From c6a1524ae54c709ea206792b0d2383e2620c0e11 Mon Sep 17 00:00:00 2001 From: Showmic Islam <57932760+showmic09@users.noreply.github.com> Date: Fri, 15 Sep 2023 11:20:28 -0500 Subject: [PATCH] Update README.md --- README.md | 22 ++++++++-------------- 1 file changed, 8 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 328ef27..d99e076 100644 --- a/README.md +++ b/README.md @@ -10,8 +10,8 @@ interfaces. For more details, check the list of [supported toolboxes](http://www and [ineligible programs](http://www.mathworks.com/products/ineligible_programs/). -All applications created with MATLAB Compiler use [MATLAB Compiler Runtime™ (MCR)](http://www.mathworks.com/products/compiler/mcr/), which enables royalty-free deployment and use. We assume you have access to a server that has MATLAB compiler because the compiler is not available on OSG Connect. MATLAB Runtime is available -on OSG Connect. +All applications created with MATLAB Compiler use [MATLAB Compiler Runtime™ (MCR)](http://www.mathworks.com/products/compiler/mcr/), which enables royalty-free deployment and use. We assume you have access to a server that has MATLAB compiler because the compiler is not available on OSG. MATLAB Runtime is available +on OSG. Although the compiled binaries are portable, they need to have a compatible, OS-specific matlab runtime to interpret the binary. We recommend the compilation of your matlab program against matlab versions that match the OSG [containers](https://portal.osg-htc.org/documentation/htc_workloads/using_software/available-containers-list/), with the compilation executed on a server with @@ -33,7 +33,7 @@ Lets start with a simple MATLAB script `hello_world.m` that prints `Hello World! ### Compilation -*OSG connect does not have a license to use the MATLAB compiler*. On a Linux server with a MATLAB +*OSG does not have a license to use the MATLAB compiler*. On a Linux server with a MATLAB license, invoke the compiler `mcc`. We turn off all graphical options (`-nodisplay`), disable Java (`-nojvm`), and instruct MATLAB to run this application as a single-threaded application (`-singleCompThread`): mcc -m -R -singleCompThread -R -nodisplay -R -nojvm hello_world.m @@ -46,7 +46,7 @@ The file `hello_world` is the standalone executable. The file `run_hello_world.s ## Running standalone binary applications on OSG -To see which releases are available on OSG visit our available [containers](https://portal.osg-htc.org/documentation/htc_workloads/using_software/available-contaners-list/) page : +To see which releases are available on OSG visit our available [containers](https://portal.osg-htc.org/documentation/htc_workloads/using_software/available-containers-list/) page : ### Tutorial files @@ -78,14 +78,12 @@ The above command sets up the environment to run the matlab/2018b runtime applic Hello, World! ============= -If you get the above output, the binary execution is successful. Now, exit from the apptainer/singularity environment typing `exit`. Next, we see how to submit the job on a remote execute point using HTcondor. +If you get the above output, the binary execution is successful. Now, exit from the apptainer/singularity environment typing `exit`. Next, we see how to submit the job on a remote execute point using HTCondor. ### Job execution and submission files Let us take a look at `hello_world.submit` file: - - universe = vanilla # One OSG Connect vanilla, the preffered job universe is "vanilla" +SingularityImage = "/cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-matlab-runtime:R2018b" executable = hello_world @@ -94,11 +92,10 @@ Let us take a look at `hello_world.submit` file: Error = Log/job.$(Process).err # standard error Log = Log/job.$(Process).log # log information about job execution - requirements = HAS_SINGULARITY == TRUE - queue 10 # Submit 10 jobs + queue 10 # Submit 10 jobs -Before we submit the job, make sure that the directory `Log` exists on the current working directory. Because HTcondor looks for `Log` directory to copy the standard output, error and log files as specified in the job description file. +Before we submit the job, make sure that the directory `Log` exists on the current working directory. Because HTCondor looks for `Log` directory to copy the standard output, error and log files as specified in the job description file. From your work directory, type @@ -110,7 +107,7 @@ Absence of `Log` directory would send the jobs to held state. We submit the job using the `condor_submit` command as follows - $ condor_submit hello_world.submit //Submit the condor job description file "hello_world.submit" + $ condor_submit hello_world.submit # Submit the condor job description file "hello_world.submit" Now you have submitted an ensemble of 10 MATLAB jobs. Each job prints `hello world` on the standard output. Check the status of the submitted job, @@ -125,6 +122,3 @@ The `hello_world.m` script sends the output to standard output. In the condor jo ## What's next? Sure, it is not very exciting to print the same message on 10 output files. In the subsequent MATLAB examples, we see how to scale up MATLAB computation on HTC environment. - -## Getting help -For assistance or questions, please email the OSG User Support team at [support@osg-htc.org](mailto:support@osg-htc.org) or visit the [help desk and community forums](https://portal.osg-htc.org/documentation/).