This page contains information about using EPICS with MATLAB 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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We can directly call Python library functionality from MATLAB or write Python programs that work with MATLAB.
For information on compatible Python versions, refer to the link: https://www.mathworks.com/support/requirements/python-compatibility.html
To check the Python version in MATLAB, use the following command:
>> 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
The library conflicts between MATLAB's and Python's libraries can result in segmentation faults.
If the Python version in the MATLAB environment differs from the one in the Linux environment (the version used in DEV and PROD, you need to update the "startup.m" file located at "$TOOLS/matlab/toolbox/."
# 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: Integrate EPICS7 into MATLAB using PVAccess for Python (P4P) module
Link to the GitHub Repository: https://github.com/slaclab/matpva
How to test Matpva in DEV and PROD (lcls and facet)
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:
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:
The EPICS Java APIs are located at:
At these locations you will be able to find the following libraries:
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.
Click the version name of MATLAB shown below to move to the detailed instructions for each version.
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 |
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:
export MLM_LICENSE_FILE=27010@license701,27010@license702,27010@license703
If you are using csh or tcsh, the equivalent command is:
setenv MLM_LICENSE_FILE "27010@license701,27010@license702,27010@license703"
https://slacprod.servicenowservices.com/kb_view.do?sysparm_article=KB0011921
# 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.)
$ 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.)
$ 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
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
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
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
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.
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.
The bug has been resolved in the following versions: R2023b, R2023a Update 3, and R2022b Update 6.
>> exit finish.m about to lcaClear Entering labca finalizer -------------------------------------------------------------------------------- Segmentation violation detected at 2023-03-07 23:18:49 -0800 -------------------------------------------------------------------------------- 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