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-bash-3.2$ module load ImageMagick How to display a picture using Imagemagick's display command without running the interface |
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Matlab related:
- How do I get matlab command line options?*
-bash-3.2$ srun ... matlab -help
How do I run a matlab batch job?
-bash-3.2$ module load matlab -bash-3.2$ sbatch ...options... --warp="matlab -nojvm -nodisplay < your-matlab-code.m" |
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This will submit your code to the slurm partition you choose in the sbatch options. Matlab has several ways to direct output and results by use of matlab commands such as: diary, print and several other commands.
How do I speed up my Matlab calculations?
By default Matlab on the cluster has multi-thread parallelism enabled. Many Matlab functions will automatically use the threaded libraries. The number of threads obtained is equal to the number of cores on the node your job is placed on. Currently it is either 8 or 12. You no longer need to request exclusive node access via bsub.
How do I access the Parallel capability of Matlab?
Matlab can make use of MPI parallelism if you modify your code accordingly(see Parallel computing documentation within Matlab) and setup your session to instruct Matlab to use slurm. Currently Distributed Computing Engine Toolbox is licensed for 32 cores. It is strongly recommended to initially use 4, 8 or 16 cores while you explore how your code scales. Depending on what you are doing, execution times may not benefit from additional cores. To setup this feature, import a working configuration found at:
----Currently this has not been tested with slurm. Matlab R2015b, expected Fall 2015 will have slurm support -----
To view an older lsf based config file:
/cluster/shared/dmarshal/ISO/matlab-R2012-lsfconfig16.settings
Use Matlab's Cluster Profile Manager Tool to import the settings. Choose the menu options Parallel -> Import Cluster Profile and browse to the config file.
To test this out, you may run the Validation tests by choosing Start Validation. This will take several minutes and should result in five passed tests.
I want to run hundreds of matlab jobs using my matlab scripts. What do I need to know?
Your jobs will end up on a partition with a limit of 512 concurrent jobs/cores/user.
Is Matlab MCR available to run compiled jobs?
Yes. You will need to load the MCR version corresponding to the Matlab version you used to compile your standalone executable. The Matlab example called magicsquare in the documentation can be used as an example. Once compiled the named executable, magicsquare, can be run without loading Matlab nor checking out licenses. Such an example is available below. Note, be sure to quote any needed command line arguments to your named executable.
> module load MCR/R2012a > srun ... "/cluster/shared/dmarshal/ISO/magicsquare 3" |
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How do I access the public domain Matlab toolbox EDGE?
EDGE has been installed into cluster directory /opt/shared/EDGE/1.02. To use it you'll need to launch MATLAB then change into the /opt/shared/EDGE/1.0/Matlab directory by issuing the following command at the Matlab prompt:
cd /opt/shared/EDGE/1.0/Matlab
Or better yet, add this path to your Matlab path within Matlab. Choose File -> Set Path and Add with subfolders.
To launch the Importer tool from within Matlab type on the command line:
semiauto
See the EDGE website for additional documentation.
How do I access the public domain Matlab toolbox WaveLab?
Load the corresponding module:
> module load Wavelab
> module load matlab
In Matlab choose File -> Set Path and then Add with Subfolders. Add the following: /opt/shared/Wavelab/Wavelab850
Then issue the command startup at the Matlab command line.
At this point you can issue commands and demos. Check the website for documentation.
Mathematica related:
Where can I find more Mathematica documentation?
The vendor's website and the online help in the application. In addition look at the broadcast section on the vendor site to view various movies on how to do many tasks in Mathematica. Also check out some paper based options.
My Mathematica notebook file doesn't work like it did before, what is up?
The following explanation is a good starting point to explore this issue.
How does one submit a mathematica batch job?
Suppose you have a text file called my_mathematica.m created with a text editor with the following tasks:
AppendTo[$Echo, "stdout"] To submit as a batch job through the batch partition, but not the Mathematica gui interface: |
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I get an error about Mathematica missing fonts,etc... What does this mean?
The cluster does not provide a Font Server supporting Mathematica font sets. Whereas a local install of Mathematica on your desktop includes this font set. Remote users need to provide access to the fonts locally.
For linux desktops, the easy way is to obtain the Mathematica helper program called, Mathematica Player. You may download this from the vendor website. Before you start Mathematica on the cluster for display on your computer, start the helper program locally. This will provide the font support.
For MacOSx desktops you need to either install Mathematica or the Mathematica Player and then point to the installed fonts. For example if you have Mathematica installed, to use it's fonts, open a terminal window(shell) and type:
> xset fp+ /Applications/Mathematica.app/SystemFiles/Fonts/Type1/
> xset fp rehash
Assuming that is the path to the fonts.
Then connect to the cluster and start Mathematica normally.
NCAR related:
How do I start NCAR?
NCAR has lots of separate programs. These are all available to you after you setup the environment.
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