This page contains information about using EPICS with MATLAB and Java in the LCLS Development and Production environments.
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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): 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: |
Python with MATLABWe can directly call Python library functionality from MATLAB or write Python programs that work with MATLAB.
Versions of Python Compatible with MATLAB: https://www.mathworks.com/support/requirements/python-compatibility.html
To check the Python version in the MATLAB,
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>> pyenv
ans =
PythonEnvironment with properties:
Version: "3.8"
Executable: "/usr/local/lcls/package/anaconda/envs/python3_env/bin/python"
Library: "/usr/local/lcls/package/anaconda/envs/python3_env/lib/libpython3.8.so"
Home: "/usr/local/lcls/package/anaconda/envs/python3_env"
Status: NotLoaded
ExecutionMode: InProcess |
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The library conflicts between MATLAB's and Python's libraries could result in segmentation faults. |
If the Python version in the MATLAB environment is different from the one in the Linux environment, which is the released version in DEV and PROD, you need to update "startup.m" file, which is located at $TOOLS/matlab/toolbox/.
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# A snippet of the file:
if strcmp(version('-release'),'2020a') | strcmp(version('-release'),'2022b') | strcmp(version('-release'),'2023a')
% Setup Python Environment:
package_top = getenv('PACKAGE_TOP');
pyenv_path = [package_top '/anaconda/envs/python3_rhel7_env/bin/python'];
pyenv('Version', pyenv_path,'ExecutionMode','InProcess');
%% Change default add-ons installation folder for Monkey Proof Code Checker
theSettings = settings();
theSettings.matlab.addons.InstallationFolder.TemporaryValue = [package_top '/matlab/2020a/SupportPackages'];
end |
matpva- matpva is a powerful extension that provides seamless integration between MATLAB and EPICS 7 through the Python P4P module.
How to use matpva
Matpva: Integrate EPICS7 into MATLAB using PVAccess for Python (P4P) module
Link to the GitHub Repository: https://github.com/slaclab/matpva
How to test matpva
How to test Matpva in DEV and PROD (lcls and facet)
JavaAt 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:
- Development
/afs/slac/g/lcls/physics/setup/javaSetup-R1.8.0_181.bash - Production
/usr/local/lcls/physics/setup/javaSetup-R1.8.0_181.bash
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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
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EPICS Java APIs
The EPICS Java APIs are located at:
- Development
/afs/slac/g/lcls/epics/java - Production
/usr/local/lcls/epics/java
At these locations you will be able to find the following libraries:
- epicsCoreJava
Includes EPICS 7 (pvaccess, ntypes, pvdata) and JCA libraries - pvaClientJava
Includes 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.
exampleJava
Includes a set of examples of client and server code for PVAcess.
MATLABClick the version name of MATLAB shown below to move to the detailed instructions for each version.
MATLAB R2012a
MATLAB R2019a
MATLAB R2020a
MATLAB R2022b
MATLAB R2023a
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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, 2023a etc.
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 |
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physics | 2020a |
softegr | 2020a |
laci | 2012a |
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License servers for Matlab network licenses
In order to support the latest version of Matlab, the network license service had to be migrated to a newer operating system. The new service is running on servers license701, license702, and license703 (replacing license1, license2, and license3).
Linux users using bash or similar shells should update their environment with the command:
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export MLM_LICENSE_FILE=27010@license701,27010@license702,27010@license703 |
If you are using csh or tcsh, the equivalent command is:
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setenv MLM_LICENSE_FILE "27010@license701,27010@license702,27010@license703" |
https://slacprod.servicenowservices.com/kb_view.do?sysparm_article=KB0011921
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Running MATLAB
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# Launch in desktop mode:
$ run_matlab.bash -m <matlab_version> -d # ex) run_matlab.bash -m 2023a -d
# Launch in terminal mode:
$ run_matlab.bash -m <matlab_version> # ex) run_matlab.bash -m 2023a |
To use one of the supported versions of MATLAB for development and configuration setup purposes, you need to follow the appropriate setup procedures.
Development (MATLAB should be run on lcls-dev3 in DEV. Do not run MATLAB instances on login nodes such as centos7.)
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$ source /afs/slac/g/lcls/epics/setup/epicsenv-7.0.3.1-1.0.bash
$ source /afs/slac/g/lcls/tools/oracle/oracleSetup-R11.2.0.4.bash
$ export MATLAB_VER=<matlab_version> # Currently supported MATLAB versions: 2020a, 2022b, 2023a
$ export MLM_LICENSE_FILE="27010@license701,27010@license702,27010@license703"
$ source /afs/slac/g/lcls/tools/matlab/setup/matlabSetup64.bash
# Launch in desktop mode:
$ LD_PRELOAD=${FACILITY_ROOT}/epics/base/R7.0.3.1-1.0/lib/rhel7-x86_64/libCom.so matlab &
$ LD_PRELOAD=${FACILITY_ROOT}/epics/base/R7.0.3.1-1.0/lib/rhel7-x86_64/libCom.so /afs/slac/g/lcls/package/matlab/<matlab_version>/bin/matlab & # If "matlab &" couldn't find the correct location, use the absolute path
$ run_matlab.bash -m <matlab_version> -d # ex) run_matlab.bash -m 2023a -d
# Launch in terminal mode:
$ run_matlab.bash -m <matlab_version> # ex) run_matlab.bash -m 2023a |
Production (Run on softegr@lcls-srv01 or physics@lcls-ssrv01 in PROD. Do not run MATLAB instances on mcclogin.)
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$ source /usr/local/lcls/epics/epicsenv-7.0.3.1-1.0.bash
$ source /usr/local/lcls/tools/oracle/oracleSetup-R11.2.0.4.bash
$ export MATLAB_VER=<matlab_version> # Currently supported MATLAB versions: 2020a, 2022b, 2023a
$ source /usr/local/lcls/tools/matlab/setup/matlabSetup64.bash
# Launch in desktop mode:
$ LD_PRELOAD=${FACILITY_ROOT}/epics/base/R7.0.3.1-1.0/lib/rhel7-x86_64/libCom.so matlab &
$ LD_PRELOAD=${FACILITY_ROOT}/epics/base/R7.0.3.1-1.0/lib/rhel7-x86_64/libCom.so /usr/local/lcls/package/matlab/<matlab_version>/bin/matlab & # If "matlab &" couldn't find the correct location, use the absolute path
$ run_matlab.bash -m <matlab_version> -d # ex) run_matlab.bash -m 2023a -d
# Launch in terminal mode:
$ run_matlab.bash -m <matlab_version> # ex) run_matlab.bash -m 2023a |
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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:
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
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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
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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
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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.
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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. |
Known issues1. When MATLAB 2022b starts, you will see the following error message: Warning: X does not support locale en_US.UTF-8
This is a known issue in MATLAB R2022b Update 5. The bug that triggers the warning when starting up MATLAB will be resolved in the upcoming update.
https://www.mathworks.com/matlabcentral/answers/1929870-why-do-i-get-warning-on-startup-x-does-not-support-locale-en_us-utf-8-when-startup-matlab-with-r2?s_tid=answers_rc1-2_p2_MLT
The bug has been resolved in the following versions: R2023b, R2023a Update 3, and R2022b Update 6.
2. When using matpva in MATLAB and then exiting, it generates a segmentation violation message. While labCA closes, it displays the message "Entering labca finalizer." Ideally, it should complete this process and then show another message, such as "Leavving labca finalizer."
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>> exit
finish.m about to lcaClear
Entering labca finalizer
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Segmentation violation detected at 2023-03-07 23:18:49 -0800
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Configuration:
Crash Decoding : Disabled - No sandbox or build area path
Crash Mode : continue (default)
Default Encoding : UTF-8
Deployed : false
GNU C Library : 2.17 stable
Graphics Driver : Uninitialized software
Graphics card 1 : 0x102b ( 0x102b ) 0x534 Version 0.0.0.0 (0-0-0)
Java Version : Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
MATLAB Architecture : glnxa64
MATLAB Entitlement ID : 6397849
MATLAB Root : /afs/slac.stanford.edu/g/lcls/vol9/package/matlab/2022b
MATLAB Version : 9.13.0.2166757 (R2022b) Update 4
OpenGL : software
Operating System : "Red Hat Enterprise Linux Server release 7.9 (Maipo)"
Process ID : 29718
Processor ID : x86 Family 6 Model 63 Stepping 2, GenuineIntel
Session Key : 455c04fb-90e4-445d-a778-ba3106ff69bd
Static TLS mitigation : Enabled: Full
Window System : The X.Org Foundation (11906000), display localhost:25.0
Fault Count: 1
Abnormal termination:
Segmentation violation
Current Thread: 'MCR 0 interpret' id 140077373851392
Register State (from fault):
RAX = 00007f6691d5e7a0 RBX = 00007f64b9b92e50
RCX = 00007f64a80939b0 RDX = 00007f64b9c85df0
RSP = 00007f664e1bf690 RBP = 0000000000000000
RSI = 00007f64b9b92e50 RDI = 0000000000000000
R8 = 0000000000000000 R9 = 00007f64b9ba2870
R10 = 00007f664e1bf120 R11 = 00007f6691b39570
R12 = 00007f64b9ba83c0 R13 = 00007f64b9ba83c0
R14 = 00007f64b9ba8378 R15 = 0000000000000000
RIP = 00007f6691b27f24 EFL = 0000000000010206
CS = 0033 FS = 0000 GS = 0000
Stack Trace (from fault):
[ 0] 0x00007f6691b27f24 /afs/slac/g/lcls/epics/base/R7.0.3.1-1.0/lib/rhel7-x86_64/libCom.so+00249636 _ZN10epicsMutex4lockEv+00000004
[ 1] 0x00007f64b9ba81b0 <unknown-module>+00000000
** This crash report has been saved to disk as /u/gu/ktkim/matlab_crash_dump.29718-1 **
MATLAB is exiting because of fatal error |