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Warning

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):

ypchsh -s /bin/bash

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:

echo $SHELL

Anchor
java_top
java_top
Java

At the time of this writing, the latest version of Java available in Development and Production is 1.8.0_181 (64-bit). In order to use this Java version, source the following scripts depending on your environment:

...

Note

For Oracle compatibility, the Oracle client used must also be compiled for 64-bit. In order to use the supported 64-bit Oracle client, source the following scripts depending on your environment:

  • Development
    /afs/slac/g/lcls/tools/oracle/oracleSetup-R11.2.0.4.bash
  • Production
    /usr/local/lcls/tools/oracle/oracleSetup-R11.2.0.4.bash

EPICS Java APIs

The EPICS Java APIs are located at:

...

  • epicsCoreJava
    Includes EPICS 7 (pvaccess, ntypes, pvdata) and JCA libraries
  • pvaClientJava
    Inlcudes pvaClientJava library developed by Marty Kraimer
  • phoebus
    This repository contains the whole phoebus code (replacement for the CS-Studio backend) but it also contains the new pva client library developed by Kay Kasemir.

  • pva
    Includes the pva library

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matlab_top
matlab_top
MATLAB

Anchor
matlab_installation
matlab_installation
Installation

For MATLAB admins (epicsmgr group members) only:

...

AccountDefault MATLAB version
physics2012a
softegr2019a
laci2012a

Anchor
matlab_2012a_installation
matlab_2012a_installation
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/matlab/2012a

Anchor
matlab_2019a_installation
matlab_2019a_installation
2019a

This is 64-bit software.
The Java version used by this Matlab is Java 8.

  • Development
    /afs/slac/g/lcls/package/matlab/2019a
  • Production
    /usr/local/lcls/package/matlab/2019a

Anchor
matlab_2020a_installation
matlab_2020a_installation
2020a

This is 64-bit software.
The Java version used by this Matlab is Java 8.

  • Development
    /afs/slac/g/lcls/package/matlab/2020a
  • Production
    /usr/local/lcls/package/matlab/2020a

Anchor
running_matlab
running_matlab
Running MATLAB

In order to set up your environment to use one of the supported versions of MATLAB, follow one of the appropriate procedures below.

Anchor
running_matlab_2012a
running_matlab_2012a
2012a

  • Development

    Warning

    Do not run MATLAB instances on mcclogin or lcls-prod02. MATLAB should be run on mcc-simul in DEV.

    Code Block
    languagebash
    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

    Code Block
    languagebash
    source /usr/local/lcls/tools/script/ENVS.bash
    
    # Launch in desktop mode: 
    matlab &
    
    # Launch in terminal mode:
    run_matlab.bash --matlab=2012a

Anchor
running_matlab_2019a
running_matlab_2019a
2019a

  • Development

    Warning

    Do not run MATLAB instances on mcclogin or lcls-prod02. MATLAB should be run on mcc-simul in DEV.

    Code Block
    languagebash
    source /afs/slac/g/lcls/epics/setup/epicsenv-7.0.2-1.0.bash
    source /afs/slac/g/lcls/tools/oracle/oracleSetup-R11.2.0.4.bash
    export MATLAB_VER=2019a  export MLM_LICENSE_FILE="27010@license1,27010@license2,27010@license3" 
    source /afs/slac/g/lcls/tools/matlab/setup/matlabSetup64.bash
    
    # Launch in desktop mode: 
    matlab &
    
    # Launch in terminal mode: 
    run_matlab.bash --matlab=2019a



  • Production

    Code Block
    languagebash
    source /usr/local/lcls/epics/setup/epicsenv-7.0.2-1.0.bash
    source /usr/local/lcls/tools/oracle/oracleSetup-R11.2.0.4.bash
    export MATLAB_VER=2019a 
    source /usr/local/lcls/tools/matlab/setup/matlabSetup64.bash
    
    # Launch in desktop mode: 
    matlab &
    
    # Launch in terminal mode: 
    run_matlab.bash --matlab=2019a

Anchor
running_matlab_2020a
running_matlab_2020a
2020a

  • Development

    Warning

    Do not run MATLAB instances on mcclogin or lcls-prod02. MATLAB should be run on mcc-simul in DEV.

    Code Block
    languagebash
    source /afs/slac/g/lcls/epics/setup/epicsenv-7.0.2-1.0.bash
    source /afs/slac/g/lcls/tools/oracle/oracleSetup-R11.2.0.4.bash
    export MATLAB_VER=2020a   
    export MLM_LICENSE_FILE="27010@license1,27010@license2,27010@license3"
    source /afs/slac/g/lcls/tools/matlab/setup/matlabSetup64.bash
    
    # Launch in desktop mode: 
    matlab &
    
    # Launch in terminal mode: 
    run_matlab.bash --matlab=2020a
  • Production

    Code Block
    languagebash
    source /usr/local/lcls/epics/setup/epicsenv-7.0.2-1.0.bash
    source /usr/local/lcls/tools/oracle/oracleSetup-R11.2.0.4.bash
    export MATLAB_VER=2020a 
    source /usr/local/lcls/tools/matlab/setup/matlabSetup64.bash
    
    # Launch in desktop mode: 
    matlab &
    
    # Launch in terminal mode: 
    run_matlab.bash --matlab=2020a

Anchor
configuring_matlab
configuring_matlab
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:

...

Anchor
matlab_jvm
matlab_jvm
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
Code Block
languagetext
-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
Code Block
languagetext
-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

2019a and 2020a

Development
Code Block
languagetext
-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
-Dgov.aps.jca.jni.JNIContext.jca.use_env=true
-Djca.use_env=true
-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
Production
Code Block
languagetext
-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
-Dgov.aps.jca.jni.JNIContext.jca.use_env=true
-Djca.use_env=true
-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

Anchor
matlab_classpath
matlab_classpath
classpath.txt

Description: This file is used to augment the Java classpath used by MATLAB.
Location:
<matlabroot>/toolbox/local/classpath.txt
e.g., in Development environment: /afs/slac/g/lcls/package/matlab/2019a/toolbox/local/classpath.txt

...

Note

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
Code Block
languagetext
# 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
Code Block
languagetext
# 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
2019a and 2020a
Development
Code Block
languagetext
# Additions to classpath.txt
# ****************************************************************************************************************
# EPICS 7 Java Interface
# ****************************************************************************************************************
/afs/slac/g/lcls/epics/java/epicsCoreJava/R7.0.2-1.0.0/products/epics-pvdata-6.1.2.jar
/afs/slac/g/lcls/epics/java/epicsCoreJava/R7.0.2-1.0.0/products/epics-pvaccess-5.1.2.jar
/afs/slac/g/lcls/epics/java/epicsCoreJava/R7.0.2-1.0.0/products/epics-ntypes-0.3.2.jar
/afs/slac/g/lcls/epics/java/epicsCoreJava/R7.0.2-1.0.0/products/epics-util-1.0.0.jar
/afs/slac/g/lcls/epics/java/epicsCoreJava/R7.0.2-1.0.0/products/jca-2.4.2.jar
#/afs/slac/g/lcls/epics/extensions/R0.5.0/javalib/jca.jar
/afs/slac/g/lcls/epics/java/pvaClientJava/R4.3.2-0.0.1/products/epics-pvaclient-4.3.2.jar
# ****************************************************************************************************************
# ****************************************************************************************************************
# Oracle Database connectivity
# ****************************************************************************************************************
/afs/slac/g/lcls/package/oracle/product/11.2.0.4/linux-x86_64/jdbc/lib/ojdbc5.jar
# ****************************************************************************************************************
# ****************************************************************************************************************
# IONA ORBacus ==> CORBA-based Client Server API
# ****************************************************************************************************************
/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
# ****************************************************************************************************************
# ****************************************************************************************************************
# AIDA Interface
# ****************************************************************************************************************
/afs/slac/g/lcls/physics/package/aida/lib/aida.jar
/afs/slac/g/lcls/physics/package/aida/lib/aidadp.jar
/afs/slac/g/lcls/physics/package/err/lib/err.jar
/afs/slac/g/lcls/package/except/lib/except.jar
# ****************************************************************************************************************
# ****************************************************************************************************************
# SLAC Java APIs
# ****************************************************************************************************************
/afs/slac/g/lcls/physics/release/hlaExtensions/hlaExtensions-R2-0-0/jar/hlaExtensions.jar
/afs/slac/g/lcls/physics/release/xal4lcls/xal4lcls-R1-0-0/build/jar/ext.jar
/afs/slac/g/lcls/physics/release/xal4lcls/xal4lcls-R1-0-0/build/jar/xal.jar
/afs/slac/g/lcls/physics/release/hlaCommon/hlaCommon-R2-0-0/jar/hlaCommon.jar
/afs/slac/g/lcls/epics/extensions/R0.5.0/lib/rhel6-x86_64
/afs/slac/g/lcls/physics/release/MessageLogAPI/MessageLogAPI-R1-0-0/jar/MessageLogAPI.jar
# ****************************************************************************************************************
Production
Code Block
languagetext
# Additions to classpath.txt
# ****************************************************************************************************************
# EPICS 7 Java Interface
# ****************************************************************************************************************
/usr/local/lcls/epics/java/epicsCoreJava/R7.0.2-1.0.0/products/epics-pvdata-6.1.2.jar
/usr/local/lcls/epics/java/epicsCoreJava/R7.0.2-1.0.0/products/epics-pvaccess-5.1.2.jar
/usr/local/lcls/epics/java/epicsCoreJava/R7.0.2-1.0.0/products/epics-ntypes-0.3.2.jar
/usr/local/lcls/epics/java/epicsCoreJava/R7.0.2-1.0.0/products/epics-util-1.0.0.jar
/usr/local/lcls/epics/java/epicsCoreJava/R7.0.2-1.0.0/products/jca-2.4.2.jar
#/usr/local/lcls/epics/extensions/R0.5.0/javalib/jca.jar
/usr/local/lcls/epics/java/pvaClientJava/R4.3.2-0.0.1/products/epics-pvaclient-4.3.2.jar
# ****************************************************************************************************************
# ****************************************************************************************************************
# Oracle Database connectivity
# ****************************************************************************************************************
/usr/local/lcls/package/oracle/product/11.2.0.4/linux-x86_64/jdbc/lib/ojdbc5.jar
# ****************************************************************************************************************
# ****************************************************************************************************************
# IONA ORBacus ==> CORBA-based Client Server API
# ****************************************************************************************************************
/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
# ****************************************************************************************************************
# ****************************************************************************************************************
# AIDA Interface
# ****************************************************************************************************************
/usr/local/lcls/physics/package/aida/lib/aida.jar
/usr/local/lcls/physics/package/aida/lib/aidadp.jar
/usr/local/lcls/physics/package/err/lib/err.jar
/usr/local/lcls/package/except/lib/except.jar
# ****************************************************************************************************************
# ****************************************************************************************************************
# SLAC Java APIs
# ****************************************************************************************************************
/usr/local/lcls/physics/release/hlaExtensions/hlaExtensions-R2-0-0/jar/hlaExtensions.jar
/usr/local/lcls/physics/release/xal4lcls/xal4lcls-R1-0-0/build/jar/ext.jar
/usr/local/lcls/physics/release/xal4lcls/xal4lcls-R1-0-0/build/jar/xal.jar
/usr/local/lcls/physics/release/hlaCommon/hlaCommon-R2-0-0/jar/hlaCommon.jar
/usr/local/lcls/epics/extensions/R0.5.0/lib/rhel6-x86_64
/usr/local/facet/tools/matlab/sdds/java/SDDS.jar
/usr/local/lcls/physics/release/MessageLogAPI/MessageLogAPI-R1-0-0/jar/MessageLogAPI.jar
# ****************************************************************************************************************

Anchor
matlab_librarypath
matlab_librarypath
librarypath.txt

Description: This file is used to augment the library search path used by MATLAB.

...

Note

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.


2012a

Development
Code Block
languagetext
/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
Code Block
languagetext
/usr/local/lcls/epics/extensions/extensions-R3-14-12/lib/linux-x86
/usr/local/lcls/epics/base/base-R3-14-12/lib/linux-x86

2019a and 2020a

Development
Code Block
languagetext
/afs/slac/g/lcls/epics/extensions/R0.5.0/lib/rhel6-x86_64
/afs/slac/g/lcls/epics/base/R7.0.2-1.0/lib/rhel6-x86_64
/afs/slac/g/lcls/package/oracle/product/11.2.0.4/linux-x86_64/lib
Production
Code Block
languagetext
/usr/local/lcls/epics/extensions/R0.5.0/lib/rhel6-x86_64
/usr/local/lcls/epics/base/R7.0.2-1.0/lib/rhel6-x86_64
/usr/local/lcls/package/oracle/product/11.2.0.4/linux-x86_64/lib


Anchor
custom_matlab_env
custom_matlab_env
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.

...