M01 How to Obtain and Run ParaDiS - Revision history

Wcash: added notes on Nvidia card

2008-03-20T21:39:26Z

added notes on Nvidia card

← Older revision		Revision as of 21:39, 20 March 2008
Line 48:		Line 48:

	<font color="red">If you are using Ubuntu Linux or GCC and are unable to compile, please see the following [[Media:ParaDiS_Ubuntu.pdf\|guide]] for instructions on installing '''version 2.2'''.</font>		<font color="red">If you are using Ubuntu Linux or GCC and are unable to compile, please see the following [[Media:ParaDiS_Ubuntu.pdf\|guide]] for instructions on installing '''version 2.2'''.</font>

			===Issues with Nvidia Linux graphics card driver===
			The X11 display has consistently crashed when running ParaDiS versions 2.0 and 2.2 and MD++ on a Dell Latitude D630 with an Nvidia Quadro 130M running Ubuntu 7.10. The window would render correctly for a few seconds, but then freeze. However, the simulation would still continue running. This error appears to be unique to Nvidia cards, because ParaDiS has been successfully ran on other Ubuntu machines. After hours spent reconfiguring the xorg.conf and searching for other libraries, the only solution found was to not use the closed-source Nvidia driver. Instead, the open-source nv driver had to be installed. This effectively renders the graphics card useless, and is thus not an ideal solution. If you have have a similar problem contact [[William Cash]] with the details of your system and any solution you might have found.

	==How to run a single-CPU ParaDiS simulation==		==How to run a single-CPU ParaDiS simulation==

Wcash: Updated reference to Ubuntu

2008-03-20T21:06:35Z

Updated reference to Ubuntu

← Older revision		Revision as of 21:06, 20 March 2008
Line 47:		Line 47:
	You can compile ParaDiS on Windows if [[http://en.wikipedia.org/wiki/Cygwin cygwin]] installed. Set <tt>SYS = cygwin</tt> in <tt>makefile.setup</tt>.		You can compile ParaDiS on Windows if [[http://en.wikipedia.org/wiki/Cygwin cygwin]] installed. Set <tt>SYS = cygwin</tt> in <tt>makefile.setup</tt>.

	If you are using Ubuntu Linux and are unable to compile, please see the following [[Media:ParaDiS_Ubuntu.pdf\|guide]] for ~~additional~~ ~~installation~~ ~~instructions~~.		<font color="red">If you are using Ubuntu Linux or GCC and are unable to compile, please see the following [[Media:ParaDiS_Ubuntu.pdf\|guide]] for instructions on installing '''version 2.2'''.</font>

	==How to run a single-CPU ParaDiS simulation==		==How to run a single-CPU ParaDiS simulation==

Wcash: Added link to Ubuntu installation guide

2008-01-12T10:00:43Z

Added link to Ubuntu installation guide

← Older revision		Revision as of 10:00, 12 January 2008
Line 46:		Line 46:

	You can compile ParaDiS on Windows if [[http://en.wikipedia.org/wiki/Cygwin cygwin]] installed. Set <tt>SYS = cygwin</tt> in <tt>makefile.setup</tt>.		You can compile ParaDiS on Windows if [[http://en.wikipedia.org/wiki/Cygwin cygwin]] installed. Set <tt>SYS = cygwin</tt> in <tt>makefile.setup</tt>.

			If you are using Ubuntu Linux and are unable to compile, please see the following [[Media:ParaDiS_Ubuntu.pdf\|guide]] for additional installation instructions.

	==How to run a single-CPU ParaDiS simulation==		==How to run a single-CPU ParaDiS simulation==

Jieyin: /* ParaDiS input and output */

2007-12-21T19:35:28Z

ParaDiS input and output

← Older revision		Revision as of 19:35, 21 December 2007
Line 116:		Line 116:
	<tt>dirname</tt> specifies the directory in which all output files are created. Simulation output styles are specified by groups of variables. For example, <tt>saveprop</tt>, <tt>saveprop_freq</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_time</tt> specifies how frequent and how detailed the simulation properties should be saved. The simulation property files are saved in the <tt>properties</tt> sub-directory, which contains the stress-strain curve (<tt>stress_Total_strain</tt> file) and the dislocatoin density (<tt>density</tt> file). Similarly, <tt>gnuplot</tt>, <tt>gnuplot_freq</tt>, <tt>gnuplot_counter</tt>, <tt>gnuplot_dt</tt>, <tt>gnuplot_timie</tt> together specify whether and how ParaDiS will output snapshots of dislocation structures in the [[http://en.wikipedia.org/wiki/Gnuplot gnuplot]] format.		<tt>dirname</tt> specifies the directory in which all output files are created. Simulation output styles are specified by groups of variables. For example, <tt>saveprop</tt>, <tt>saveprop_freq</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_time</tt> specifies how frequent and how detailed the simulation properties should be saved. The simulation property files are saved in the <tt>properties</tt> sub-directory, which contains the stress-strain curve (<tt>stress_Total_strain</tt> file) and the dislocatoin density (<tt>density</tt> file). Similarly, <tt>gnuplot</tt>, <tt>gnuplot_freq</tt>, <tt>gnuplot_counter</tt>, <tt>gnuplot_dt</tt>, <tt>gnuplot_timie</tt> together specify whether and how ParaDiS will output snapshots of dislocation structures in the [[http://en.wikipedia.org/wiki/Gnuplot gnuplot]] format.

	Within the directory specified by <tt>dirname</tt>, the <tt>restart<tt> sub-directory contains restart files, e.g. <tt>rs0001</tt> (control file) and <tt>rs0001.data</tt> (nodal data file), which are saved periodically during the simulation. The <tt>restart</tt> and <tt>restart.data</tt> files are saved at the end of the simulation. The <tt>timers</tt> sub-directory contains computational time information for different parts of the program.		Within the directory specified by <tt>dirname</tt>, the <tt>restart</tt> sub-directory contains restart files, e.g. <tt>rs0001</tt> (control file) and <tt>rs0001.data</tt> (nodal data file), which are saved periodically during the simulation. The <tt>restart</tt> and <tt>restart.data</tt> files are saved at the end of the simulation. The <tt>timers</tt> sub-directory contains computational time information for different parts of the program.



	==How to run a parallel ParaDiS simulation==		==How to run a parallel ParaDiS simulation==

Jieyin: /* How to run a single-CPU ParaDiS simulation */

2007-12-20T23:58:42Z

How to run a single-CPU ParaDiS simulation

New page

<H1 ALIGN="CENTER"><FONT SIZE="-1">Manual 01 for ParaDiS </FONT>
<BR>
How to obtain and run ParaDiS</H1>
<DIV>

<P ALIGN="CENTER"><STRONG>Sylvie Aubry and Wei Cai</STRONG></P>
</DIV>
<P ALIGN="CENTER">[[ Dec. 14 ]], [[2007]]</P>
<P>
<BR><HR>

==What is ParaDiS and how to obtain a copy==

[http://paradis.stanford.edu ParaDiS] is a free large scale dislocation dynamics simulation code to study the fundamental mechanisms of plasticity. It was originally developed at the Lawrence Livermore National Laboratory. It is written in C (with a little C++) and uses the MPI library for communication between processors. It runs routinely on 100-1000 processors and scalability on 132,000 processors of BlueGene/L has been demonstrated.

You can go to http://paradis.stanford.edu to obtain a free copy of the source code of ParaDiS. You will need to requestion an account by submitting a username, a password and a brief description of yourself and your research interests. Once your account request is approved, you will receive a confirmation email and you can download the ParaDiS source code. The same web site also contains the documentation of the ParaDiS code, including tutorials and reference manuals.

The source file you obtain should look something like <tt>pub-dd3d.v2.0.tar.gz</tt>. It is recommended that you create a <tt>~/Codes</tt> directory and extract the source code there.

<pre>
cd ~/Codes
tar zxvf pub-dd3d.v2.0.tar.gz
cd dd3dv2.0
</pre>

This should create a <tt>~/Codes/dd3dv2.0</tt> directory. We will refer to it as <tt>$ParaDiS</tt> in the following. Check that you have the following directories within your <tt>$ParaDiS</tt> directory: <tt>Inputs</tt>, <tt>Tests</tt>, <tt>Tools</tt>, <tt>Utilities</tt>.

==How to compile ParaDiS==

Go to the <tt>$ParaDiS</tt> directory. You may need to edit the <tt>makefile.setup</tt> file. The most important variables are <tt>SYS</tt> and <tt>MODE</tt>. <tt>SYS</tt> specifies the type of your computer and <tt>MODE</tt> can be either <tt>SERIAL</tt> or <tt>PARALLEL</tt>. For example, suppose you want to compile ParaDiS on a Linux/Intel workstation with 1 processor. You want to set <tt>SYS = i386</tt> and <tt>MODE = SERIAL</tt> in the <tt>makefile.setup</tt> file. Then, you can just type

<pre>
make dd3d
</pre>

If the compilation is successful, this creates the main executable <tt>dd3d</tt> in your <tt>$ParaDiS</tt> directory. If you type

<pre>
make
</pre>

instead, then in addition to <tt>dd3d</tt>, a few useful executables will be created in the <tt>$ParaDiS/Utilities</tt> directory.

If there are some problems during compilation, you should then look into the <tt>makefile.setup</tt> file, and check whether the lines <tt>CC_SERIAL.i386</tt>, <tt>CPP_SERIAL.i386</tt>, <tt>CCFLAG_SERIAL.i386</tt>, <tt>CPPFLAG_SERIAL.i386</tt> correctly specify the C/C++ compilers on your computer.

You can compile ParaDiS on Windows if [[http://en.wikipedia.org/wiki/Cygwin cygwin]] installed. Set <tt>SYS = cygwin</tt> in <tt>makefile.setup</tt>.

==How to run a single-CPU ParaDiS simulation==

Using the <tt>dd3d</tt> executable compiled as described above, we can run a few test cases in the <tt>Tests</tt> directory. Each ParaDiS run is described in two input files: a <tt>.cn</tt> file (specifying simulation control parameters) and a <tt>.data</tt> with the same name (specifying the dislocation structure). For example, we can run

<pre>
./dd3d Tests/frank_read_src.cn
</pre>

In this run, ParaDiS will automatically look for file <tt>Tests/fread_read_src.data</tt> to read the dislocation (nodal) structure. The output for this run should look something like:

<pre>
***********************************************************
****
**** Time of run: Fri Nov 30 20:37:40 2007
**** Executable name: dd3d
**** Executable path: .
**** Working dir: ....
**** Execution host: .... i686
**** User name: Wei Cai
**** Number of tasks: 1
**** Command line: Tests/frank_read_src.cn
****
***********************************************************
Initialize: Parsing control file Tests/frank_read_src.cn
Initialize: Control file parsing complete
ReadNodeDataFile: dataFile = Tests/frank_read_src.data
node count: 3

...

chdir successful on all tasks.
DD3dInit finished
cycle=1 realdt=5.953988e-10 timeNow=1.511247e-06 Fri Nov 30 20:37:43 2007
cycle=2 realdt=7.144786e-10 timeNow=1.511962e-06 Fri Nov 30 20:37:43 2007
cycle=3 realdt=8.573743e-10 timeNow=1.512819e-06 Fri Nov 30 20:37:43 2007

...
</pre>

After <tt>DD3dInit</tt> finishes, ParaDiS prints one line every simulation step (cycle), which includes the cycle number, physical time step (realdt), physical time (timeNow), and computer wall time. Notice that the physical time advance for each time step is not a constant during the simulation.

By default, a window will open spontaneously, which displays the evolution of the dislocations. The setting for this window is specified in the <tt>win.script</tt> file. In particular, the window will be disabled if <tt>enable_window = 0</tt>. By default <tt>enable_window = 1</tt> is set in this file. You can rotate the 3-dimensional dislocation structure by dragging your mouse in the display window. You can also zoom in and out, as well as save a snapshot into file. Press <tt>F1</tt> in the window, and a list of short-keys will be printed in your terminal. For example, the <tt>F9</tt> key saves the current window into a <tt>.gif</tt> file and the <tt>F10</tt> saves a <tt>.ps</tt> file.

==ParaDiS input and output==

The content of ParaDiS control files, e.g. <tt>Tests/frank_read_src.cn</tt> look something like this:

<pre>
### DD3d configuration file (use -*-shell-script-*- format)
#
# Sample control file to be used in conjunction with
# the frank_read_src.data file.
#
dirname = "Tests/frank_read_src_results"
Rijmfile = "Inputs/Rijm.cube.out"
RijmPBCfile = "Inputs/RijmPBC.cube.out"
numXdoms = 1
numYdoms = 1
numZdoms = 1

...
</pre>

Anything following the pound sign <tt>#</tt> is a comment. The values of the parameters are specified by the syntax <tt>var_name = value</tt>. A list of all ParaDiS input variables is available [[http://paradis.stanford.edu/docs here]]. In the following we describe a few of the most important ones.

For single CPU runs, <tt>numXdoms</tt>, <tt>numYdoms</tt> and <tt>numZdoms</tt> should all be set to <tt>1</tt>. For parallel runs, the total number of CPUs must match <tt>numXdoms</tt> * <tt>numYdoms</tt> * <tt>numZdoms</tt>. <tt>maxstep</tt> specifies the total number of time steps (cycles) for the simulation.

<tt>dirname</tt> specifies the directory in which all output files are created. Simulation output styles are specified by groups of variables. For example, <tt>saveprop</tt>, <tt>saveprop_freq</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_time</tt> specifies how frequent and how detailed the simulation properties should be saved. The simulation property files are saved in the <tt>properties</tt> sub-directory, which contains the stress-strain curve (<tt>stress_Total_strain</tt> file) and the dislocatoin density (<tt>density</tt> file). Similarly, <tt>gnuplot</tt>, <tt>gnuplot_freq</tt>, <tt>gnuplot_counter</tt>, <tt>gnuplot_dt</tt>, <tt>gnuplot_timie</tt> together specify whether and how ParaDiS will output snapshots of dislocation structures in the [[http://en.wikipedia.org/wiki/Gnuplot gnuplot]] format.

Within the directory specified by <tt>dirname</tt>, the <tt>restart<tt> sub-directory contains restart files, e.g. <tt>rs0001</tt> (control file) and <tt>rs0001.data</tt> (nodal data file), which are saved periodically during the simulation. The <tt>restart</tt> and <tt>restart.data</tt> files are saved at the end of the simulation. The <tt>timers</tt> sub-directory contains computational time information for different parts of the program.

==How to run a parallel ParaDiS simulation==

Compiling and running ParaDiS in parallel depends on the specific settings of your computer cluster. Here we explain the main steps using our own cluster [[http://hpcc.stanford.edu mc-cc.stanford.edu]] as an example.

First, ParaDiS need to be compiled in the parallel mode. You need to set <tt>MODE = PARALLEL</tt> in <tt>makefile.setup</tt>. You also need to choose the correct <tt>SYS</tt> or write your own to use the correct MPI compiler. For example, we wrote our own settings for <tt>SYS = mc-cc</tt> in the <tt>makefile.sys</tt> file. You may try <tt>SYS = i386</tt> or <tt>SYS = linux</tt> if you have an Intel cluster.

In a shared cluster, you need to submit the parallel job into a queue, usually by the <tt>qsub</tt> command, such as

<pre>
qsub run_dd3d.qsub
</pre>

where <tt>run_dd3d.qsub</tt> may look like the following

<pre>
#!/bin/bash
#PBS -N my-paradis-run
#PBS -j oe
#PBS -l nodes=2:ppn=4,walltime=48:00:00
#PBS -V

### ---------------------------------------
### BEGINNING OF EXECUTION
### ---------------------------------------

echo The master node of this job is `hostname`
echo The working directory is `echo $PBS_O_WORKDIR`
echo This job runs on the following nodes:
echo `cat $PBS_NODEFILE`

ncpu=`cat $PBS_NODEFILE | wc -w`
echo "Number of processors = $ncpu "
### end of information preamble

cd $PBS_O_WORKDIR
echo $PWD
./dd3d Outputs/myrun/restart.cn > dd3d_output

</pre>

In this example, ParaDiS will re-run a restart file (saved from a previous simulation) in the <tt>Outputs/myrun</tt> directory, using 8 CPUs. The total number of domains in the input file has to be modified to match this number, e.g. <tt>numXdoms = 2</tt>, <tt>numYdoms = 2</tt>, <tt>numZdoms = 2</tt>.

Usually you need to specify some environment variables for parallel programs to run successfully. For example, you may need to add the following lines to your <tt>~/.bash_profile</tt> file.

<pre>
PATH=$PATH:/share/apps/lib
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/lib
</pre>

Caiwei at 05:56, 1 December 2007

2007-12-01T05:56:32Z

← Older revision		Revision as of 05:56, 1 December 2007
Line 126:		Line 126:
	<pre>		<pre>
	#!/bin/bash		#!/bin/bash
	#PBS -N si-~~orig~~-~~7.1-1800K~~		#PBS -N my-paradis-run
	#PBS -j oe		#PBS -j oe
	#PBS -l nodes=2:ppn=4,walltime=48:00:00		#PBS -l nodes=2:ppn=4,walltime=48:00:00

Caiwei at 05:54, 1 December 2007

2007-12-01T05:54:53Z

← Older revision		Revision as of 05:54, 1 December 2007
Line 152:		Line 152:
	In this example, ParaDiS will re-run a restart file (saved from a previous simulation) in the <tt>Outputs/myrun</tt> directory, using 8 CPUs. The total number of domains in the input file has to be modified to match this number, e.g. <tt>numXdoms = 2</tt>, <tt>numYdoms = 2</tt>, <tt>numZdoms = 2</tt>.		In this example, ParaDiS will re-run a restart file (saved from a previous simulation) in the <tt>Outputs/myrun</tt> directory, using 8 CPUs. The total number of domains in the input file has to be modified to match this number, e.g. <tt>numXdoms = 2</tt>, <tt>numYdoms = 2</tt>, <tt>numZdoms = 2</tt>.

	Usually you need to specify some environment variables for parallel programs to run successfully. For example, you may need to add the following lines to your <tt>.bash_profile</tt> file.		Usually you need to specify some environment variables for parallel programs to run successfully. For example, you may need to add the following lines to your <tt>~/.bash_profile</tt> file.

	<pre>		<pre>

Caiwei at 05:41, 1 December 2007

2007-12-01T05:41:43Z

← Older revision		Revision as of 05:41, 1 December 2007
Line 105:		Line 105:

	<tt>dirname</tt> specifies the directory in which all output files are created. Simulation output styles are specified by groups of variables. For example, <tt>saveprop</tt>, <tt>saveprop_freq</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_time</tt> specifies how frequent and how detailed the simulation properties should be saved. The simulation property files are saved in the <tt>properties</tt> sub-directory, which contains the stress-strain curve (<tt>stress_Total_strain</tt> file) and the dislocatoin density (<tt>density</tt> file). Similarly, <tt>gnuplot</tt>, <tt>gnuplot_freq</tt>, <tt>gnuplot_counter</tt>, <tt>gnuplot_dt</tt>, <tt>gnuplot_timie</tt> together specify whether and how ParaDiS will output snapshots of dislocation structures in the [[http://en.wikipedia.org/wiki/Gnuplot gnuplot]] format.		<tt>dirname</tt> specifies the directory in which all output files are created. Simulation output styles are specified by groups of variables. For example, <tt>saveprop</tt>, <tt>saveprop_freq</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_time</tt> specifies how frequent and how detailed the simulation properties should be saved. The simulation property files are saved in the <tt>properties</tt> sub-directory, which contains the stress-strain curve (<tt>stress_Total_strain</tt> file) and the dislocatoin density (<tt>density</tt> file). Similarly, <tt>gnuplot</tt>, <tt>gnuplot_freq</tt>, <tt>gnuplot_counter</tt>, <tt>gnuplot_dt</tt>, <tt>gnuplot_timie</tt> together specify whether and how ParaDiS will output snapshots of dislocation structures in the [[http://en.wikipedia.org/wiki/Gnuplot gnuplot]] format.

			Within the directory specified by <tt>dirname</tt>, the <tt>restart<tt> sub-directory contains restart files, e.g. <tt>rs0001</tt> (control file) and <tt>rs0001.data</tt> (nodal data file), which are saved periodically during the simulation. The <tt>restart</tt> and <tt>restart.data</tt> files are saved at the end of the simulation. The <tt>timers</tt> sub-directory contains computational time information for different parts of the program.



Line 122:		Line 125:

	<pre>		<pre>
			#!/bin/bash
			#PBS -N si-orig-7.1-1800K
			#PBS -j oe
			#PBS -l nodes=2:ppn=4,walltime=48:00:00
			#PBS -V

			### ---------------------------------------
⚫	</pre>
			### BEGINNING OF EXECUTION
			### ---------------------------------------

			echo The master node of this job is `hostname`
			echo The working directory is `echo $PBS_O_WORKDIR`
			echo This job runs on the following nodes:
			echo `cat $PBS_NODEFILE`

			ncpu=`cat $PBS_NODEFILE \| wc -w`
			echo "Number of processors = $ncpu "
			### end of information preamble

			cd $PBS_O_WORKDIR
			echo $PWD
			./dd3d Outputs/myrun/restart.cn > dd3d_output

		⚫	</pre>
	==ParaDiS input parameters==

			In this example, ParaDiS will re-run a restart file (saved from a previous simulation) in the <tt>Outputs/myrun</tt> directory, using 8 CPUs. The total number of domains in the input file has to be modified to match this number, e.g. <tt>numXdoms = 2</tt>, <tt>numYdoms = 2</tt>, <tt>numZdoms = 2</tt>.

			Usually you need to specify some environment variables for parallel programs to run successfully. For example, you may need to add the following lines to your <tt>.bash_profile</tt> file.

			<pre>
			PATH=$PATH:/share/apps/lib
			LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/lib
			</pre>

Caiwei: Add parallel run

2007-12-01T05:26:29Z

Add parallel run

← Older revision		Revision as of 05:26, 1 December 2007
Line 80:		Line 80:


		⚫	==ParaDiS input and output==
⚫	==~~A few~~ ParaDiS ~~control~~ parameters==

	The content of ParaDiS control files, e.g. <tt>Tests/frank_read_src.cn</tt> look something like this:		The content of ParaDiS control files, e.g. <tt>Tests/frank_read_src.cn</tt> look something like this:
Line 109:		Line 109:
	==How to run a parallel ParaDiS simulation==		==How to run a parallel ParaDiS simulation==

			Compiling and running ParaDiS in parallel depends on the specific settings of your computer cluster. Here we explain the main steps using our own cluster [[http://hpcc.stanford.edu mc-cc.stanford.edu]] as an example.

			First, ParaDiS need to be compiled in the parallel mode. You need to set <tt>MODE = PARALLEL</tt> in <tt>makefile.setup</tt>. You also need to choose the correct <tt>SYS</tt> or write your own to use the correct MPI compiler. For example, we wrote our own settings for <tt>SYS = mc-cc</tt> in the <tt>makefile.sys</tt> file. You may try <tt>SYS = i386</tt> or <tt>SYS = linux</tt> if you have an Intel cluster.

			In a shared cluster, you need to submit the parallel job into a queue, usually by the <tt>qsub</tt> command, such as

			<pre>
			qsub run_dd3d.qsub
			</pre>

			where <tt>run_dd3d.qsub</tt> may look like the following

			<pre>
⚫	==ParaDiS input ~~parameters~~==

			</pre>




	==ParaDiS outputs==
		⚫	==ParaDiS input parameters==

Caiwei: Add simple parameters

2007-12-01T05:12:48Z

Add simple parameters

← Older revision		Revision as of 05:12, 1 December 2007
Line 100:		Line 100:
	</pre>		</pre>

	Anything following the pound sign <tt>#</tt> is a comment. The values of the parameters are specified by the syntax <tt>var_name = value</tt>. A list of all ParaDiS input variables is available [[http://paradis.stanford.edu/docs here]]. ~~Here~~ we describe a few of the most important ones.		Anything following the pound sign <tt>#</tt> is a comment. The values of the parameters are specified by the syntax <tt>var_name = value</tt>. A list of all ParaDiS input variables is available [[http://paradis.stanford.edu/docs here]]. In the following we describe a few of the most important ones.

		⚫	For single CPU runs, <tt>numXdoms</tt>, <tt>numYdoms</tt> and <tt>numZdoms</tt> should all be set to <tt>1</tt>. For parallel runs, the total number of CPUs must match <tt>numXdoms</tt> * <tt>numYdoms</tt> * <tt>numZdoms</tt>. <tt>maxstep</tt> specifies the total number of time steps (cycles) for the simulation.

			<tt>dirname</tt> specifies the directory in which all output files are created. Simulation output styles are specified by groups of variables. For example, <tt>saveprop</tt>, <tt>saveprop_freq</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_dt</tt>, <tt>saveprop_time</tt> specifies how frequent and how detailed the simulation properties should be saved. The simulation property files are saved in the <tt>properties</tt> sub-directory, which contains the stress-strain curve (<tt>stress_Total_strain</tt> file) and the dislocatoin density (<tt>density</tt> file). Similarly, <tt>gnuplot</tt>, <tt>gnuplot_freq</tt>, <tt>gnuplot_counter</tt>, <tt>gnuplot_dt</tt>, <tt>gnuplot_timie</tt> together specify whether and how ParaDiS will output snapshots of dislocation structures in the [[http://en.wikipedia.org/wiki/Gnuplot gnuplot]] format.

⚫	For single CPU runs, <tt>numXdoms</tt>, <tt>numYdoms</tt> and <tt>numZdoms</tt> should all be set to <tt>1</tt>. For parallel runs, the total number of CPUs must match <tt>numXdoms</tt> * <tt>numYdoms</tt> * <tt>numZdoms</tt>. <tt>maxstep</tt> specifies the total number of time steps (cycles) for the simulation. Simulation output styles are specified by groups of variables. For example, <tt>gnuplot</tt>, <tt>gnuplot_freq</tt>, <tt>gnuplot_counter</tt>, <tt>gnuplot_dt</tt>, <tt>gnuplot_timie</tt> together specify whether and how ParaDiS will output snapshots of dislocation structures in the [[http://en.wikipedia.org/wiki/Gnuplot gnuplot]] format.

	==How to run a parallel ParaDiS simulation==		==How to run a parallel ParaDiS simulation==