Difference between revisions of "LGI/Rlgi"
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Rlgi is a package for the [http://www.r-project.org/ programming language R] to seamlessly run on an [[LGI]] grid. Instead of using the family of <tt>apply</tt> functions on a heavy computation, you use one of the <tt>lgi.par?apply</tt> functions. This splits the data in chunks, and runs them on several nodes on the LGI grid. In usage it is similar to the R package [http://cran.r-project.org/web/packages/Rsge/index.html Rsge]. | Rlgi is a package for the [http://www.r-project.org/ programming language R] to seamlessly run on an [[LGI]] grid. Instead of using the family of <tt>apply</tt> functions on a heavy computation, you use one of the <tt>lgi.par?apply</tt> functions. This splits the data in chunks, and runs them on several nodes on the LGI grid. In usage it is similar to the R package [http://cran.r-project.org/web/packages/Rsge/index.html Rsge]. | ||
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#* Store this file as <tt>LGI.cfg</tt> in your home directory ''(Unix/Mac)'' or your profile directory ''(Windows)''. | #* Store this file as <tt>LGI.cfg</tt> in your home directory ''(Unix/Mac)'' or your profile directory ''(Windows)''. | ||
#* Please make sure that this file is secure. It contains your private key and should not be readable by others. | #* Please make sure that this file is secure. It contains your private key and should not be readable by others. | ||
| − | # Install the Rlgi package | + | # Install the Rlgi package (Linux & MacOS): |
| − | + | #* [https://github.com/downloads/wvengen/Rlgi/Rlgi_0.0.10.tar.gz Download] the Rlgi package | |
| − | #* [https://github.com/downloads/wvengen/Rlgi/Rlgi_0.0. | + | #* Install this package: <tt>R CMD INSTALL Rlgi_0.0.10.tar.gz</tt> |
| − | #* Install this package: <tt>R CMD INSTALL Rlgi_0.0. | + | # Install the Rlgi package (Windows): |
| + | #* Follow these [[InstallRlgiOnWindows|instructions]] | ||
===Example session=== | ===Example session=== | ||
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</code> | </code> | ||
| + | For more information, look in the [https://github.com/wvengen/Rlgi/wiki Rlgi wiki] | ||
===Moving your credentials file=== | ===Moving your credentials file=== | ||
If you find the location of <tt>LGI.cfg</tt> in your home directory disturbing, you can move it to another place. In that case, you'll have to load the configuration after loading Rlgi, like this: | If you find the location of <tt>LGI.cfg</tt> in your home directory disturbing, you can move it to another place. In that case, you'll have to load the configuration after loading Rlgi, like this: | ||
| − | library(Rlgi) | + | library(Rlgi); |
lgi.readConfig(path.expand("~/.config/LGI.cfg")); | lgi.readConfig(path.expand("~/.config/LGI.cfg")); | ||
| − | Alternatively, you can use the <tt>~/.LGI</tt> configuration directory, as explained [https://github.com/wvengen/Rlgi/blob/master/QUICKSTART here]. All the information required is present in your <tt>LGI.cfg</tt> file. | + | Alternatively, you can use the <tt>~/.LGI</tt> configuration directory, as explained [https://github.com/wvengen/LGI/wiki/User-configuration here] and [https://github.com/wvengen/Rlgi/blob/master/QUICKSTART here]. All the information required is present in your <tt>LGI.cfg</tt> file. |
===Further information=== | ===Further information=== | ||
This package is being developed at [https://github.com/wvengen/Rlgi github]. | This package is being developed at [https://github.com/wvengen/Rlgi github]. | ||
Latest revision as of 12:40, 1 March 2012
Rlgi is a package for the programming language R to seamlessly run on an LGI grid. Instead of using the family of apply functions on a heavy computation, you use one of the lgi.par?apply functions. This splits the data in chunks, and runs them on several nodes on the LGI grid. In usage it is similar to the R package Rsge.
Getting started
- Obtain your LGI credentials.
- These are supplied by your service provider (like BiG Grid). They either give you
- A login for the LGI portal. You'll be able to download a credentials file from the Settings menu, or
- the LGI.cfg credentials file directly.
- Store this file as LGI.cfg in your home directory (Unix/Mac) or your profile directory (Windows).
- Please make sure that this file is secure. It contains your private key and should not be readable by others.
- These are supplied by your service provider (like BiG Grid). They either give you
- Install the Rlgi package (Linux & MacOS):
- Download the Rlgi package
- Install this package: R CMD INSTALL Rlgi_0.0.10.tar.gz
- Install the Rlgi package (Windows):
- Follow these instructions
Example session
> library(Rlgi)
Loading required package: snow
Loading required package: XML
Welcome to Rlgi
Version: 0.0.7
> # non-cluster-aware call, runs locally
> sapply(c(10:20), function(x){x^3})
[1] 1000 1331 1728 2197 2744 3375 4096 4913 5832 6859 8000
> # use Rlgi's function to do sapply, but run locally for testing
> lgi.parSapply(c(10:20), function(x){x^3}, cluster=FALSE)
[Rlgi] Running locally
[1] 1000 1331 1728 2197 2744 3375 4096 4913 5832 6859 8000
> # now run remotely, block until all computations are finished
> lgi.parSapply(c(10:20), function(x){x^3})
[Rlgi] Submitting 1 jobs...
[Rlgi] All jobs submitted, waiting for completion.
[Rlgi] Waiting for jobs: 0 queued; 0 running; 1 other
[1] 1000 1331 1728 2197 2744 3375 4096 4913 5832 6859 8000
For more information, look in the Rlgi wiki
Moving your credentials file
If you find the location of LGI.cfg in your home directory disturbing, you can move it to another place. In that case, you'll have to load the configuration after loading Rlgi, like this:
library(Rlgi);
lgi.readConfig(path.expand("~/.config/LGI.cfg"));
Alternatively, you can use the ~/.LGI configuration directory, as explained here and here. All the information required is present in your LGI.cfg file.
Further information
This package is being developed at github.