOldGen total 269568K, used 154289K [0x00007f5cd38c0000,
0x00007f5ce4000000, 0x00007f5d86b70000)
object space 269568K, 57% used
[0x00007f5cd38c0000,0x00007f5cdcf6c7f8,0x00007f5ce4000000)
PSPermGen total 155968K, used 78071K [0x00007f5cc48c0000,
0x00007f5cce110000, 0x00007f5cd38c0000)
object space 155968K, 50% used
[0x00007f5cc48c0000,0x00007f5cc94fdd98,0x00007f5cce110000)
Dynamic libraries:
Can not get library information for pid = 14560
VM Arguments:
jvm_args: -Xmx4300m -XX:MaxPermSize=240m
-Draven.profile=file:conf/current-profile.xml -Dtaverna.startup=.
-Djava.system.class.loader=net.sf.taverna.raven.prelauncher.BootstrapClassLoader
-Dapple.laf.useScreenMenuBar=true -Dapple.awt.graphics.UseQuartz=false
-Dsun.swing.enableImprovedDragGesture
java_command: lib/prelauncher-2.0.jar
Launcher Type: SUN_STANDARD
Environment Variables:
JAVA_HOME=/usr/local/java64
PATH=/usr/local/java64/bin:/local/uludag/embossCVS/bin:/bin:/usr/local/libtool/bin:/usr/local/java64/bin:/local/uludag/embossCVS/bin:/bin:/usr/local/libtool/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/bin:/shared/software/bin/:/homes/uludag/naccess2.1.1:/homes/uludag/stamp_4_2/bin:/bin:/usr/bin:/homes/uludag/hmmer-2.3.2.bin.intel-linux/binaries:/shared/software/bin:~/eclipse-workspace/bio-bwa/:~/eclipse-workspace/samtools/:/homes/uludag/eclipse-workspace/libdivsufsort/build/examples/:/bin:/shared/software/bin/:/homes/uludag/naccess2.1.1:/homes/uludag/stamp_4_2/bin:/bin:/usr/bin:/homes/uludag/hmmer-2.3.2.bin.intel-linux/binaries:/shared/software/bin:~/eclipse-workspace/bio-bwa/:~/eclipse-workspace/samtools/:/homes/uludag/eclipse-workspace/libdivsufsort/build/examples/
USERNAME=uludag
LD_LIBRARY_PATH=/local/local/jdk1.6.0_18_64/jre/lib/amd64/server:/local/local/jdk1.6.0_18_64/jre/lib/amd64:/local/local/jdk1.6.0_18_64/jre/../lib/amd64
SHELL=/usr/local/bin/bash
DISPLAY=:0.0
Signal Handlers:
SIGSEGV: [libjvm.so+0x70f1a0], sa_mask[0]=0x7ffbfeff,
sa_flags=0x10000004
SIGBUS: [libjvm.so+0x70f1a0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGFPE: [libjvm.so+0x5d7f70], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGPIPE: [libjvm.so+0x5d7f70], sa_mask[0]=0x7ffbfeff,
sa_flags=0x10000004
SIGXFSZ: [libjvm.so+0x5d7f70], sa_mask[0]=0x7ffbfeff,
sa_flags=0x10000004
SIGILL: [libjvm.so+0x5d7f70], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGUSR1: SIG_DFL, sa_mask[0]=0x00000000, sa_flags=0x00000000
SIGUSR2: [libjvm.so+0x5da790], sa_mask[0]=0x00000000,
sa_flags=0x10000004
SIGHUP: [libjvm.so+0x5da4e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGINT: [libjvm.so+0x5da4e0], sa_mask[0]=0x7ffbfeff, sa_flags=0x10000004
SIGTERM: [libjvm.so+0x5da4e0], sa_mask[0]=0x7ffbfeff,
sa_flags=0x10000004
SIGQUIT: [libjvm.so+0x5da4e0], sa_mask[0]=0x7ffbfeff,
sa_flags=0x10000004
--------------- S Y S T E M ---------------
OS:Linux
uname:Linux 2.6.31.12-174.2.19.fc12.x86_64 #1 SMP Thu Feb 11 07:07:16
UTC 2010 x86_64
libc:glibc 2.11.1 NPTL 2.11.1
rlimit: STACK 10240k, CORE 0k, NPROC 1024, NOFILE 1024, AS infinity
load average:0.00 0.00 0.00
CPU:total 4 (4 cores per cpu, 1 threads per core) family 6 model 23
stepping 10, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1
Memory: 4k page, physical 8130380k(52252k free), swap
16386260k(16281368k free)
vm_info: Java HotSpot(TM) 64-Bit Server VM (16.0-b13) for linux-amd64
JRE (1.6.0_18-b07), built on Dec 17 2009 13:42:22 by "java_re" with gcc
3.2.2 (SuSE Linux)
time: Thu Feb 18 11:41:12 2010
elapsed time: 64 seconds
#
# If you would like to submit a bug report, please visit:
# http://java.sun.com/webapps/bugreport/crash.jsp
#
Aborted (core dumped)
------------------------------------------------------------------------------
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