New Tutorial for New Users - Revision history

Rhaas: remove new tutorial for new users since it is orphaned and we no longer use QueenBee

2018-08-31T14:16:27Z

remove new tutorial for new users since it is orphaned and we no longer use QueenBee

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Knarf at 08:24, 10 April 2017

2017-04-10T08:24:04Z

Rhaas: add future location of GetComponents release branch

2011-10-25T14:29:55Z

add future location of GetComponents release branch

Rhaas: update some references to perl simfactory files, use $HOME/scratch/simulations instead of construct using

2011-10-25T14:18:46Z

update some references to perl simfactory files, use $HOME/scratch/simulations instead of construct using <user>

131.215.195.89: fix URL of ET release thorn list, simfactory path, use nano instead of vi

2011-10-25T11:58:51Z

fix URL of ET release thorn list, simfactory path, use nano instead of vi

Eschnett at 21:33, 23 October 2011

2011-10-23T21:33:40Z

Eschnett: /* Development version */

2011-10-23T21:32:01Z

‎Development version

Eschnett at 21:31, 23 October 2011

2011-10-23T21:31:34Z

Eschnett: /* Additional Simulation Factory Configuration */

2011-10-23T21:29:41Z

‎Additional Simulation Factory Configuration

Eschnett: /* Using simfactory to manage simulations */

2011-10-23T21:24:21Z

‎Using simfactory to manage simulations

@@ Line 3: / Line 3: @@
 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 require compiling with MPI and then running the resulting application in a batch queue. This complexity is hidden as much as possible in Cactus and accompanying tools such as the Simulation Factory.
-The example worked through below 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/documentation/request request an account] to use for these examples.
+The example worked through below 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/request_testaccount request an account] to use for these examples.
 ==Prepare Tools==

@@ Line 15: / Line 15: @@
 Download [https://github.com/gridaphobe/CRL/raw/ET-2011-10/GetComponents GetComponents] to checkout all the components of the Einstein Toolkit, and ensure it is executable:
-  wget --no-check-certificate https://github.com/gridaphobe/CRL/raw/ET-2011-10/GetComponents
+  wget --no-check-certificate https://github.com/gridaphobe/CRL/raw/ET_2011_10/GetComponents
   chmod 755 GetComponents

@@ Line 28: / Line 28: @@
 ===Configure the Simulation Factory===
   cd Cactus
   cp simfactory/etc/defs.local.ini.simple simfactory/etc/defs.local.ini
@@ Line 51: / Line 54: @@
 From the Cactus directory, create a batch queue script and submit it to queue an example simulation:
-  ./bin/sim submit static_tov --parfile=par/static_tov.par --procs=32 --walltime=8:0:0
+  ./simfactory/bin/sim submit static_tov --parfile=par/static_tov.par --procs=32 --walltime=8:0:0
 This parameter file sets up a static TOV star (a model of a single neutron star) with a mass of 1.4 solar masses and integrates the combined relativistic fluid dynamics and spacetime evolution equations in time. The spacetime is evolved using the BSSN 3+1 formulation of Einstein's equations and the fluid is evolved using a high resolution shock capturing method.
@@ Line 57: / Line 60: @@
 To check the status of the simulation, use
-  ./bin/sim list-simulations
+  ./simfactory/bin/sim list-simulations
 ==Look at Results==
@@ Line 66: / Line 69: @@
 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):
+(qb.loni.org) the command will be:
-  cd /scratch/<user>/simulations/static_tov/output-0000/static_tov
+  cd ~/scratch/simulations/static_tov/output-0000/static_tov
 You should see a number of files with the extenstion  ''.asc''. These are 0-D
@@ Line 103: / Line 106: @@
 The first (ks-mclachlan.par) evolves a single isolated rotating black hole with the initial data (M=1 and a/M=0.8) specified in Kerr-Schild coordinates. The second (qc0-mclachlan.par) evolves a binary black hole system using the moving puncture technique. The black holes start at a close separation and only complete about one half of an orbit before merging. You can run these additional parameter files using a similar command in the Cactus directory as for the TOV star above:
-  ./bin/sim submit ks-mclachlan --parfile=par/ks-mclachlan.par --procs=32 --walltime=8:0:0
+  ./simfactory/bin/sim submit ks-mclachlan --parfile=par/ks-mclachlan.par --procs=32 --walltime=8:0:0
 and
-  ./bin/sim submit qc0-mclachlan --parfile=par/qc0-mclachlan.par --procs=32 --walltime=8:0:0
+  ./simfactory/bin/sim submit qc0-mclachlan --parfile=par/qc0-mclachlan.par --procs=32 --walltime=8:0:0
 ==Additional Simulation Factory Configuration==
@@ Line 127: / Line 130: @@
 your application and run your simulation or how the file system tree
 is organized. Simulation Factory keeps a database for several different
-machines. You can peek at simfactory/mdb.pm to have an idea of the list
+machines. You can peek at simfactory/mdb/machines to have an idea of the list
 of machines and what the default configuration is for each of them.
 In particular for Ranger, the configuration for the source code path and
@@ Line 139: / Line 142: @@
 if your group number is '05555'. With these basic changes to
-simfactory/udb.pm, you are all set to configure and build the
+simfactory/etc/defs.local.ini you are all set to configure and build the
 Einstein Toolkit application on Ranger as well.
@@ Line 152: / Line 155: @@
 Instead of using the release version listed above, you might want the latest development version.  Proceed as above, but download from the trunk:
    (GetComponents from trunk)
-   ....  -a http://svn.einsteintoolkit.org/manifest/ET-2011-10/einsteintoolkit.th
+   ....  -a http://svn.einsteintoolkit.org/manifest/trunk/einsteintoolkit.th
 ===More about Cactus===

@@ Line 22: / Line 22: @@
 Checkout the Einstein Toolkit using anonymous authentication (this may take a few minutes):
-  ./GetComponents -a http://svn.einsteintoolkit.org/manifest/ET-2011-10/einsteintoolkit.th
+  ./GetComponents -a http://svn.einsteintoolkit.org/manifest/branches/ET_2011_10/einsteintoolkit.th
 This checks out Cactus, the Einstein Toolkit thorns, the Simulation Factory and example parameter files into a directory named Cactus.
@@ Line 30: / Line 30: @@
   cd Cactus
   cp simfactory/etc/defs.local.ini.simple simfactory/etc/defs.local.ini
-  vi simfactory/etc/defs.local.ini
+  nano simfactory/etc/defs.local.ini
 Edit defs.local.ini and replace
@@ Line 42: / Line 42: @@
 ===Compile Executable===
-  ./bin/sim build
+  ./simfactory/bin/sim build
 This may take a few minutes. You may receive an error message that building the utilities

@@ Line 13: / Line 13: @@
   export PATH=$PATH:/home/eschnett/mercurial-1.9.3/bin
-Download [https://github.com/gridaphobe/CRL/raw/master/GetComponents GetComponents] to checkout all the components of the Einstein Toolkit, and ensure it is executable:
+Download [https://github.com/gridaphobe/CRL/raw/ET-2011-10/GetComponents GetComponents] to checkout all the components of the Einstein Toolkit, and ensure it is executable:
-  wget --no-check-certificate https://github.com/gridaphobe/CRL/raw/master/GetComponents
+  wget --no-check-certificate https://github.com/gridaphobe/CRL/raw/ET-2011-10/GetComponents
   chmod 755 GetComponents
@@ Line 22: / Line 22: @@
 Checkout the Einstein Toolkit using anonymous authentication (this may take a few minutes):
-  ./GetComponents -a http://svn.einsteintoolkit.org/manifest/trunk/einsteintoolkit.th
+  ./GetComponents -a http://svn.einsteintoolkit.org/manifest/ET-2011-10/einsteintoolkit.th
 This checks out Cactus, the Einstein Toolkit thorns, the Simulation Factory and example parameter files into a directory named Cactus.
@@ Line 152: / Line 152: @@
 Instead of using the release version listed above, you might want the latest development version.  Proceed as above, but download from the trunk:
    (GetComponents from trunk)
-   ....  -a http://svn.einsteintoolkit.org/manifest/trunk/einsteintoolkit.th
+   ....  -a http://svn.einsteintoolkit.org/manifest/ET-2011-10/einsteintoolkit.th
 ===More about Cactus===

@@ Line 148: / Line 148: @@
 This and other topics are explained in the [[Simulation_Factory_Advanced_Tutorial]].
-===Development version===
+===Development version of the Einstein Toolkit===
 Instead of using the release version listed above, you might want the latest development version.  Proceed as above, but download from the trunk:

@@ Line 142: / Line 142: @@
 Einstein Toolkit application on Ranger as well.
-==Using Simfactory to manage simulations==
+==Going further==
-''FAQ''
+===Adding a new machine to Simfactory===
-==Going further==
+This and other topics are explained in the [[Simulation_Factory_Advanced_Tutorial]].
 ===Development version===

@@ Line 114: / Line 114: @@
 You may also be interested though in configuring the Simulation Factory for your
 own machine or other Teragrid machines. In this section we provide a quick
-example of what need to be changed or considered in simfactory/etc/defs.local.ini
+example of what needs to be changed or considered in simfactory/etc/defs.local.ini
 in order to configure Simulation Factory for your needs. More specifically
 we are going to work out an example for the TeraGrid machine Ranger.
-The first step is to set your username for the machine. This means
+Simfactory already knows about Ranger, so we only need to provide the settings specific to your account. To do this, you create a section for Ranger machine in defs.local.ini:
-    set_option 'ranger', 'user',          'YOUR_LOGIN'
+ [ranger]
+ user = YOUR_RANGER_USERNAME
-You also need to provide your allocation.  For example, if your allocation
+  allocation = YOUR_RANGER_ALLOCATION
 Each machine has different policies on which file system to use to build
@@ Line 138: / Line 133: @@
 '/scratch/00507/@USER@/simulations' respectively. You may need to
 change it to reflect the group number (00507 here) you belong to.
-For example you could just set:
+For example you could set (in the [ranger] section):
-    set_option 'ranger'  , 'sourcebasedir', '/work/05555/@USER@';
+  sourcebasedir = /work/05555/@USER@
-    set_option 'ranger'  , 'basedir', '/work/05555/@USER@/simulations';
+  basedir = /work/05555/@USER@/simulations
 if your group number is '05555'. With these basic changes to
 simfactory/udb.pm, you are all set to configure and build the
 Einstein Toolkit application on Ranger as well.
 ==Using Simfactory to manage simulations==

@@ Line 169: / Line 169: @@
 If you are using Mac OS X, then [[ConfiguringMacOSX|here]] are instructions for setting it up for Cactus.
-==Using simfactory to manage simulations==
+==Using Simfactory to manage simulations==
 <tt>simfactory</tt> is a wrapper to download, compile, and run code on available machines.  See [[Simulation_Factory_Advanced_Tutorial]] for more details.