# define arguments
mainclass=cbit.vcell.solver.test.HybridSolverTester
jvmmem=-Xmx1000M
siteResDir=/share/apps/vcell/deployed/test/resources

# add gcc and sonic to path
export PATH=/share/apps/vcell/deployed/test/lib:$PATH
export LD_LIBRARY_PATH=/share/apps/vcell/deployed/test/lib


jre=java 
jvm_jars=${siteResDir}/vcellAll.jar:${siteResDir}/bioformats.jar:${siteResDir}/jta.jar:${siteResDir}/activemq-core-5.6.0.jar:${siteResDir}/camel-jms-2.9.2.jar:${siteResDir}/geronimo-j2ee-management_1.1_spec-1.0.1.jar:${siteResDir}/geronimo-jms_1.1_spec-1.1.1.jar:${siteResDir}/geronimo-jta_1.0.1B_spec-1.0.1.jar:${siteResDir}/slf4j-api-1.6.4.jar:${siteResDir}/slf4j-log4j12-1.6.4.jar:${siteResDir}/log4j-1.2.16.jar:${siteResDir}/kahadb-5.6.0.jar:${siteResDir}/xercesImpl-2.7.1.jar:${siteResDir}/icu4j-3.4.4.jar:${siteResDir}/iri-0.7.jar:${siteResDir}/lucene-core-2.3.1.jar:${siteResDir}/stax-api-1.0.1.jar:${siteResDir}/wstx-asl-3.2.9.jar:${siteResDir}/xml-apis.jar:${siteResDir}/new_activation.jar:${siteResDir}/NetCDF2_2_20_VCell.jar:${siteResDir}/new_mail.jar:${siteResDir}/GlgGraphLayoutNG.jar:${siteResDir}/thirdParty.jar:${siteResDir}/sonic_Client.jar:${siteResDir}/sonic_XA.jar:${siteResDir}/sonic_Crypto.jar:${siteResDir}/sonic_Selector.jar:${siteResDir}/jai_codec.jar:${siteResDir}/jai_core.jar:${siteResDir}/jdom_1.0.jar:${siteResDir}/js.jar:${siteResDir}/script-api.jar:${siteResDir}/script-js.jar:${siteResDir}/sesame-rio-turtle-2.6.2.jar:${siteResDir}/sesame-util-2.6.2.jar:${siteResDir}/apache_commons_math_2.2.jar:${siteResDir}/ojdbc5.jar:${siteResDir}/libsbmlj.jar:${siteResDir}/jmf.jar:${siteResDir}/axis.jar:${siteResDir}/jaxrpc.jar:${siteResDir}/commons-discovery-0.2.jar:${siteResDir}/commons-logging-1.0.4.jar:${siteResDir}/wsdl4j-1.5.1.jar:${siteResDir}/jhall.jar:${siteResDir}/netty-3.2.5.Final.jar:${siteResDir}/sesame-model-2.6.2.jar:${siteResDir}/sesame-rio-api-2.6.2.jar:${siteResDir}/sesame-rio-n3-2.6.2.jar:${siteResDir}/sesame-rio-rdfxml-2.6.2.jar:${siteResDir}/jamtio.jar:${siteResDir}/jhdf5.jar:${siteResDir}/jhdf5obj.jar:${siteResDir}/jhdfobj.jar:${siteResDir}/mongo-2.8.0.jar:${siteResDir}/ucp.jar:${siteResDir}/ucpdemos.jar:${siteResDir}/bcprov-jdk15on-147.jar:${siteResDir}/sshj-0.8.1.jar:/share/apps/vcell/deployed/test/testHybrid/cbit/vcell/resource/linux:/share/apps/vcell/deployed/test/numerics/cmake-build/bin
#:${localServiceDir}/.jar

# arguments=/share/apps/vcell/users/liye/SimID_xxxx_.vcml 1 1000 U_average:G0_total
echo "starting hybrid solver ..."
echo ${jre} -cp ${jvm_jars} -Dvcell.finiteVolumeExecutableProperty=/share/apps/vcell/deployed/test/numerics/cmake-build/bin/FiniteVolume_x64 ${mainclass} $@
nice ${jre} -cp ${jvm_jars} -Dvcell.finiteVolumeExecutableProperty=/share/apps/vcell/deployed/test/numerics/cmake-build/bin/FiniteVolume_x64 ${mainclass} $@
#echo ${jre} -cp ${jvm_jars} ${mainclass} $@
#nice ${jre} -cp ${jvm_jars} ${mainclass} $@

exit 0


