[Gate-users] Using Multicore Computers to Run GATE Simulations Simultaneously

[Geron Bindseil]

Dear Gate Users:

A couple days ago I mentioned I had written a script for running multiple
Gate simulations simultaneously on multicore computers. Many people have
written asking for this script, so I decided to send it over the list in
case anyone else could benefit from it.

I have attached an example Perl script and README file that explains how to
run multiple GATE simulations simultaneously on one computer with more than
one logical CPU. This method runs a set of Gate simulations with different
parameters and if the number of simulations to be run are greater than the
number of logical CPUs, the script will wait until a CPU is available before
starting the next Gate simulation.

N.B. In my response to a question on July 16, I accidentally gave the
incorrect syntax for the terminal command ("<" should have been ">"). The
correct syntax for storing the output in a file (rather than printing it in
the terminal is): "Gate -a ParameterName ParameterValue my_macro.mac >
terminal_output.out". If you just want to run a bunch of macros
simultaneously in the background manually, you can do so by inserting an
ampersand "&" at the end of each command.

Kind Regards,
Geron

---

Geron Bindseil
PhD Candidate, Physics
University of Western Ontario
London, Ontario, Canada
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\f0\fs24 \cf0 Using Multicore Computers to Run GATE Simulations Simultaneously\
Geron Bindseil\
gbindsei at uwo.ca\
July 18 2011\
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Summary: This is a small tutorial that explains how to run multiple GATE simulations simultaneously on one computer with more than one logical CPU. This method runs a set of Gate simulations and if the number of simulations to be run are greater than the number of logical CPUs, the script will wait until a CPU is available before starting the next Gate simulation.\
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Requirements: This method requires GATE to be installed and the env_gate.sh or env_gate.csh shell script to have been sourced. Perl and several perl modules are required.\
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[[Configuring Perl to Install Modules]]\
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Make sure you have perl installed on your computer. After that, install the cpanm module installer which is a tool that automatically configures and installs perl modules. Install cpanm by typing the following on the terminal (use 'sudo' if your local account doesn't have write privileges to system directories):\
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sudo cpan App::cpanminus\
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After that, any modules can be installed by typing the following:\
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sudo cpanm Module::Name\
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The instructions for doing this and installing CPAN modules can be found here:\
http://www.cpan.org/modules/INSTALL.html\
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[[Installing Required Perl Modules]]\
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The script requires a couple modules to be installed. Install them by typing the following into a terminal window:\
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sudo cpanm Forks::Super (required: for managing the queue of GATE jobs)\
sudo cpanm File::Path (optional: to make creating directories easier)\
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[[Running GATE script.]]\
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Make a Gate macro and put the gate_batch.pl perl script into the same directory. Modify gate_batch.pl to set the number of logical CPUs your computer has (double the number of physical cores if your computer has hyper-threading). You may also wish to modify the default path for storage of the output root data files.\
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To run the code, in a terminal window with the env_gate shell script already sourced, execute the following command:\
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perl gate_batch.pl\
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The words "End of perl batch script." will be printed when all the macros have completed.\
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[[Notes]]\
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- Originally, my script included a step to automatically determine the number of CPUs but it did not treat hyper-threaded CPUs properly.\
- Originally, my script called a print statement when any particular macro had finished running, but this was not working as indented.}
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