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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

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matpva_top
matpva_top
Python with MATLAB

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:

Code Block

language	bash

>> 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

Note
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/."

Code Block

language	bash

# 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

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matpva_top
matpva_top
matpva

matpva is a powerful extension that provides seamless integration between MATLAB and EPICS 7 through the Python P4P module.

How to use matpva

matpvaMatpva: 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 Matpva in DEV and PROD (lcls and facet)

...

MATLAB R2020a

MATLAB R2022b

MATLAB R2023a

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matlab_installation
matlab_installation
Installation

...

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 2022b2023a.

Individual AFS user accounts in the LCLS Development environment default to set up and use MATLAB 2012a 2020a unless overridden.

The default MATLAB versions for shared login accounts in Production are as follows:

Account	Default MATLAB version
physics	2012a2020a
softegr	2019a2020a
laci	2012a

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matlab_license
matlab_license
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:

Code Block

language	bash

export MLM_LICENSE_FILE=27010@license701,27010@license702,27010@license703

If you are using csh or tcsh, the equivalent command is:

Code Block

language	bash

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
running_matlab
Running MATLAB

Code Block

language	bash

# 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 set up your environment following 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.)

Code Block

language	bash

$ 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.)

Code Block

language	bash

$ 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

Anchor
configuring_matlab
configuring_matlab
Configuring MATLAB

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1. 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."

Code Block

>> 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

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Python with MATLAB

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How to test matpva

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Installation

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License servers for Matlab network licenses

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Running MATLAB

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configuring_matlab
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Configuring MATLAB

1. When MATLAB 2022b starts, you will see the following error message: Warning: X does not support locale en_US.UTF-8

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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Anchormatpva_topmatpva_topPython with MATLAB

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How to use matpva

How to test matpva

Anchormatlab_installationmatlab_installationInstallation

Anchormatlab_licensematlab_licenseLicense servers for Matlab network licenses

Anchorrunning_matlabrunning_matlabRunning MATLAB

Anchorconfiguring_matlabconfiguring_matlabConfiguring MATLAB

1. When MATLAB 2022b starts, you will see the following error message: Warning: X does not support locale en_US.UTF-8

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."

Anchor
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matpva_top
Python with MATLAB

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matpva_top
matpva

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matlab_installation
Installation

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matlab_license
License servers for Matlab network licenses

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running_matlab
Running MATLAB

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configuring_matlab
configuring_matlab
Configuring MATLAB