I'm running a SeqWare VM on an amazon EC2 instance I'm trying to use the SeqWare query engine to query data from VCF files. When I first launch the instance and follow the instructions to import data, It works fine, and continues to work until I stop the instance. When I restart it. It won't let me import anything, nor create a new workspace. It always returns the error below. I looked at the processes and found that none of the required nodes were running, so I logged into root and went to the etc/init.d directory and start everything again, at which point, when T try to import data, I don't even get an error and I have to stop the process.
[seqware#master target]$ java -classpath seqware-distribution-0.13.6.7-qe-full.jar com.github.seqware.queryengine.system.importers.SOFeatureImporter -i ../../seqware-queryengine/src/test/resources/com/github/seqware/queryengine/system/FeatureImporter/consequences_annotated.vcf ALL.chr3.phase1_release_v3.20101123.snps_indels_svs.genotypes.3_100001-101000.vcf -o keyValueVCF.out -r hg_19 -s c111aea5-5e18-4c62-a8a7-ec82fe151301 -a ad_hoc -w VCFVariantImportWorker
[SeqWare Query Engine] 0 [main] ERROR org.apache.hadoop.hbase.zookeeper.RecoverableZooKeeper - ZooKeeper exists failed after 3 retries
[SeqWare Query Engine] 1 [main] ERROR org.apache.hadoop.hbase.zookeeper.ZooKeeperWatcher - hconnection Received unexpected KeeperException, re-throwing exception
org.apache.zookeeper.KeeperException$ConnectionLossException: KeeperErrorCode = ConnectionLoss for /hbase/master
at org.apache.zookeeper.KeeperException.create(KeeperException.java:99)
at org.apache.zookeeper.KeeperException.create(KeeperException.java:51)
at org.apache.zookeeper.ZooKeeper.exists(ZooKeeper.java:1021)
at org.apache.hadoop.hbase.zookeeper.RecoverableZooKeeper.exists(RecoverableZooKeeper.java:154)
at org.apache.hadoop.hbase.zookeeper.ZKUtil.watchAndCheckExists(ZKUtil.java:226)
at org.apache.hadoop.hbase.zookeeper.ZooKeeperNodeTracker.start(ZooKeeperNodeTracker.java:82)
at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.setupZookeeperTrackers(HConnectionManager.java:580)
at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.<init>(HConnectionManager.java:569)
at org.apache.hadoop.hbase.client.HConnectionManager.getConnection(HConnectionManager.java:186)
at org.apache.hadoop.hbase.client.HBaseAdmin.<init>(HBaseAdmin.java:100)
at com.github.seqware.queryengine.impl.HBaseStorage.<init>(HBaseStorage.java:89)
at com.github.seqware.queryengine.factory.SWQEFactory$Storage_Type$3.buildStorage(SWQEFactory.java:109)
at com.github.seqware.queryengine.factory.SWQEFactory.getStorage(SWQEFactory.java:174)
at com.github.seqware.queryengine.factory.SWQEFactory.getQueryInterface(SWQEFactory.java:199)
at com.github.seqware.queryengine.impl.SimpleModelManager.<init>(SimpleModelManager.java:49)
at com.github.seqware.queryengine.impl.HBaseModelManager.<init>(HBaseModelManager.java:36)
at com.github.seqware.queryengine.impl.MRHBaseModelManager.<init>(MRHBaseModelManager.java:32)
at com.github.seqware.queryengine.factory.SWQEFactory.getModelManager(SWQEFactory.java:211)
at com.github.seqware.queryengine.system.importers.FeatureImporter.performImport(FeatureImporter.java:66)
at com.github.seqware.queryengine.system.importers.SOFeatureImporter.runMain(SOFeatureImporter.java:141)
at com.github.seqware.queryengine.system.importers.SOFeatureImporter.main(SOFeatureImporter.java:60)
[SeqWare Query Engine] 3 [main] FATAL org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation - Unexpected exception during initialization, aborting
org.apache.zookeeper.KeeperException$ConnectionLossException: KeeperErrorCode = ConnectionLoss for /hbase/master
at org.apache.zookeeper.KeeperException.create(KeeperException.java:99)
at org.apache.zookeeper.KeeperException.create(KeeperException.java:51)
at org.apache.zookeeper.ZooKeeper.exists(ZooKeeper.java:1021)
at org.apache.hadoop.hbase.zookeeper.RecoverableZooKeeper.exists(RecoverableZooKeeper.java:154)
at org.apache.hadoop.hbase.zookeeper.ZKUtil.watchAndCheckExists(ZKUtil.java:226)
at org.apache.hadoop.hbase.zookeeper.ZooKeeperNodeTracker.start(ZooKeeperNodeTracker.java:82)
at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.setupZookeeperTrackers(HConnectionManager.java:580)
at org.apache.hadoop.hbase.client.HConnectionManager$HConnectionImplementation.<init>(HConnectionManager.java:569)
at org.apache.hadoop.hbase.client.HConnectionManager.getConnection(HConnectionManager.java:186)
at org.apache.hadoop.hbase.client.HBaseAdmin.<init>(HBaseAdmin.java:100)
at com.github.seqware.queryengine.impl.HBaseStorage.<init>(HBaseStorage.java:89)
at com.github.seqware.queryengine.factory.SWQEFactory$Storage_Type$3.buildStorage(SWQEFactory.java:109)
at com.github.seqware.queryengine.factory.SWQEFactory.getStorage(SWQEFactory.java:174)
at com.github.seqware.queryengine.factory.SWQEFactory.getQueryInterface(SWQEFactory.java:199)
at com.github.seqware.queryengine.impl.SimpleModelManager.<init>(SimpleModelManager.java:49)
at com.github.seqware.queryengine.impl.HBaseModelManager.<init>(HBaseModelManager.java:36)
at com.github.seqware.queryengine.impl.MRHBaseModelManager.<init>(MRHBaseModelManager.java:32)
at com.github.seqware.queryengine.factory.SWQEFactory.getModelManager(SWQEFactory.java:211)
at com.github.seqware.queryengine.system.importers.FeatureImporter.performImport(FeatureImporter.java:66)
at com.github.seqware.queryengine.system.importers.SOFeatureImporter.runMain(SOFeatureImporter.java:141)
at com.github.seqware.queryengine.system.importers.SOFeatureImporter.main(SOFeatureImporter.java:60)
I figured it out.The apache services were installed from the cloudera package. They weren't being restarted when the instance was being restarted and apparently, just running their script from the etc/init.d was the incorrect way to do it. I found the commands to restart them in the cloudera documentation.
I too faced this problem.I was able to solve this problem by providing jute.maxbuffer parameter while starting zookeeper.
For more info you can refer
https://issues.apache.org/jira/browse/SOLR-4793
Related
Trying the give the details of snowfalke in dbt profiles.yml file . but as soon as when ran the command i,e
$atom /home/myname/.dbt/profiles.yml gives below error:
/usr/bin/atom: line 190: 1705 Trace/breakpoint trap (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$#" > "$ATOM_HOME/nohup.out" 2>&1
Failed to move to new namespace: PID namespaces supported, Network namespace supported, but failed: errno = Permission denied
Following things i tried: Ran below commands but still no luck:
1)
$google-chrome --no-gpu --no-sandbox --disable-setuid-sandbox --headless --dump-dom http://www.chromestatus.com
Error:
[0627/161930.251811:ERROR:udev_watcher.cc(61)] Failed to enable receiving udev events.
[0627/161932.565713:ERROR:platform_shared_memory_region_posix.cc(46)] Descriptor access mode (0) differs from expected (2)
[0627/161932.566251:WARNING:crash_handler_host_linux.cc(366)] Could not translate tid - assuming crashing thread is thread group leader; syscall_supported=0
[0627/161932.769040:WARNING:crash_handler_host_linux.cc(366)] Could not translate tid - assuming crashing thread is thread group leader; syscall_supported=0
--2020-06-27 16:19:32-- https://clients2.google.com/cr/report
Resolving clients2.google.com (clients2.google.com)... 2404:6800:4009:805::200e, 172.217.174.238
Connecting to clients2.google.com (clients2.google.com)|2404:6800:4009:805::200e|:443... [0627/161933.036124:ERROR:headless_shell.cc(399)] Abnormal renderer termination.
connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/plain]
Saving to: ‘/dev/fd/4’
0K
Crash dump id: e870824b56e91b9f
$ google-chrome
Error:
Failed to move to new namespace: PID namespaces supported, Network namespace supported, but failed: errno = Permission denied
Trace/breakpoint trap (core dumped)
[1772:1772:0100/000000.825375:ERROR:zygote_linux.cc(653)] write: Broken pipe (32)
[0627/162152.831614:ERROR:nacl_helper_linux.cc(308)] NaCl helper process running without a sandbox!
Most likely you need to configure your SUID sandbox correctly
Could any one advise on the above issue.
This could be an atom error. Could be packages or something that they installed. I could be wrong, but I don’t see anything in that error message that indicates it’s a profiles.yml thing. I wonder if they can open other files in atom just fine?
Alternatively, use a text editor that isn’t based on chrome
Thanks #jake and #Christine from FishTown Analytics.
Here are a few helpful links.
Atom issue;
Blogpost!
I have a 2 node OpenStack Mitaka environment consisting of a controller/compute node and a compute node.
I've followed the setup guide to enable instance live migration using LVM block storage. I.e.: There's no shared storage backend, just local LVM block storage.
Using OpenStack Horizon to perform the live migration a success message is displayed, however, the migration is far from successful. This worked pretty much out-of-the-box with our Juno installation. I've exhausted Google and cannot find any other instances of people facing the same problem. I thought it might have been a time synchronisation problem so have set both nodes to UTC. Still the problems persists.
Source machine /var/log/nova/nova-compute.log
2016-08-12 15:56:42.120 2230 ERROR nova.virt.libvirt.driver [req-b71ea7b0-5fa8-4b57-92d2-4edec62135c2 b017d86d1143461a92a267d4b912c104 88c686f09e1b427fb750f5c00716f84e - - -] [instance: 5763b6b6-370c-448c-8e8f-8b71eafaa8f1] Migration operation has aborted
2016-08-12 15:56:42.470 2230 ERROR nova.virt.libvirt.driver [req-b71ea7b0-5fa8-4b57-92d2-4edec62135c2 b017d86d1143461a92a267d4b912c104 88c686f09e1b427fb750f5c00716f84e - - -] [instance: 5763b6b6-370c-448c-8e8f-8b71eafaa8f1] Live Migration failure: internal error: unable to execute QEMU command 'migrate': Migration disabled: failed to allocate shared memory
Target node /var/log/libvirt/libvirtd.log
2016-08-12 15:56:41.864+0000: 2170: error : qemuMonitorJSONGetMigrationStatsReply:2443 : internal error: info migration reply was missing return status
2016-08-12 15:56:41.864+0000: 2170: error : virNetClientProgramDispatchError:177 : Cannot open log file: '/var/log/libvirt/qemu/instance-0000006a.log': Device or resource busy
There are no other events captured in the source or target nova or libvirt logs.
I should also note that I am trying to use qemu+tcp (libvirt listening enabled, default tcp port, no auth) rather than qemu+ssh in order to keep things simple while testing. In fact, I intend to only use qemu+tcp anyway.
Which version of ubuntu did you deploy?
I had the same error with ubuntu 14.04 and mitaka version.
And I figured out that default kernel (3.13) makes this problem.
I upgraded the kernel from 3.13 to 4.40 and this problem is gone now.
I hope my experience help you solve this problem out.
Thanks
Can anyone please help me to resolve this error?
Below is the weblogic server log...
I'm using Jdk 7, and Java Developer for ADF
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Unrecognized option: -jrockit
Process exited.
--Weblogic server log-------
*** Using HTTP port 7101 ***
*** Using SSL port 7102 ***
C:\Users\inatar\AppData\Roaming\JDeveloper\system11.1.2.4.39.64.36.1\DefaultDomain\bin\startWebLogic.cmd
[waiting for the server to complete its initialization...]
.
.
JAVA Memory arguments: -Xms256m -Xmx512m
.
WLS Start Mode=Development
.
CLASSPATH=C:\Oracle\Middleware\oracle_common\modules\oracle.jdbc_11.1.1\ojdbc6dms.jar;C:\Oracle\Middl
eware\patch_wls1035\profiles\default\sys_manifest_classpath\weblogic_patch.jar;C:\Oracle\Middleware\p
atch_jdev1112\profiles\default\sys_manifest_classpath\weblogic_patch.jar;C:\PROGRA~1\Java\jdk1.7.0_67
\lib\tools.jar;C:\Oracle\Middleware\wlserver_10.3\server\lib\weblogic_sp.jar;C:\Oracle\Middleware\wls
erver_10.3\server\lib\weblogic.jar;C:\Oracle\Middleware\modules\features\weblogic.server.modules_10.3
.5.0.jar;C:\Oracle\Middleware\wlserver_10.3\server\lib\webservices.jar;C:\Oracle\Middleware\modules\o
rg.apache.ant_1.7.1/lib/ant-all.jar;C:\Oracle\Middleware\modules\net.sf.antcontrib_1.1.0.0_1-
0b2/lib/ant-
contrib.jar;C:\Oracle\Middleware\oracle_common\modules\oracle.jrf_11.1.1\jrf.jar;C:\Oracle\Middleware
\wlserver_10.3\common\derby\lib\derbyclient.jar;C:\Oracle\Middleware\wlserver_10.3\server\lib\xqrl.jar
.
PATH=C:\Oracle\Middleware\patch_wls1035\profiles\default\native;C:\Oracle\Middleware\patch_jdev1112\p
rofiles\default\native;C:\Oracle\Middleware\wlserver_10.3\server\native\win\32;C:\Oracle\Middleware\w
lserver_10.3\server\bin;C:\Oracle\Middleware\modules\org.apache.ant_1.7.1\bin;C:\PROGRA~1\Java\jdk1.7
.0_67\jre\bin;C:\PROGRA~1\Java\jdk1.7.0_67\bin;E:\DB\app\oracle\product\11.2.0\server\bin;;c:\Program
Files\RSA SecurID Token Common;C:\Program Files\Intel\iCLS
Client\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell
\v1.0\;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program
Files\Intel\Intel(R) Management Engine Components\IPT;C:\Program
Files\Java\jdk1.7.0_67\bin;C:\Oracle\Middleware\wlserver_10.3\server\native\win\32\oci920_8
.
***************************************************
* To start WebLogic Server, use a username and *
* password assigned to an admin-level user. For *
* server administration, use the WebLogic Server *
* console at http:\\hostname:port\console *
***************************************************
starting weblogic with Java version:
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Unrecognized option: -jrockit
Starting WLS with line:
C:\PROGRA~1\Java\jdk1.7.0_67\bin\java -jrockit -Xms256m -Xmx512m -Dweblogic.Name=DefaultServer
-Djava.security.policy=C:\Oracle\Middleware\wlserver_10.3\server\lib\weblogic.policy -
Djavax.net.ssl.trustStore=C:\Users\inatar\AppData\Local\Temp\trustStore8547229804589400188.jks -
Doracle.jdeveloper.adrs=true -Dweblogic.nodemanager.ServiceEnabled=true -Xverify:none -da -
Dplatform.home=C:\Oracle\Middleware\wlserver_10.3 -
Dwls.home=C:\Oracle\Middleware\wlserver_10.3\server -
Dweblogic.home=C:\Oracle\Middleware\wlserver_10.3\server -Djps.app.credential.overwrite.allowed=true
-Dcommon.components.home=C:\Oracle\Middleware\oracle_common -Djrf.version=11.1.1 -
Dorg.apache.commons.logging.Log=org.apache.commons.logging.impl.Jdk14Logger -
Ddomain.home=C:\Users\inatar\AppData\Roaming\JDeveloper\system11.1.2.4.39.64.36.1\DefaultDomain -
Djrockit.optfile=C:\Oracle\Middleware\oracle_common\modules\oracle.jrf_11.1.1\jrocket_optfile.txt -
Doracle.server.config.dir=C:\Users\inatar\AppData\Roaming\JDeveloper\system11.1.2.4.39.64.36.1\Defaul
tDomain\config\fmwconfig\servers\DefaultServer -
Doracle.domain.config.dir=C:\Users\inatar\AppData\Roaming\JDeveloper\system11.1.2.4.39.64.36.1\Defaul
tDomain\config\fmwconfig -
Digf.arisidbeans.carmlloc=C:\Users\inatar\AppData\Roaming\JDeveloper\system11.1.2.4.39.64.36.1\Defaul
tDomain\config\fmwconfig\carml -
Digf.arisidstack.home=C:\Users\inatar\AppData\Roaming\JDeveloper\system11.1.2.4.39.64.36.1\DefaultDom
ain\config\fmwconfig\arisidprovider -
Doracle.security.jps.config=C:\Users\inatar\AppData\Roaming\JDeveloper\system11.1.2.4.39.64.36.1\Defa
ultDomain\config\fmwconfig\jps-config.xml -
Doracle.deployed.app.dir=C:\Users\inatar\AppData\Roaming\JDeveloper\system11.1.2.4.39.64.36.1\Default
Domain\servers\DefaultServer\tmp\_WL_user -Doracle.deployed.app.ext=\- -
Dweblogic.alternateTypesDirectory=C:\Oracle\Middleware\oracle_common\modules\oracle.ossoiap_11.1.1,C:
\Oracle\Middleware\oracle_common\modules\oracle.oamprovider_11.1.1 -
Djava.protocol.handler.pkgs=oracle.mds.net.protocol -Dweblogic.jdbc.remoteEnabled=false -
Dwsm.repository.path=C:\Users\inatar\AppData\Roaming\JDeveloper\system11.1.2.4.39.64.36.1\DefaultDoma
in\oracle\store\gmds -Dweblogic.management.discover=true -Dwlw.iterativeDev= - Dwlw.testConsole= -
Dwlw.logErrorsToConsole= -
Dweblogic.ext.dirs=C:\Oracle\Middleware\patch_wls1035\profiles\default\sysext_manifest_classpath;C:\O
racle\Middleware\patch_jdev1112\profiles\default\sysext_manifest_classpath weblogic.Server
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Unrecognized option: -jrockit
Process exited.
Unrecognized option: -jrockit Process exited. is the critical error. -jrockit is not an option available to the standard java jdk.
e.g. C:\PROGRA~1\Java\jdk1.7.0_67\bin\java -jrockit is the issue
Your JAVA_VENDOR is being set incorrectly in your setDomainEnv.cmd or startWebLogic.cmd script. It's being set to Oracle but should be set to Sun. You either need to figure out how that environment variable is being set incorrectly or manually fix one of the two .cmd files.
My last post was bad!
Here is the unwrapped set of lines I added:
echo "==> Force JAVA_VM to use -server:"
JAVA_VM=-server
export JAVA_VM
echo "."
echo "."
echo "JAVA Machine: ${JAVA_VM}"
THIS ISSUE IS RESOLVED FOR ME. I JUST WANTED TO POST THE SOLUTION SOMEWHERE...
I was working through exercise 1 on the NoSQL intro: http://www.oracle.com/technetwork/topics/bigdata/articles/intro-to-oracle-nosql-db-hol-1937059.pdf
I tried to deploy the Movieplex application to JDeveloper's internal weblogic server but kept getting hit with a -jrockit VM not found. This was difficult for me to get fixed because: 1 - I am not a heavy java programmer, and 2 - I apparently do not read very well. As for point 1, JRockit is an optimized special JAVA VM that some folks use. You can look that up oon line I guess, but it looks like we do not need it for this tutorial. As for point 2, I spent hours (I ashamedly admit) trying to figure out what .sh scripts were being run to start the Weblogic server running. I did all sorts of find commands, hunted through the binaries and folders underneath the Middleware folders. In the end, all I has to do was read the output log carefully, the script for me is: /home/oracle/.jdeveloper/system11.1.1.6.38.61.92/DefaultDomain/bin/startWebLogic.sh.
I edited the script REPLACING line 129 with below:
echo "==> Force JAVA_VM to use -server:"
JAVA_VM=-server
export JAVA_VM
echo "."
echo "."
echo "JAVA Machine: ${JAVA_VM}"
NOTE: there is another shell script that may be involved, /home/oracle/.jdeveloper/system11.1.1.6.38.61.92/Default/init-info/Domain
I connected hive, and when I try to show all databases using command below, I get the following error,:
techgene#slaveone:~/apps/hive-0.12.0$ hive
Logging initialized using configuration in jar:file:/home/techgene/apps/hive-0.12.0/lib/hive-common-0.12.0.jar!/hive-log4j.properties
hive> show databases;
FAILED: Execution Error, return code 1 from org.apache.hadoop.hive.ql.exec.DDLTask. java.lang.RuntimeException: Unable to instantiate org.apache.hadoop.hive.metastore.HiveMetaStoreClient
Can you please provide a solution for this?
This problem usually occurs when hive CLI session is improperly ended. In such case, kill the improperly closed hive CLI session as follows. After this launch hive CLI fresh.
ramisetty#aspire:~$ jps
3710 SecondaryNameNode
4103 RunJar -------------------------> hive CLI instance.
4019 TaskTracker
3467 DataNode
3242 NameNode
4366 Jps
3788 JobTracker
ramisetty#aspire:~$ kill -9 4103
ramisetty#aspire:~$
still problem persists means follow the available solutions # FAILED: Error in metadata: java.lang.RuntimeException: Unable to instantiate org.apache.hadoop.hive.metastore.HiveMetaStoreClient
I am setting up a GlassFish cluster following the guide at http://javadude.wordpress.com/2011/04/25/glassfish-3-1-clustering-tutorial/. I started from fresh installs of GlassFish 3.1.1. I also have the same architecture as in the guide: two nodes with one instance each. The DAS is on node1.
I've tried starting from scratch several times and am able to create the cluster, nodes and instances without issue. I also have the DAS communicating with node2 via SSH. However, each time when I get to the point where I attempt to start instance2 it fails:
$ ./asadmin start-local-instance --node node1 --sync normal instance2
Previous synchronization failed at Feb 23, 2012 2:41:53 PM
Will perform full synchronization.
Removing all cached state for instance instance2.
CLI802 Synchronization failed for directory config, caused by:
javax.xml.bind.JAXBException
- with linked exception:
[java.lang.ClassNotFoundException: com.sun.xml.bind.v2.ContextFactory]
Command start-local-instance failed.
I spent the day Googling and searching GlassFish's Jira, but couldn't find a solution to this issue. I'd very much appreciate any ideas you have on how to solve this problem.
My operating system is CentOS 5.7 and my Java version is 1.6.0_20
Unfortunately my instance directory is empty, I'm assuming because it never started. So there is no log file. I set AS_DEBUG=true but it gives no stack trace. The last debug lines before the error are
Removing all cached state for instance instance2.
Removing: /usr/local/glassfish3_1_1/glassfish/nodes/blade-50/instance2/config
Removing: /usr/local/glassfish3_1_1/glassfish/nodes/blade-50/instance2/applications
Removing: /usr/local/glassfish3_1_1/glassfish/nodes/blade-50/instance2/generated
Removing: /usr/local/glassfish3_1_1/glassfish/nodes/blade-50/instance2/lib
Removing: /usr/local/glassfish3_1_1/glassfish/nodes/blade-50/instance2/docroot
Got exception: javax.xml.bind.JAXBException
Acting on a tip from a user in the Glassfish forum, I learned that Java 1.6.0_20 is an older release of Java that is not supported by Glassfish 3.1.1. I worked with a sysadmin to get Java 1.6.0_31 installed on both nodes of the cluster and that did the trick--both instances start up without errors.