Regarding the issue I mentionned in 2011, I followed the instructions and ps -ef | grep jetty showed two process. (one being the command grep jetty command itself)
See below: --- root 4462 4459 2 18:35 pts/0 00:00:20 /home/krue/bin/jdk1-7/jdk1.7.0_07/jre/bin/java -Xmx2048m -Xms1024m -cp :lib/abbot.jar:lib/activation.jar:lib/ant4eclipse.jar:lib/ant-launcher.jar:lib/aopalliance.jar:lib/arq-2.8.7.jar:lib/asm-3.1.jar:lib/batik-anim.jar:lib/batik-awt-util.jar:lib/batik-css.jar:lib/batik-dom.jar:lib/batik-ext.jar:lib/batik-gui-util.jar:lib/batik-gvt.jar:lib/batik-parser.jar:lib/batik-svg-dom.jar:lib/batik-svggen.jar:lib/batik-util.jar:lib/batik-xml.jar:lib/biomart-0.8.jar:lib/biomart-string2longset.jar:lib/bsh-2.0b4.jar:lib/colt-1.2.0.jar:lib/commons-beanutils-1.7.jar:lib/commons-codec-1.3.jar:lib/commons-collections.jar:lib/commons-dbcp-1.2.2.jar:lib/commons-fileupload-1.2.1.jar:lib/commons-httpclient-3.0.1.jar:lib/commons-io-1.4.jar:lib/commons-lang.jar:lib/commons-logging-1.1.1.jar:lib/commons-pool-1.5.2.jar:lib/core-3.1.1.jar:lib/costello.jar:lib/db2jcc4.jar:lib/dna-common-0.6.jar:lib/dsn.jar:lib/ecp1_0beta.jar:lib/ensj.jar:lib/ensj-util.jar:lib/epsgraphics2d.jar:lib/ezmorph.jar:lib/gmbal-api-only.jar:lib/gnu-regexp-1.1.0.jar:lib/guava-r09.jar:lib/guice-2.0.jar:lib/guicemanaged-0.4.jar:lib/guice-servlet-2.0.jar:lib/httpclient-4.0.jar:lib/httpcore-4.0.1.jar:lib/icgc.jar:lib/icu4j-3.4.4.jar:lib/idw-gpl.jar:lib/imap.jar:lib/iri-0.8.jar:lib/iText-5.0.4.jar:lib/jackson-core-asl-1.4.0.jar:lib/jackson-jaxrs-1.4.0.jar:lib/jackson-mapper-asl-1.4.0.jar:lib/jackson-xc-1.4.0.jar:lib/jai_imageio.jar:lib/java-getopt-1.0.9.jar:lib/jaxb-api.jar:lib/jaxb-impl.jar:lib/jaxws-api.jar:lib/jaxws-rt.jar:lib/jcommon-1.0.16.jar:lib/jconsole.jar:lib/jdbc2_0-stdext.jar:lib/jdom-1.0.jar:lib/je-4.0.103.jar:lib/jena-2.6.4.jar:lib/jena-2.6.4-tests.jar:lib/jersey-bundle-1.4-SNAPSHOT.jar:lib/jersey-guice-1.4.jar:lib/jetty-6.1.23.jar:lib/jetty-j2se6-6.1.26.jar:lib/jetty-session-ext.jar:lib/jetty-setuid-6.1.23.jar:lib/jetty-util-6.1.23.jar:lib/jfreechart-1.0.13.jar:lib/jline.jar:lib/jopt-simple-3.1.jar:lib/jsp-2.1-glassfish-9.1.1.B60.25.p2.jar:lib/jsp-2.1-jetty-6.1.23.jar:lib/jsp-api-2.1-glassfish-9.1.1.B60.25.p2.jar:lib/jsr305.jar:lib/jsr311-api-1.1.1.jar:lib/jstl-api-1.2.jar:lib/jstl-impl-1.2.jar:lib/junit-4.8.2.jar:lib/jython.jar:lib/libreadline-java.jar:lib/lingpipe-3.8.2.jar:lib/log4j-1.2.15.jar:lib/lucene-core-2.3.1.jar:lib/mailapi.jar:lib/management-api.jar:lib/mysql-connector-java-5.1.15-bin.jar:lib/nekohtml-1.9.7.jar:lib/oauth-java-20100819.jar:lib/ojdbc5.jar:lib/opencsv-2.1.jar:lib/openid4java-0.9.7-SNAPSHOT-20110525-jhsu.jar:lib/optional.jar:lib/p6spy.jar:lib/policy.jar:lib/pop3.jar:lib/postgresql-9.0-801.jdbc4.jar:lib/salma-hayek.jar:lib/scribe-1.0.3.jar:lib/servlet-api-2.5.jar:lib/slf4j-api-1.5.11.jar:lib/slf4j-nop-1.5.11.jar:lib/smtp.jar:lib/sqljdbc4.jar:lib/stax-api-1.0.1.jar:lib/stax-ex.jar:lib/streambuffer.jar:lib/velocity-1.6.2.jar:lib/voldemort-0.81.jar:lib/wstx-asl-3.2.9.jar:lib/xalan.jar:lib/xercesImpl.jar:lib/xml-apis-ext.jar:lib/xml-apis.jar:lib/zzNetBoxDependencies.jar:lib/zzNetBoxModified.jar org.biomart.configurator.test.MartConfigurator krue 4635 4630 0 18:50 pts/2 00:00:00 grep jetty --- On 02/10/2012, Kevin Rue <[email protected]> wrote: > Hi, > > i just installed Biomart 0.8 candidate 6 and tried to deploy the quick > start example. I saw a similar issue posted in March 2011 > (https://lists.biomart.org/pipermail/users/2011-March/001405.html) > > Whenever I click Start Server, I see the loading bar, but then I > constantly wait 2minutes until an error message like "timeout, server > took more than 2 minutes to start, exiting now" (not the exact > message) > > Here is a copy of the messages in the terminal: > ---- > animalgenomics:/home/krue/bin/biomart/release-0_8-candidate_6# > ./dist/scripts/martconfigurator.sh > Starting MartConfigurator please wait .... > [AWT-EventQueue-0] INFO martconfigurator - ...martconfigurator started. > [AWT-EventQueue-0] INFO martconfigurator - Loading resources from > org/biomart/configurator/resources/messages > [AWT-EventQueue-0] INFO martconfigurator - Done loading resources > [AWT-EventQueue-0] INFO martconfigurator - Done loading settings > [SwingWorker-pool-1-thread-1] INFO martconfigurator - Done saving settings > [Thread-6] INFO martconfigurator - ./scripts/biomart-server.sh stop > [Thread-6] INFO martconfigurator - stop exitValue: 0 > [Thread-6] INFO martconfigurator - ./scripts/biomart-server.sh start > [Thread-6] INFO martconfigurator - <Info> > [Thread-6] INFO martconfigurator - Invalid maximum heap size: -Xmx4096m > [Thread-6] INFO martconfigurator - The specified size exceeds the > maximum representable size. > [Thread-6] INFO martconfigurator - </Info> > [Thread-6] INFO martconfigurator - start exitValue: 0 > ---- > > Nothing shows up on port 9000 after the two minutes. Although the > button now offers "Stop Server". > I did point to the xml file and the registry key. > I tried to run MartConfigurator as superuser to avoid access right > limitations. > > Any idea? > Thanks in advance, > -- > Kévin RUE-ALBRECHT > Computational Infection Biology PhD Programme > University College Dublin > Ireland > http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en > -- Kévin RUE-ALBRECHT Computational Infection Biology PhD Programme University College Dublin Ireland http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
