Einstein Toolkit Documentation - User contributions [en]

Allocation for Examples

2010-05-11T13:21:39Z

Gallen:

Thank you for your request for an Einstein Toolkit demonstration account. Please go to https://allocations.loni.org/login_request.php and request a LONI account. Enter "Erik Schnetter" as your LONI Contact/Collaborator. Enter "Einstein Toolkit" as your research area. You do not need to enter a Globus DN.

Once you have received your account (hopefully within one or two days) go to https://allocations.loni.org/balances.php and login.
Select "Request Allocation" on the right hand side, and then "Join Allocation". Enter "Erik Schnetter" and then select the "loni_cactus05" allocation. This will be approved within one or two days, and you will receive an email confirming the allocation.

Note that this allocation is reserved for running the examples for the Einstein Toolkit, please limit your total usage to 2kSUs. If you need more resources once you reach 2kSUs feel free to contact the toolkit maintainers for suggestions on where you might find a real allocation for your work. We also may remove you from the allocation if you have used over 2kSUs, but you will still be able to access all your data and files. The user guide for queen bee is at http://www.loni.org/teragrid/users_guide.php

If you continue to use the Einstein Toolkit, please join our consortium by signing up at http://einsteintoolkit.org/about/members/join

Please also write to users@einsteintoolkit.org if you have problems or questions about the examples.

Standard Emails

2010-05-11T13:13:00Z

Gallen:

* [[Allocation for Examples]]

Organization and Responsibilities

2010-05-04T10:58:38Z

Gallen:

This page is for planning out areas of responsibility for the Einstein Toolkit Maintainers.

* Web pages
* Services (email lists, SVN, etc)
* Adding new members and dealing with test accounts
* Testsuites
* Add more ...

Supported Machines

2010-04-23T15:59:42Z

Gallen: /* Kraken, TeraGrid */

Supported Machines

2010-04-23T15:59:25Z

Gallen:

Supported Machines

2010-04-23T15:57:00Z

Gallen:

This page describes some of the large scale resources on which the simulation codes using the Einstein Toolkit are being deployed. While some core machines, such as those of the NSF TeraGrid, are actively supported by the Einstein Toolkit Maintainers, others listed here are supported by members of the community who are regularly using them and are willing to act as a machine expert. If you are interested in adding a machine and supporting the Einstein Toolkit on it, please add it to these pages, along with any machine specific details important for others assembling, compiling, running or visualizing Einstein Toolkit codes. Added machines do not need to be open or community resources if you want to add your groups local machine please use our page.

Please direct questions about using these machines to the users@einsteintoolkit.org mail list.

== Abe, NCSA/TeraGrid ==

=== Status and Maintainers ===

The Einstein Toolkit is regularly tested on Abe by the Einstein Toolkit Maintainers, and is included in SimFactory. Questions about using the Einstein Toolkit should be directed to the users@einsteintoolkit.org mail list.

=== Machine Specific Information ===

Not yet added.

== Kraken, TeraGrid ==

=== Status and Maintainers ===

The Einstein Toolkit is regularly tested on Kraken by the Einstein Toolkit Maintainers, and is included in SimFactory. Questions about using the Einstein Toolkit should be directed to the users@einsteintoolkit.org mail list.

=== Machine Specific Information ===

Kraken uses grid certificates for access control. Every TeraGrid user automatically receives such a certificate, so you don't need to worry about this. However, you need to install the <tt>gsissh</tt> command on your local machine, which is available e.g. from http://grid.ncsa.illinois.edu/ssh/ .

== Mare Nostrum, BSC ==

=== Status and Maintainers ===

The Einstein Toolkit is supported on Mare Nostrum by Erik Schnetter, and is included in SimFactory. Questions about using the Einstein Toolkit should be directed to the users@einsteintoolkit.org mail list.

=== Machine Specific Information ===

Not yet added.

== Queen Bee, LONI/TeraGrid ==

=== Status and Maintainers ===

The Einstein Toolkit is regularly tested on Queen Bee by the Einstein Toolkit Maintainers, and is included in SimFactory. Questions about using the Einstein Toolkit should be directed to the users@einsteintoolkit.org mail list.

=== Machine Specific Information ===

Although <tt>git</tt> (needed for checking out some thorns) is now on the standard path for Queen Bee users, those with long term Queen Bee accounts may need to add <tt>git</tt> to their environment (<tt>soft add git</tt>), or issue the <tt>resoft</tt> command.

== Ranger, TACC/TeraGrid ==

=== Status and Maintainers ===

The Einstein Toolkit is regularly tested on Ranger by the Einstein Toolkit Maintainers, and is included in SimFactory. Questions about using the Einstein Toolkit should be directed to the users@einsteintoolkit.org mail list.

=== Machine Specific Information ===

Not yet added.

Tutorial for New Users

2010-04-23T15:45:11Z

Gallen: /* Prepare Tools */

This section provides a simple guide for compiling and running an example parameter file for the Einstein Toolkit.

One complexity of high performance computing is the heterogeneous environments presented by different resources with different core software installations and local setups. For example, Einstein Toolkit codes necessitate compiling with MPI and then running the resulting application in a batch queue. As much as possible of this complexity is hidden in Cactus and accompanying tools such as the Simulation Factory.

This worked example assumes that you are using the NSF TeraGrid resource [http://www.loni.org/systems/system.php?system=QueenBee Queen Bee]. If you don't have an existing account on Queen Bee you can [http://einsteintoolkit.org/info/documentation/request.php request an account] to use for these examples.

==Prepare Tools==

On Queen Bee (qb.loni.org), the <tt>git</tt> client may not be in your path by default. To add this type:

soft add +git

Download the [http://www.cactuscode.org/download/GetComponents GetComponents] script which will checkout all the components of the Einstein Toolkit and ensure it is executable:

wget https://svn.cactuscode.org/Utilities/trunk/Scripts/GetComponents
chmod 755 GetComponents

==Download, Configure, and Build==

Checkout the Einstein Toolkit using anonymous authentication (this may take a few minutes):

./GetComponents -a https://svn.einsteintoolkit.org/manifest/einsteintoolkit.th

This checks out Cactus, the Einstein Toolkit thorns, the Simulation Factory and example parameter files into a directory named Cactus.

===Configure the Simulation Factory===

cd Cactus
cp simfactory/udb.example.pm simfactory/udb.pm
vi simfactory/udb.pm

Edit udb.pm and replace
<ul>
<li>YOUR_LOGIN with your username on Queen Bee
<li>YOUR@EMAIL.ADDRESS with your usual email address
<li>YOUR_ALLOCATION with your project allocation on Queen Bee
</ul>

===Compile Executable===

./simfactory/sim build --thornlist=manifest/einsteintoolkit.th

This may take a few minutes. You may receive an error message that building the utilities
failed. This is fine as long as the main executable has been built correctly. You can check this with the command <tt>ls exe</tt>; if this shows a file <tt>cactus_sim</tt>, then you are fine.)

==Run a Simulation==

From the Einstein Toolkit directory, create a batch queue script and submit it to queue an example simulation:

./simfactory/sim create-submit static_tov --parfile=par/static_tov.par --procs=32 --walltime=8:0:0

To check the status of the simulation, use

./simfactory/sim list-simulations

==Look at Results==

For the following make sure that you have logged in to Queen Bee with X-forwarding enabled, i.e.

ssh -Y qb.loni.org

When the simulation is complete, move to the output directory. On Queen Bee
(qb.loni.org) the command will be (replace <user> with your own login name):

cd /scratch/<user>/simulations/static_tov/output-0000/static_tov

You should see a number of files with the extenstion ''.asc''. These are 0-D
(reductions of 3-D grid functions to scalar values) and 1-D ASCII output files that
can be plotted with gnuplot.

In this case it's interesting to look at the maximum of the density (in the file hydrobase::rho.maximum.asc). Start gnuplot with the command:

gnuplot

and at the gnuplot prompt type:

p 'hydrobase::rho.maximum.asc' u 2:3 w lp

This plots the data in column 3 (rho) as a function of the data in column 2 (time).

[[Image:rho_of_time.png]]

As can be seen from the plot, the maximum of the density oscillates with decreasing amplitude around the initial value with a small drift upwards. Even though the initial model is supposed to be in equilibrium, numerical errors means that the numerical model is not exactly in equilibrium and it starts to oscillate. The oscillation energy is slowly dissipated by shocks and the oscillation amplitude decreases and the maximum density increases as the star contracts in response.

A consistent picture can be seen by plotting the minimum of the lapse:

p 'admbase::lapse.minimum.asc' u 2:3 w lp

[[Image:Lapse_of_time.png]]

The quantity shows the same features as the maximum of the density, except the drift is downwards since as the star contracts, the curvature of spacetime increases slightly and in response the singularity avoiding lapse condition used here decreases the lapse.

As the oscillations and subsequent drift of the density and the lapse are caused by numerical error, these effects will decrease with increasing numerical resolution.

==Any Problems?==

This example should work smoothly on the TeraGrid machines Queen Bee, Ranger, Kraken and Abe. If you have any problems, please send details to [mailto:users@einsteintoolkit.org users@einsteintoolkit.org].

Supported Machines

2010-04-23T15:24:01Z

Gallen:

== Abe, NCSA/TeraGrid ==

=== Status and Maintainers ===

The Einstein Toolkit is regularly tested on Abe by the Einstein Toolkit Maintainers, and is included in SimFactory. Questions about using the Einstein Toolkit should be directed to the users@einsteintoolkit.org mail list.

=== Machine Specific Information ===

Not yet added.

== Kraken, TeraGrid ==

=== Status and Maintainers ===

The Einstein Toolkit is regularly tested on Kraken by the Einstein Toolkit Maintainers, and is included in SimFactory. Questions about using the Einstein Toolkit should be directed to the users@einsteintoolkit.org mail list.

=== Machine Specific Information ===

Not yet added.

== Mare Nostrum, BSC ==

=== Status and Maintainers ===

The Einstein Toolkit is supported on Mare Nostrum by Erik Schnetter, and is included in SimFactory. Questions about using the Einstein Toolkit should be directed to the users@einsteintoolkit.org mail list.

=== Machine Specific Information ===

Not yet added.

== Queen Bee, LONI/TeraGrid ==

=== Status and Maintainers ===

The Einstein Toolkit is regularly tested on Queen Bee by the Einstein Toolkit Maintainers, and is included in SimFactory. Questions about using the Einstein Toolkit should be directed to the users@einsteintoolkit.org mail list.

=== Machine Specific Information ===

Although <tt>git</tt> (needed for checking out some thorns) is now on the standard path for Queen Bee users, those with long term Queen Bee accounts may need to add <tt>git</tt> to their environment (<tt>soft add git</tt>), or issue the <tt>resoft</tt> command.

== Ranger, TACC/TeraGrid ==

=== Status and Maintainers ===

The Einstein Toolkit is regularly tested on Ranger by the Einstein Toolkit Maintainers, and is included in SimFactory. Questions about using the Einstein Toolkit should be directed to the users@einsteintoolkit.org mail list.

=== Machine Specific Information ===

Not yet added.

Main Page

2010-04-23T15:09:15Z

Gallen:

==Instructions==

Documentation for the Einstein Toolkit is a community effort and everyone is encouraged to contribute towards these pages. You need to login to the wiki to edit the documentation, to do this either

* if you already have a personal LDAP login with the CCT use this
* request a personal login from maintainers@einsteintoolkit.org

If you would like to make major changes to these pages please discuss first on the users@einsteintoolkit.org mail list.

Thanks for your contributions!

==Documentation==

* [[Tutorial for New Users]]
* [[Getting Started for Cactus Experts]]
* [[Einstein Toolkit standards]]: ADMBase, HydroBase, EOSBase, SphericalSurface
* [[Supported Machines]]
* Adding your own analysis method
* Adding your own [[adding initial data|initial data]]
* [[FAQ]]

== Getting Started with Wikis ==

* Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]
* [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2010-04-23T10:06:41Z

Gallen: /* Documentation */

==Instructions==

Documentation for the Einstein Toolkit is a community effort and everyone is encouraged to contribute towards these pages. You need to login to the wiki to edit the documentation, to do this either

* if you already have a personal LDAP login with the CCT use this
* request a personal login from maintainers@einsteintoolkit.org

If you would like to make major changes to these pages please discuss first on the users@einsteintoolkit.org mail list.

Thanks for your contributions!

==Documentation==

* [[Tutorial for New Users]]
* [[Getting Started for Cactus Experts]]
* [[Einstein Toolkit standards]]: ADMBase, HydroBase, EOSBase, SphericalSurface
* Adding your own analysis method
* Adding your own [[adding initial data|initial data]]
* [[FAQ]]

== Getting Started with Wikis ==

* Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]
* [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Getting Started for Cactus Experts

2010-04-23T09:48:32Z

Gallen:

Use [http://cactuscode.org/download/GetComponents GetComponents] (the new version of GetCactus) with the Einstein Toolkit [https://svn.einsteintoolkit.org/manifest/einsteintoolkit.th thornlist]. This thornlist should work on platforms supported by the Cactus team using the usual [http://www.cactuscode.org/download/configfiles configuration files] available on the Cactus web page or with the [http://www.cct.lsu.edu/~eschnett/SimFactory Simulation Factory].

Example parameter files are provided in the Einstein Toolkit SVN repository:

svn checkout https://svn.einsteintoolkit.org/EinsteinExamples

Problems should be directed to [mailto:users@einsteintoolkit.org users@einsteintoolkit.org] or [mailto:users@cactuscode.org users@cactuscode.org] as appropriate.

Tutorial for New Users

2010-04-21T09:59:50Z

Gallen:

This section provides a simple guide for compiling and running an example parameter file for the Einstein Toolkit.

One complexity of high performance computing is the heterogeneous environments presented by different resources with different core software installations and local setups. For example, Einstein Toolkit codes necessitate compiling with MPI and then running the resulting application in a batch queue. As much as possible of this complexity is hidden in Cactus and accompanying tools such as the Simulation Factory.

This worked example assumes that you are using the NSF TeraGrid resource [http://www.loni.org/systems/system.php?system=QueenBee Queen Bee]. If you don't have an existing account on Queen Bee you can [request.php request an account] to use for these examples.

==Prepare some Tools==

On Queen Bee (qb.loni.org), the <tt>git</tt> client will not be in your path by default. To add this type:

soft add +git

Download the [http://www.cactuscode.org/download/GetComponents GetComponents] script which will checkout all the components of the Einstein Toolkit and ensure it is executable:

wget http://cactuscode.org/download/GetComponents
chmod 755 GetComponents

==Download, Configure, and Build==

Checkout the Einstein Toolkit using anonymous authentication (this may take a few minutes):

./GetComponents -a https://svn.einsteintoolkit.org/manifest/einsteintoolkit.th

This checks out Cactus, the Einstein Toolkit thorns, the Simulation Factory and example parameter files into a directory named Cactus.

===Configure the Simulation Factory===

cd Cactus
cp simfactory/udb.example.pm simfactory/udb.pm
vi simfactory/udb.pm

Edit udb.pm and replace
<ul>
<li>YOUR_LOGIN with your username on Queen Bee
<li>YOUR@EMAIL.ADDRESS with your usual email address
<li>YOUR_ALLOCATION with your project allocation on Queen Bee
</ul>

===Compile Executable===

./simfactory/sim build --thornlist=manifest/einsteintoolkit.th

This may take a few minutes. You may receive an error message that building the utilities
failed. This is fine as long as the main executable has been built correctly. You can check this with the command <tt>ls exe</tt>; if this shows a file <tt>cactus_sim</tt>, then you are fine.)

==Run a Simulation==

From the Einstein Toolkit directory, create a batch queue script and submit it to queue an example simulation:

./simfactory/sim create-submit static_tov --parfile=par/static_tov.par --procs=32 --walltime=8:0:0

To check the status of the simulation, use

./simfactory/sim list-simulations

==Look at Results==

When the simulation is complete, move to the output directory (<tt>XXXX</tt>). You should see output files with the extension XXXX. These are 1D plots of the different grid variables. These can be plotted using e.g. gnuplot. An example plot of the XXXX is shown below.

==Any Problems?==

This example should work smoothly on the TeraGrid machines Queen Bee, Ranger, Kraken and Abe. If you have any problems, please send details to [mailto:users@einsteintoolkit.org users@einsteintoolkit.org].

Main Page

2010-04-21T09:41:58Z

Gallen:

==Instructions==

Documentation for the Einstein Toolkit is a community effort and everyone is encouraged to contribute towards these pages. You need to login to the wiki to edit the documentation, to do this either

* if you already have a personal LDAP login with the CCT use this
* request a personal login from maintainers@einsteintoolkit.org

If you would like to make major changes to these pages please discuss first on the users@einsteintoolkit.org mail list.

Thanks for your contributions!

==Documentation==

* [[Tutorial for New Users]]
* [[Einstein Toolkit standards]]: ADMBase, HydroBase, EOSBase, SphericalSurface
* Adding your own analysis method
* Adding your own [[adding initial data|initial data]]
* FAQ

== Getting Started with Wikis ==

* Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]
* [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2010-04-21T09:41:32Z

Gallen: /* Instructions */

==Instructions==

Documentation for the Einstein Toolkit is a community effort and everyone is encouraged to contribute towards these pages. You need to login to the wiki to edit the documentation, to do this either

* if you already have a personal LDAP login with the CCT use this
* request a personal login from maintainers@einsteintoolkit.org

If you would like to make major changes to these pages please discuss first on the users@einsteintoolkit.org mail list.

Thanks for your contributions!

==Documentation==

* [[Einstein Toolkit standards]]: ADMBase, HydroBase, EOSBase, SphericalSurface
* Adding your own analysis method
* Adding your own [[adding initial data|initial data]]
* FAQ

== Getting Started with Wikis ==

* Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]
* [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Main Page

2010-04-15T08:48:37Z

Gallen:

==Instructions==

Documentation for the Einstein Toolkit is a community effort and everyone is encouraged to contribute towards these pages. You need to login to the wiki to edit the documentation, to do this either

* login anonymously (username: einstein, password: <who is the "M" in the ADM formalism? (all lower case)>)
* if you already have a personal LDAP login with the CCT use this
* request a personal login from maintainers@einsteintoolkit.org

Using a personal login means that your contribution can be acknowledged. If you would like to make major changes to these pages please discuss first on the users@einsteintoolkit.org mail list.

Thanks for your contributions!

==Documentation==

* Einstein Toolkit standards: ADMBase, HydroBase, EOSBase
* Adding your own analysis method
* Adding your own initial data
* FAQ

== Getting Started with Wikis ==

* Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
* [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]
* [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]
* [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]