-
Notifications
You must be signed in to change notification settings - Fork 6
Update README.md #7
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Open
showmic09
wants to merge
1
commit into
master
Choose a base branch
from
showmic09-patch-matlab-typos
base: master
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
Open
Changes from all commits
Commits
File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -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 [[email protected]](mailto:[email protected]) or visit the [help desk and community forums](https://portal.osg-htc.org/documentation/). |
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Please change this to the new "HTC" images location:
/cvmfs/singularity.opensciencegrid.org/htc/matlab-runtime:R2023a
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Our container page does not show R2023a. Can I fix that from my end?