This page contains information about using EPICS with MATLAB R2012a and Java in the LCLS Development and Production environments.
Attention:
All scripts in this page are assuming that your current shell is Bash.
In order to change your default shell at login from tcsh (or any other shell) to Bash, please execute the following command on a Linux server on the AFS network, such as a rhel6-64* node. (You will be prompted for your password during this process):
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After that, close the terminal and open a new one. You will be using Bash as the default shell.
You can check if all went well with the following command in a new Terminal window:
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For MATLAB admins (epicsmgr group members) only:
At the time of this writing, the latest version of MATLAB deployed for LCLS Development and Production is 2023a.
Individual AFS user accounts in the LCLS Development environment default to set up and use MATLAB 2020a unless overridden.
The default MATLAB versions for shared login accounts in Production are as follows:
Account | Default MATLAB version |
---|---|
physics | 2020a |
softegr | 2020a |
laci | 2012a |
This is 32-bit software and will no longer be supported with OS versions later than RHEL6.
The Java version used by this Matlab is Java 6.
/afs/slac/g/lcls/package/matlab/2012a
In order to set up your environment to use MATLAB R2012a, follow one of the appropriate procedures below.
Development
Do not run MATLAB instances on mcclogin or lcls-prod02. MATLAB should be run on mcc-simul in DEV.
$ source /afs/slac/g/lcls/epics/setup/epicsenv-3.14.12.bash $ source /afs/slac/g/lcls/tools/oracle/oracleSetup_11g.bash $ source /afs/slac/g/lcls/tools/matlab/setup/matlabSetup_dev.bash # Launch in desktop mode: $ matlab & # Launch in terminal mode: $ run_matlab.bash --matlab=2012a
Production
$ source /usr/local/lcls/tools/script/ENVS.bash # Launch in desktop mode: $ matlab & # Launch in terminal mode: $ run_matlab.bash --matlab=2012a
For the Development and Production environments, a set of working configuration files is already provided for users and invoked upon login. Users can override the usage of these files by having their own custom files in the folder where they launch MATLAB (see: Creating A Custom MATLAB Environment).
MATLAB is non-standard Unix software and does not adhere to values set by PATH, LD_LIBRARY_PATH, CLASSPATH, and other global environment variables that are used by most other Unix software. Instead, MATLAB uses the following configuration files to set its environment:
For questions on the installation and deployment of MATLAB in Development or Production, please contact:
Description: This file is used to pass variables and configurations to the Java JVM used by MATLAB.
Location:
<matlabroot>/bin/<architecture>/java.opts
e.g., in Development environment: /afs/slac/g/lcls/package/matlab/2019a/bin/glnxa64/java.opts
Below are the working java.opts files for Development and Production.
-Xbootclasspath/p:/afs/slac/g/lcls/package/iona/orbacus/prod/JOB/lib/OB.jar -DAIDA_NAMESERVER_IOR_URL=http://mccas0.slac.stanford.edu/aida/NameServerPROD.ior -DOOC_COSEVENTCONFIG_PATHNAME=/afs/slac/g/lcls/package/err/common/script/ooc_CosEvent_server.conf -DAIDA_CLIENT_TIMEOUT=90 -DEPICS_PVA_SERVER_PORT=5075 -DEPICS_PVA_BROADCAST_PORT=5076 -DEPICS_PVA_AUTO_ADDR_LIST=FALSE -DEPICS_PVA_ADDR_LIST=134.79.219.255 lcls-dev1.slac.stanford.edu mcc-simul.slac.stanford.edu -Dcom.cosylab.epics.caj.CAJContext.addr_list=134.79.219.255 172.26.97.63 -Dcom.cosylab.epics.caj.CAJContext.auto_addr_list=false -Dcom.cosylab.epics.caj.CAJContext.max_array_bytes=80000000 -Dcom.cosylab.epics.caj.CAJContext.repeater_port=5067 -Dcom.cosylab.epics.caj.CAJContext.server_port=5066
-Xbootclasspath/p:/usr/local/lcls/package/iona/orbacus/prod/JOB/lib/OB.jar -DAIDA_NAMESERVER_IOR_URL=http://mccas0.slac.stanford.edu/aida/NameServerPROD.ior -DOOC_COSEVENTCONFIG_PATHNAME=/u1/lcls/tools/orbacus/ooc_CosEvent_server.conf -DAIDA_CLIENT_TIMEOUT=90 -DEPICS_PVA_SERVER_PORT=5075 -DEPICS_PVA_BROADCAST_PORT=5076 -DEPICS_PVA_AUTO_ADDR_LIST=FALSE -DEPICS_PVA_ADDR_LIST=172.27.3.255 172.27.131.255 172.27.43.255 172.21.40.63 mcc-dmz mccas0.slac.stanford.edu -Dcom.cosylab.epics.caj.CAJContext.addr_list=172.27.3.255:5068 mcc-dmz 172.21.40.63:5064 172.27.72.24:5070 172.27.131.255:5068 172.27.43.255:5068 -Dcom.cosylab.epics.caj.CAJContext.auto_addr_list=false -Dcom.cosylab.epics.caj.CAJContext.max_array_bytes=80000000 -Dcom.cosylab.epics.caj.CAJContext.repeater_port=5069 -Dcom.cosylab.epics.caj.CAJContext.server_port=5068
Description: This file is used to augment the Java classpath used by MATLAB.
Location:
<matlabroot>/toolbox/local/classpath.txt
e.g., in the Development environment: /afs/slac/g/lcls/package/matlab/2019a/toolbox/local/classpath.txt
Below are the working changes to the default MATLAB classpath.txt files for Development and Production.
The lines listed for each file below must be APPENDED to the end of the existing default MATLAB classpath.txt file for the configuration to work. Do not remove the preceding lines in the default MATLAB classpath.txt file.
# Additions to classpath.txt /afs/slac/g/lcls/package/oracle/product/11.1.0.6/client/jdbc/lib/ojdbc5.jar /afs/slac/g/lcls/package/iona/orbacus/prod/JOB/lib/OB.jar /afs/slac/g/lcls/package/iona/orbacus/prod/JOB/lib/OBEvent.jar /afs/slac/g/lcls/package/iona/orbacus/prod/JOB/lib/OBUtil.jar /afs/slac/g/lcls/physics/package/except/lib/except.jar /afs/slac/g/lcls/physics/package/err/lib/err.jar /afs/slac/g/lcls/physics/package/aida/lib/aida.jar /afs/slac/g/lcls/physics/release/hlaExtensions/hlaExtensions-R1-2-13/jar/hlaExtensions.jar /afs/slac/g/lcls/physics/release/xal4lcls-R0-8-4A/build/jar/ext.jar /afs/slac/g/lcls/physics/release/xal4lcls-R0-8-4A/build/jar/xal.jar /afs/slac/g/lcls/physics/release/hlaCommon/hlaCommon-R1-0-16/jar/hlaCommon.jar /afs/slac/g/lcls/epics/extensions/extensions-R3-14-12/lib/linux-x86 #/usr/local/facet/tools/matlab/sdds/java/SDDS.jar /afs/slac/g/lcls/physics/release/MessageLogAPI-R0-0-1A/jar/MessageLogAPI.jar # integration with EPICSv4 (greg) # Note that the following MUST be compiled so as to target a Java 6 compiler at most, # since matlab 2012b of LCLS is shipped with Java 6. pvAccess as shipped requires Java 7. # But we use a special source version, adapted by Matej to compile under java 6. /afs/slac/g/lcls/epics/base/base-java6-R4-4-0/easyPVAJava-0.4.3.jar /afs/slac/g/lcls/epics/base/base-java6-R4-4-0/pvAccessJava-4.2.0-Java6-SNAPSHOT.jar /afs/slac/g/lcls/epics/base/base-java6-R4-4-0/pvDataJava-4.0.2.jar
# Additions to classpath.txt /usr/local/lcls/package/oracle/product/11.1.0.6/client/jdbc/lib/ojdbc5.jar /usr/local/lcls/package/iona/orbacus/prod/JOB/lib/OB.jar /usr/local/lcls/package/iona/orbacus/prod/JOB/lib/OBEvent.jar /usr/local/lcls/package/iona/orbacus/prod/JOB/lib/OBUtil.jar /usr/local/lcls/physics/package/except/lib/except.jar /usr/local/lcls/physics/package/err/lib/err.jar /usr/local/lcls/physics/package/aida/lib/aida.jar /usr/local/lcls/physics/release/hlaExtensions/hlaExtensions-R1-2-13/jar/hlaExtensions.jar /usr/local/lcls/physics/release/xal4lcls-R0-8-4A/build/jar/ext.jar /usr/local/lcls/physics/release/xal4lcls-R0-8-4A/build/jar/xal.jar /usr/local/lcls/physics/release/hlaCommon/hlaCommon-R1-0-16/jar/hlaCommon.jar /usr/local/lcls/epics/extensions/extensions-R3-14-12/lib/linux-x86 /usr/local/facet/tools/matlab/sdds/java/SDDS.jar /usr/local/lcls/physics/release/MessageLogAPI-R0-0-1A/jar/MessageLogAPI.jar # integration with EPICSv4 (greg) # Note that the following MUST be compiled so as to target a Java 6 compiler at most, # since matlab 2012b of LCLS is shipped with Java 6. pvAccess as shipped requires Java 7. # But we use a special source version, adapted by Matej to compile under java 6. /usr/local/lcls/epics/base/base-java6-R4-4-0/easyPVAJava-0.4.3.jar /usr/local/lcls/epics/base/base-java6-R4-4-0/pvAccessJava-4.2.0-Java6-SNAPSHOT.jar /usr/local/lcls/epics/base/base-java6-R4-4-0/pvDataJava-4.0.2.jar
Description: This file is used to augment the library search path used by MATLAB.
Location:
<matlabroot>/toolbox/local/librarypath.txt
e.g., in Development environment: /afs/slac/g/lcls/package/matlab/2019a/toolbox/local/librarypath.txt
Below are the working librarypath.txt files for Development and Production.
The lines listed for each file below must be APPENDED to the end of the existing default MATLAB librarypath.txt file for the configuration to work. Do not remove the preceding lines in the default MATLAB librarypath.txt file.
/afs/slac/g/lcls/epics/extensions/extensions-R3-14-12/lib/linux-x86 /afs/slac/g/lcls/epics/base/base-R3-14-12/lib/linux-x86
/usr/local/lcls/epics/extensions/extensions-R3-14-12/lib/linux-x86 /usr/local/lcls/epics/base/base-R3-14-12/lib/linux-x86
If you need to use a MATLAB environment configuration that does not match the default environment provided in Development or Production, you will need to create your own java.opts, classpath.txt or librarypath.txt files in your working directory prior to launching MATLAB.
It is strongly recommended to only override the files needed in your local workspace, since MATLAB will inspect your current working directory before looking at the global configuration files.
If you need to connect to a different set of EPICS servers, copy the java.opts file from one of the locations above to your local working directory and modify it according to your needs.
If you need to test a new JAR file, copy the classpath.txt file from one of the locations above to your local working directory and modify it according to your needs.
If you need to test a new library to add to the library path, copy the librarypath.txt file from one of the locations above to your local working directory and modify it according to your needs.
Never try to modify the existing global configuration files. If you need changes made to the global configuration files, consult the MATLAB admins for LCLS Development and Production (TID-ACS and EED Systems Group). Any changes to the global MATLAB configuration must be approved and implemented by those groups.