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| − | The Simulation Factory simplifies many aspects of running Cactus-based
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| − | simulations. It provides a central facility for managing authoritative
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| − | source tree versions, providing convenient access to remote HPC
| |
| − | systems, building Cactus source configurations, and managing
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| − | simulations all the way from submission to archiving their output.
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| − | | |
| − | | |
| − | | |
| − | == Getting Started ==
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| − | | |
| − | To begin using The Simulation Factory, it needs to be checked out from
| |
| − | '''svn'''. The Simulation Factory is typically placed into a
| |
| − | '''simfactory''' folder inside a Cactus source tree. This can be
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| − | accomplished with the following '''svn''' command:
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| − | | |
| − | svn co https://svn.cct.lsu.edu/repos/numrel/simfactory/branches/PYSIM_2010 simfactory
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| − | | |
| − | The Simulation Factory could also be placed in an independent location
| |
| − | to be used with multiple Cactus source trees. This approach will be
| |
| − | described later.
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| − | | |
| − | | |
| − | | |
| − | == Initial Setup ==
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| − | | |
| − | Once the Simulation Factory has been checked out from svn, the next
| |
| − | step is to configure it, telling it e.g. about your user name. The
| |
| − | Simulation Factory comes with example configuration files that you can
| |
| − | copy and modify. Assuming The Simulation Factory has been checked out
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| − | into the '''simfactory''' folder, this initial configuration can be
| |
| − | accomplished with the following commands:
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| − |
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| − | cp simfactory/etc/defs.local.ini.simple simfactory/etc/defs.local.ini
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| − | | |
| − | Edit '''simfactory/etc/defs.local.ini''' and replace
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| − | <ul>
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| − | <li>YOUR_LOGIN with your usual username
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| − | <li>YOUR@EMAIL.ADDRESS with your usual email address
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| − | <li>YOUR_ALLOCATION with your usual allocation
| |
| − | </ul>
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| − | | |
| − | === Additional Configurations ===
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| − | | |
| − | The Simulation Factory contains a database known as the Machine
| |
| − | Database. This collection of information describes all the aspects
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| − | that are unique about each individual HPC system, so that the
| |
| − | Simulation Factory can provide a common interface for all systems that
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| − | hides these differences.
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| − | | |
| − | The Machine Database consists of different sections, one for each
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| − | machine. The section name is given in square brackets, e.g.
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| − | '''[queenbee]'''. There is a special section '''[default]''' that
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| − | provides default values for those properties that are not explicitly
| |
| − | set in the machine-specific entries.
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| − | | |
| − | The Machine Database is an authoritative collection of information,
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| − | and is generally not meant to contain modification that are only
| |
| − | relevant for individual people. These local modifications are instead
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| − | maintained in the file '''simfactory/etc/defs.local.ini''' described
| |
| − | above, where one can add, change, or overwrite properties of Machine
| |
| − | Database entries. For instance, if an alternative username,
| |
| − | allocation, and sourcebasedir is needed for the machine
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| − | '''queenbee''', you would add the following section there:
| |
| − | | |
| − | [queenbee]
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| − | user = QUEENBEE_USERNAME
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| − | allocation = QUEENBEE_ALLOCATION
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| − | sourcebasedir = /work/@USER@
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| − | | |
| − | There are several macros that help simplifying configuration entries.
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| − | The most useful is probably '''@USER@''', which expands to the
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| − | '''user''' property of the Machine Database entry.
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| − | | |
| − | For example, if you are using the same user name on many systems, but
| |
| − | have a different user name on some systems, then you would set the
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| − | common user name in the '''[default]''' section, and override this for
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| − | those machines where your user name differs. The example
| |
| − | '''simfactory/etc/defs.local.ini.complex''' has examples for this.
| |
| − | | |
| − | Most of the macros available in the Simulation Factory are described
| |
| − | in the section [[#Macros]] below.
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| − | | |
| − | The command
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| − |
| |
| − | simfactory/sim list-machines
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| − | | |
| − | outputs a list of all preconfigured machines that the Simulation
| |
| − | Factory knows about.
| |
| − | | |
| − | === Local Workstation Configuration ===
| |
| − | | |
| − | The Simulation Factory can only be used on a machine known to the
| |
| − | Simulation Factory. This means that you may have to add an entry for
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| − | your workstation or notebook.
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| − | | |
| − | The first step is to determine the hostname of the local machine. It
| |
| − | is through this hostname that the Simulation Factory matches a Machine
| |
| − | Database entry to the machine on which it executes. The hostname can
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| − | be determined using the following command:
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| − |
| |
| − | hostname
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| − | | |
| − | Once you know the hostname, issue the following command to create a
| |
| − | new Machine Database entry, starting from a generic example:
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| − | | |
| − | cp simfactory/etc/mdb/generic.ini simfactory/etc/mdb/<hostname>.ini
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| − | | |
| − | Then edit '''simfactory/etc/mdb/<hostname>.ini''' and replace
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| − | | |
| − | <ul>
| |
| − | <li> '''[generic]''' with '''[<hostname>]'''
| |
| − | <ul>
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| − | <li>The section header for this machine database entry must be unique
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| − | among all Machine Database entries, and must match the '''nickname'''
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| − | property exactly.
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| − | </ul>
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| − | <li> '''nickname = generic''' with '''nickname = <hostname>'''
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| − | <li> '''hostname = generic''' with '''hostname = <hostname>'''
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| − | <li> '''sourcebasedir = /home/@USER@''' with the correct '''root'''
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| − | path under which all your Cactus source trees reside. (This is not
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| − | the Cactus directory itself, but the directory that contains the
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| − | Cactus directory.)
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| − | <li> '''basedir = /home/@USER@/simulations''' with the desired folder
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| − | that will contain all simulation output. (This is explained in more
| |
| − | detail below in the section [[#Managing Simulations]].)
| |
| − | </ul>
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| − | You can ignore the properties '''user''', '''email''', and
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| − | '''allocation''', as the values from the '''[default]''' section of
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| − | '''simfactory/etc/defs.local.ini''' will propagate to this entry.
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| − | | |
| − | | |
| − | | |
| − | == Accessing Remote Systems ==
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| − | | |
| − | The Simulation Factory simplifies access to remote systems, both for
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| − | transferring files and logging in. You can synchronise (replicate) an
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| − | authoritative version of your Cactus source tree to remote systems,
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| − | obtain an interactive shell, or execute commands.
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| − | | |
| − | === Information Commands ===
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| − | | |
| − | The following commands can be used to discover information about a
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| − | machine, or list all known machines.
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| − | | |
| − | List all known machines:
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| − | | |
| − | simfactory/sim list-machines | |
| − | | |
| − | List details about a single machine:
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| − |
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| − | simfactory/sim list-machine <machine>
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| − | | |
| − | Print the complete Machine Database to the screen:
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| − | | |
| − | simfactory/sim print-mdb
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| − | | |
| − | Print the Machine Database entry for a single machine:
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| − | | |
| − | simfactory/sim print-mdb <machine>
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| − | | |
| − | Print the name of the machine on which the Simulation Factory is
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| − | currently being executed:
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| − |
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| − | simfactory/sim print-machine
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| − | | |
| − | === Syncing ===
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| − | | |
| − | Historically, Cactus and the Einstein Toolkit have not been installed
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| − | into a central location on each machine, but are instead built
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| − | on-demand by every user for a certain thorn list. (One of the
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| − | advantages is that people can thus easily add their own thorns.) To
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| − | help with this approach, the Simulation Factory provides a facility to
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| − | synchronize a Cactus user's local, authoritative source tree to remote
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| − | HPC systems, where it can then be compiled and run.
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| − | | |
| − | Remote access is implemented on top of ssh and other ssh-like
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| − | mechanisms such as gsi-ssh. Currently, you must still manage all ssh
| |
| − | keys and passwords manually. (We highly recommend to use ssh keychain
| |
| − | and ssh agents to avoid having to enter passwords multiple times.)
| |
| − | | |
| − | ==== Configuration ====
| |
| − | | |
| − | Before syncing a source tree to a remote system, a small amount of
| |
| − | configuration must be performed. It is necessary to either verify that
| |
| − | the defaults are correct, or to define the correct values for the
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| − | following keys for the remote system in the Machine Database:
| |
| − | | |
| − | <ul>
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| − | <li> '''sourcebasedir'''
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| − | <ul>
| |
| − | <li>The root directory under which the Cactus source tree will reside
| |
| − | </ul>
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| − | <li> '''basedir'''
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| − | <ul>
| |
| − | <li>The root directory in which all simulation output will reside
| |
| − | </ul>
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| − | <li> '''user'''
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| − | <ul>
| |
| − | <li>The user name on the remote system
| |
| − | </ul>
| |
| − | </ul>
| |
| − | | |
| − | You can output the currently configured values by issuing the command
| |
| − |
| |
| − | simfactory/sim print-mdb <machine>
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| − | | |
| − | If you need to change these values, then edit (on the local system)
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| − | the file '''simfactory/etc/defs.local.ini''' and add a section for the
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| − | remote machine. This entry will augment the existing Machine Database
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| − | entry and updating/replace the corresponding values. An example for
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| − | the machine '''queenbee''' can be see in the [[#Additional
| |
| − | Configuration]] section.
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| − | | |
| − | To see the list of files and directories that are synchronized, look
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| − | at '''simfactory/etc/defs.ini''' and find the following two keys
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| − | | |
| − | <ul>
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| − | <li> '''sync-sources'''
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| − | <ul>
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| − | <li>The list of files and directories that will be transferred when
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| − | the option '''--sync-sourcetree''' is enabled (on by default)
| |
| − | </ul>
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| − | <li> '''sync-parfiles'''
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| − | <ul>
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| − | <li>The list of files and directories that will be copied when the
| |
| − | option '''--sync-parfiles''' is enabled (also on by default). This
| |
| − | list of files typically includes just parameter files.
| |
| − | </ul>
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| − | <li> '''sync-excludes'''
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| − | <ul>
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| − | <li>A list of files and directories that will be expressly excluded
| |
| − | from syncing, such as e.g. '''CVS''' or '''.svn''' directories.
| |
| − | </ul>
| |
| − | </ul>
| |
| − | | |
| − | ==== Performing a Sync ====
| |
| − | | |
| − | A sync command takes two options, both of which default to '''true'''.
| |
| − | | |
| − | <ul>
| |
| − | <li> '''sync-sourcetree'''
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| − | <ul>
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| − | <li>Synchronise the complete source tree, as specified in the
| |
| − | aforementioned '''rsync-sources''' configuration entry. This takes a
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| − | few seconds or minutes, depending on the connection.
| |
| − | </ul>
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| − | <li> '''sync-parfiles'''
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| − | <ul>
| |
| − | <li>Synchronise parameter files, as specified by the aforementioned
| |
| − | '''rsync-parfiles''' configuration entry. This is typically faster
| |
| − | than synchronising the source tree.
| |
| − | </ul>
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| − | </ul>
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| − | | |
| − | Usually, you would issue the command:
| |
| − | | |
| − | simfactory/sim sync <machine>
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| − | | |
| − | To synchronise only parfiles, you can negate the
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| − | '''--sync-sourcetree''' argument with the following command
| |
| − | | |
| − | simfactory/sim sync <machine> --nosync-sourcetree
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| − | | |
| − | If you want to synchronise not from the local machine, but from
| |
| − | another remote machine, then use
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| − | | |
| − | simfactory/sim --remote=<frommachine> sync <tomachine>
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| − | | |
| − | This executes the synchronisation command on the machine
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| − | '''<frommachine>'''.
| |
| − | | |
| − | === Remote Login ===
| |
| − | | |
| − | The Simulation Factory provides the ability to log in to a remote
| |
| − | system. This is initiated with the command
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| − | | |
| − | simfactory/sim login <machine>
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| − | | |
| − | This will automatically cd into the Cactus directory on the remote
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| − | system.
| |
| − | | |
| − | === Local/Remote Command Execution ===
| |
| − | | |
| − | To execute a command (locally) via the Simulation Factory, use the
| |
| − | command
| |
| − | | |
| − | simfactory/sim execute <command>
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| − | | |
| − | The command will be executed in the Cactus directory on the remote
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| − | system.
| |
| − | | |
| − | If the command is complex, and requires arguments, the command must be
| |
| − | quoted. For example
| |
| − | | |
| − | simfactory/sim execute 'ls -al'
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| − | | |
| − | To execute a remote command, use the command
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| − | | |
| − | simfactory/sim --remote-machine=<machine> execute <command>
| |
| − | | |
| − | An example of a complex command being executed remotely is
| |
| − |
| |
| − | simfactory/sim --remote-machine=queenbee execute 'find . -name *.py -exec sed -i .bk -n s/foo/bar/g {} \;'
| |
| − | | |
| − | == Build Cactus Configurations ==
| |
| − | | |
| − | The Simulation Factory provides a central facility for configuring and
| |
| − | building Cactus source trees. When a Cactus source tree is compiled,
| |
| − | the Simulation Factory creates a '''configuration''' for the compiled
| |
| − | executable, storing with it related information such as the Cactus
| |
| − | options list, and the scripts necessary to submit and run jobs in a
| |
| − | queuing system. This configuration is thus a self-contained entity
| |
| − | containing everything that is necessary to perform Cactus simulations.
| |
| − | | |
| − | === Information Commands ===
| |
| − | | |
| − | To list all existing Cactus configurations, use the following command
| |
| − |
| |
| − | simfactory/sim list-configurations
| |
| − | | |
| − | === Building a Configuration ===
| |
| − | | |
| − | To build a configuration, four pieces of information are required:
| |
| − | | |
| − | <ul>
| |
| − | <li>Thorn list
| |
| − | <ul>
| |
| − | <li>This defines which thorns are to be included into the configuration.
| |
| − | <li>Default: '''thornlist''' parameter of the Machine Database entry
| |
| − | <li>Override: '''--thornlist=<thornlist>'''
| |
| − | <li>The default option list is probably not useful in many cases.
| |
| − | </ul>
| |
| − | <li>Option List
| |
| − | <ul>
| |
| − | <li>This specifies the compiler and build options that need to be used
| |
| − | to build Cactus on a particular system.
| |
| − | <li>Default: '''optionlist''' parameter of the Machine Database entry
| |
| − | <li>Override: '''--optionlist=<optionlist>'''
| |
| − | <li>The Simulation Factory is supposed to contain good, working
| |
| − | default option lists for all supported systems. In fact, this is one
| |
| − | of the main strengths of the Simulation Factory. You should normally
| |
| − | not need to override the default.
| |
| − | </ul>
| |
| − | <li>Submission Script
| |
| − | <ul>
| |
| − | <li>This specifies how to submit a job to the queueing system on a
| |
| − | particular system.
| |
| − | <li>Default: '''submitscript''' parameter of the Machine Database entry
| |
| − | <li>Override: '''--submitscript=<submitscript>'''
| |
| − | <li>Similar to the option list, the Simulation Factory is supposed to
| |
| − | contain good, working default submission scripts for all supported
| |
| − | systems.
| |
| − | </ul>
| |
| − | <li>Run Script
| |
| − | <ul>
| |
| − | <li>This specifies to how execute an MPI process on a particular
| |
| − | system; it is closely connected to the submission script.
| |
| − | <li>Default: '''runscript''' parameter of the Machine Database entry
| |
| − | <li>Override: '''--runscript=<runscript>'''
| |
| − | <li>Same as with the the submission script, the Simulation Factory is
| |
| − | supposed to contain good, working default run scripts for all
| |
| − | supported systems.
| |
| − | </ul>
| |
| − | </ul>
| |
| − | | |
| − | To build a configuration with a specific thornlist, issue the
| |
| − | following command:
| |
| − | | |
| − | simfactory/sim build [<configurationname>] --thornlist=<thornlist>
| |
| − | | |
| − | If you choose to omit the configuration name, it will default to
| |
| − | 'sim'. (We recommend this.) You can in addition specify any of the
| |
| − | options
| |
| − | <ul>
| |
| − | <li>--debug
| |
| − | <li>--optimise (default)
| |
| − | <li>--profile
| |
| − | </ul>
| |
| − | These options create configurations for debugging, optimisation (this
| |
| − | is the default), or profiling enabled.
| |
| − | If any of these options is specified, then the configuration name will
| |
| − | be modified correspondingly, e.g. to 'sim-debug'.
| |
| − | | |
| − | ==== Additional Options ====
| |
| − | | |
| − | <ul>
| |
| − | | |
| − | <li>'''--reconfig'''
| |
| − | <ul>
| |
| − | <li>Reconfigure before building, i.e. re-examine the configuration
| |
| − | options and re-run the CST stage. This happens automatically when
| |
| − | the option list changes.
| |
| − | </ul>
| |
| − | | |
| − | <li>'''--clean'''
| |
| − | <ul>
| |
| − | <li>Clean the configuration (remove all object files etc.) before
| |
| − | building.
| |
| − | </ul>
| |
| − | | |
| − | </ul>
| |
| − | | |
| − | cbZsul <a href="http://wlswjasvvkxf.com/">wlswjasvvkxf</a>, [url=http://aegknafsayjg.com/]aegknafsayjg[/url], [link=http://erlxqmjagmjm.com/]erlxqmjagmjm[/link], http://rbnzmidhcrnk.com/
| |
| − | | |
| − | === Script Locations ===
| |
| − | | |
| − | The Simulation Factory provides default scripts for all its
| |
| − | preconfigured machines. These scripts can be found in the following
| |
| − | locations
| |
| − | | |
| − | <ul>
| |
| − | | |
| − | <li>'''Option Lists'''
| |
| − | <ul>
| |
| − | <li>MDB Key: optionlist
| |
| − | <li>Location: simfactory/etc/optionlists
| |
| − | </ul>
| |
| − | | |
| − | <li>'''Submit Scripts'''
| |
| − | <ul>
| |
| − | <li>MDB Key: submitscript
| |
| − | <li>Location: simfactory/etc/submitscripts
| |
| − | </ul>
| |
| − | | |
| − | <li>'''Run Scripts'''
| |
| − | <ul>
| |
| − | <li>MDB Key: runscript
| |
| − | <li>Location: simfactory/etc/runscripts
| |
| − | </ul>
| |
| − | | |
| − | </ul>
| |
| − | | |
| − | To determine, for instance, which option list Queen Bee uses by
| |
| − | default, issue the command
| |
| − | | |
| − | simfactory/sim print-mdb queenbee | grep optionlist
| |
| − | | |
| − | | |
| − | | |
| − | == Managing Simulations ==
| |
| − | | |
| − | The Simulation Factory provides a convenient, consistent facility for
| |
| − | submitting, running, and managing simulations. This is accomplished
| |
| − | through two main commands '''submit''' and '''run'''.
| |
| − | | |
| − | === Information Commands ===
| |
| − | | |
| − | The status of all simulations on a particular machine can be seen with
| |
| − | the following command
| |
| − | | |
| − | simfactory/sim list-simulations
| |
| − | | |
| − | If a more detailed look at each simulation is required, the verbose
| |
| − | option can be specified
| |
| − | | |
| − | simfactory/sim list-simulations --verbose
| |
| − | | |
| − | === Submitting a Simulation ===
| |
| − | | |
| − | Four primary pieces of information are necessary when submitting a
| |
| − | simulation to the host queuing system. They are
| |
| − | | |
| − | <ul>
| |
| − | | |
| − | <li>'''Configuration'''
| |
| − | <ul>
| |
| − | <li>The Cactus configuration to run
| |
| − | <li>'''option''': --configuration
| |
| − | <li>'''default''': "sim"
| |
| − | </ul>
| |
| − | | |
| − | <li>'''Parfile'''
| |
| − | <ul>
| |
| − | <li>The Cactus parameter file to use
| |
| − | <li>'''option''': --parfile
| |
| − | </ul>
| |
| − | | |
| − | <li>'''Walltime'''
| |
| − | <ul>
| |
| − | <li>The total amount of wall time required
| |
| − | <li>'''option''': --walltime
| |
| − | <li>'''default''': MDB Key '''maxwalltime'''
| |
| − | </ul>
| |
| − | | |
| − | <li>Processors
| |
| − | <ul>
| |
| − | <li>The total number of processors to use
| |
| − | <li>'''option''': --procs
| |
| − | <li>'''default''': 1
| |
| − | </ul>
| |
| − | | |
| − | </ul>
| |
| − | | |
| − | The option '''--configuration''' only needs to be specified the first
| |
| − | time you submit a simulation. Subsequent re-submissions of the same
| |
| − | simulation (for restarting from checkpoints) will always use the same
| |
| − | configuration that was specified the first time. Here is an example of
| |
| − | submitting a simulation named "static_tov" using the aforementioned
| |
| − | options:
| |
| − | | |
| − | simfactory/sim submit static_tov --configuration sim-debug --parfile=par/static_tov.par --walltime=4:00:00 --procs=8
| |
| − | | |
| − | It is possible to submit a simulation using shorthand notation where
| |
| − | you do not need to specify the option names, but have to specify the
| |
| − | options in a certain order. If you don't specify a simulation name
| |
| − | using the shorthand syntax, a simulation name will be derived from
| |
| − | from the parameter file name.
| |
| − | | |
| − | simfactory/sim submit [<simulationname>] <parfile> <walltime> <procs>
| |
| − | | |
| − | An example is
| |
| − | | |
| − | simfactory/sim submit par/static_tov.par 4:00:00 8
| |
| − | | |
| − | ==== Additional Options: Submission ====
| |
| − | | |
| − | <ul>
| |
| − | | |
| − | <li>Number of OpenMP Threads
| |
| − | <ul>
| |
| − | <li>The number of OpenMP threads per MPI process. (You specify the
| |
| − | total number of processors (cores), and the number of OpenMP
| |
| − | threads; the number of MPI processes is then calculated
| |
| − | automatically.)
| |
| − | <li>option: --num-threads
| |
| − | <li>default: 1 (as if OpenMP was not used)
| |
| − | </ul>
| |
| − | | |
| − | <li>Allocation
| |
| − | <ul>
| |
| − | <li>The allocation for the simulation, overriding the corresponding
| |
| − | MDB entry
| |
| − | <li>option: --allocation
| |
| − | <li>default: taken from the MDB
| |
| − | </ul>
| |
| − | | |
| − | <li>Queue
| |
| − | <ul>
| |
| − | <li>The queue for the simulation, overriding the corresponding MDB
| |
| − | entry
| |
| − | <li>option: --queue
| |
| − | <li>default: taken from the MDB
| |
| − | </ul>
| |
| − | | |
| − | <li>Processors per node
| |
| − | <ul>
| |
| − | <li>The number of processors per node requested from the queueing system
| |
| − | <li>option: --ppn
| |
| − | <li>default: all processors on a node
| |
| − | </ul>
| |
| − | | |
| − | <li>Used processors per node
| |
| − | <ul>
| |
| − | <li>The number of processors per node that should actually be used,
| |
| − | allowing under-using nodes even if the queueing system does not
| |
| − | allow it. (The remaining processors will idle and will remain
| |
| − | unused.)
| |
| − | <li>option: --ppn-used
| |
| − | <li>default: all processors on a node
| |
| − | </ul>
| |
| − | | |
| − | </ul>
| |
| − | | |
| − | === Running a Simulation ===
| |
| − | | |
| − | The Simulation Factory can execute a simulation directly, bypassing
| |
| − | the queuing system. Running a simulation directly uses the same
| |
| − | options, but ignores wall time limit etc. You use the '''run'''
| |
| − | command for this:
| |
| − | | |
| − | simfactory/sim run static_tov --configuration sim-debug --parfile=par/static_tov.par --procs=8
| |
| − | | |
| − | ==== Additional Options: Running ====
| |
| − | | |
| − | See [[#Aditional Options: Submission]]
| |
| − | | |
| − | === Other Simulation Commands ===
| |
| − | | |
| − | To launch an interactive session on a compute node, use the command
| |
| − | | |
| − | simfactory/sim interactive --procs=8 --walltime=4:00:00
| |
| − | | |
| − | This leads to a login shell on the compute node, but is otherwise
| |
| − | similar to the submit command.
| |
| − | | |
| − | To stop a simulation:
| |
| − |
| |
| − | simfactory/sim stop <simulationname>
| |
| − | | |
| − | To purge (put in the basedir/TRASH folder) an existing simulation:
| |
| − | | |
| − | simfactory/sim purge <simulationname> [--restart-id=<restartid>]
| |
| − | | |
| − | To show the current output (stdout and stderr) for a given simulation:
| |
| − | | |
| − | simfactory/sim show-output <simulationname> [--restart-id=<restartid>]
| |
| − | | |
| − | === What's Produced ===
| |
| − | | |
| − | When a simulation is submitted for the first time, all necessary
| |
| − | information from the Cactus build configuration is brought into a
| |
| − | specific simulation folder created underneath the '''basedir'''
| |
| − | directory. Contained inside this folder, which has the same name as
| |
| − | the specified simulation, are the executable, run script, submit
| |
| − | script, a SIMFACTORY folder, a log file, and the output directories
| |
| − | for each individual restart.
| |
| − | | |
| − | Simulations are self-contained, and once created do not rely on
| |
| − | outside information. For example, recompiling the executable or
| |
| − | changing the parameter file that were used to submit a simulation will
| |
| − | not influence the simulation, since the simulation contains copies of
| |
| − | both. This ensures that simulations can continue to run unperturbed
| |
| − | even weeks after they have been created.
| |
| − | | |
| − | Here is the contents of the simulation folder "static_tov" with
| |
| − | several restarts in it:
| |
| − | | |
| − | [mwt@eric2 simulations]$ ls -l static_tov
| |
| − | total 32
| |
| − | -rw-r--r-- 1 mwt lsuusers 0 Sep 30 13:30 LOG
| |
| − | drwxr-xr-x 3 mwt lsuusers 4096 Aug 20 10:19 output-0000
| |
| − | drwxr-xr-x 4 mwt lsuusers 4096 Aug 20 10:19 output-0001
| |
| − | drwxr-xr-x 4 mwt lsuusers 4096 Aug 20 10:24 output-0002
| |
| − | drwxr-xr-x 3 mwt lsuusers 4096 Aug 20 23:57 output-0003
| |
| − | drwxr-xr-x 4 mwt lsuusers 4096 Sep 17 09:02 output-0004
| |
| − | drwxr-xr-x 7 mwt lsuusers 4096 Aug 20 10:18 SIMFACTORY
| |
| − | | |
| − | The SIMFACTORY folder contains the executable, the necessary script
| |
| − | files for submission and execution, and a properties.ini file that is
| |
| − | used by the Simulation Factory to store information about the
| |
| − | simulation.
| |
| − | | |
| − | Each time a simulation is either run or submitted, a restart directory
| |
| − | is created underneath the simulation directory. This restart folder
| |
| − | has a name of the format "output-####", starting with "output-0000".
| |
| − | Contained inside the restart folder are several internal files, the
| |
| − | output written to stdout and stderr from the simulation, and the
| |
| − | simulation output itself. The simulation output is typically stored
| |
| − | inside a directory named after the basename of the parameter file. An
| |
| − | example output directory is:
| |
| − | | |
| − | [mwt@eric2 output-0001]$ ls -l
| |
| − | total 172
| |
| − | -rw-r--r-- 1 mwt lsuusers 0 Sep 17 09:06 LOG
| |
| − | -rw-r--r-- 1 mwt lsuusers 9 Sep 17 09:06 mpd_nodefile
| |
| − | -rw-r--r-- 1 mwt lsuusers 32 Sep 17 09:06 mpi_nodefile
| |
| − | -rw-r--r-- 1 mwt lsuusers 33 Sep 17 09:06 NODELIST
| |
| − | drwxr-xr-x 3 mwt lsuusers 20480 Sep 17 16:12 qc0-mclachlan
| |
| − | -rw------- 1 mwt lsuusers 2520 Sep 17 21:06 qc0-mclachlan.err
| |
| − | -rw------- 1 mwt lsuusers 108210 Sep 17 21:06 qc0-mclachlan.out
| |
| − | -rw-r--r-- 1 mwt lsuusers 13621 Sep 17 09:06 qc0-mclachlan.par
| |
| − | lrwxrwxrwx 1 mwt lsuusers 23 Sep 17 09:06 scratch -> /var/scratch/mwt/250072
| |
| − | drwxr-xr-x 2 mwt lsuusers 4096 Sep 17 09:06 SIMFACTORY
| |
| − | | |
| − | === Script Locations ===
| |
| − | | |
| − | When a simulation is created, it copies the submit script and the run
| |
| − | script from the build configuration into the folder
| |
| − | "basedir/<simulation>/SIMFACTORY". The executable goes in the "exe/"
| |
| − | folder, the run and submit scripts into the "run/" folder, the Cactus
| |
| − | options list into the "cfg/" folder, and the parfile into the "par/"
| |
| − | folder. Below shows an example SIMFACTORY directory
| |
| − | | |
| − | [mwt@eric2 SIMFACTORY]$ ls -lR
| |
| − | .:
| |
| − | total 32
| |
| − | drwxr-xr-x 2 mwt lsuusers 4096 Sep 17 09:06 cfg
| |
| − | drwxr-xr-x 2 mwt lsuusers 4096 Sep 17 09:05 data
| |
| − | drwxr-xr-x 2 mwt lsuusers 4096 Sep 17 09:05 exe
| |
| − | drwxr-xr-x 2 mwt lsuusers 4096 Sep 17 09:06 par
| |
| − | -rw-r--r-- 1 mwt lsuusers 740 Sep 17 09:06 properties.ini
| |
| − | drwxr-xr-x 2 mwt lsuusers 4096 Sep 17 09:06 run
| |
| − | | |
| − | ./cfg:
| |
| − | total 12
| |
| − | -rw-r--r-- 1 mwt lsuusers 4041 Sep 17 09:06 OptionList
| |
| − | | |
| − | ./exe:
| |
| − | total 121408
| |
| − | -rwxr-xr-x 1 mwt lsuusers 124306159 Sep 17 09:06 cactus_sim
| |
| − | | |
| − | ./par:
| |
| − | total 24
| |
| − | -rw-r--r-- 1 mwt lsuusers 13621 Sep 17 09:06 qc0-mclachlan.par
| |
| − | | |
| − | ./run:
| |
| − | total 16
| |
| − | -rw-r--r-- 1 mwt lsuusers 1162 Sep 17 09:06 RunScript
| |
| − | -rw-r--r-- 1 mwt lsuusers 410 Sep 17 09:06 SubmitScript
| |
| − | | |
| − | | |
| − | | |
| − | == Other Advanced Features ==
| |
| − | | |
| − | === Archiving ===
| |
| − | | |
| − | Preliminary support for archiving of simulations has been added to the
| |
| − | Simulation Factory using the PetaShare data storage system on LONI.
| |
| − | This archiving system can only be used from machines that have access
| |
| − | to PetaShare. The currently supported machines that have access to
| |
| − | Petashare are
| |
| − | | |
| − | bluedawg
| |
| − | ducky
| |
| − | eric
| |
| − | lacumba
| |
| − | louie
| |
| − | neptune
| |
| − | oliver
| |
| − | painter
| |
| − | poseidon
| |
| − | queenbee
| |
| − | spider
| |
| − | tezpur
| |
| − | zeke
| |
| − | | |
| − | To use the PetaShare archiving system, the PetaShare
| |
| − | [http://www.cct.lsu.edu/~sreekanth/petashare/downloads/pcommands/pcommands-2.3.tar.gz
| |
| − | Pcommands],
| |
| − | [http://www.cct.lsu.edu/~sreekanth/petashare/pcommands-manual(2.0).php
| |
| − | (manual)] must be downloaded and installed onto your machine. Once
| |
| − | that is done, add a new section in '''etc/defs.local.ini''' for the
| |
| − | machine from which you wish to access PetaShare, and add the necessary
| |
| − | MDB keys. An example for the machine Queen Bee is:
| |
| − | | |
| − | [queenbee]
| |
| − | # archive information
| |
| − | archivetype = petashare
| |
| − | archiveuser = numrel
| |
| − | archivetoolspath = /home/mwt/tools/pcommands-2.3/bin
| |
| − | archivebasepath = /tempZone/home/numrel/mwt/simulations
| |
| − | | |
| − | '''archivebasepath''' is where the simulations will be stored on
| |
| − | PetaShare.
| |
| − | | |
| − | Once this setup has been completed, you can archive an entire
| |
| − | simulation (including all restarts) using the command
| |
| − | | |
| − | simfactory/sim archive <simulationname>
| |
| − | | |
| − | To archive just a single restart for a given simulation, issue the
| |
| − | command
| |
| − |
| |
| − | simfactory/sim archive <simulationname> --restart-id=<restartid>
| |
| − | | |
| − | To print a list of all archived simulations, use the command
| |
| − | | |
| − | simfactory/sim list-archived-simulations
| |
| − | | |
| − | To retreive an archived simulation, first use the
| |
| − | '''list-archived-simulations''' command to retrieve the unique
| |
| − | identifier for the simulation, and then issue the following command to
| |
| − | retrieve a simulation. It will place the simulation in the current
| |
| − | directory.
| |
| − | | |
| − | simfactory/sim get-archived-simulation <archiveid>
| |
