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.
- If you are using some other shell such as tcsh, you can switch to bash in your current session by typing "bash" in your terminal.
- If you wish to switch permanently to Bash as your default shell here are some instructions:
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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MATLAB
Installation
For MATLAB admins (epicsmgr group members) only:
- New versions (versions later than 2012a) of MATLAB should be installed in the 3rd-party software package area under the matlab folder:
- Development: /afs/slac/g/lcls/package/matlab
- Production: /usr/local/lcls/package/matlab - Inside the matlab directory, versions should be installed in folders that correspond to their MATLAB version, e.g. 2012a, 2019a, 2020a, 2022b, etc.
At the time of this writing, the latest version of MATLAB deployed for LCLS Development and Production is 2022b.
Individual AFS user accounts in the LCLS Development environment default to set up and use MATLAB 2012a unless overridden.
The default MATLAB versions for shared login accounts in Production are as follows:
| Account | Default MATLAB version |
|---|---|
| physics | 2012a |
| softegr | 2019a |
| laci | 2012a |
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.
- Development Environment
/afs/slac/g/lcls/package/matlab/2012a
- Production Environment
- /usr/local/lcls/package/matlab/2012a
- In production, make sure to copy the licenses folder from other MATLAB version:
/usr/local/lcls/package/matlab/2012a/licenses
Running MATLAB
In order to set up your environment to use MATLAB R2012a, follow one of the appropriate procedures below.
2012a
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
Configuring MATLAB
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:
- Parameters for the Java JVM that runs inside of MATLAB are configured via a java.opts file
- The classpath is configured via a classpath.txt file
- The library search path is configured via a librarypath.txt file
For questions on the installation and deployment of MATLAB in Development or Production, please contact:
- Kuktae Kim (TID-ACS)
- Pascual, Patrick James (EED Systems Group)
java.opts
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.
2012a
Development
-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
Production
-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
classpath.txt
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.
2012a
Development
# 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
Production
# 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
librarypath.txt
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.
2012
Development
/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
Production
/usr/local/lcls/epics/extensions/extensions-R3-14-12/lib/linux-x86 /usr/local/lcls/epics/base/base-R3-14-12/lib/linux-x86
Creating A Custom MATLAB Environment
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.
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