MCNP - Revision history

Ondrejch at 17:09, 16 October 2018

2018-10-16T17:09:16Z

WikiSysop: /* Common Problems */

2014-08-27T21:47:12Z

Common Problems

Ondrejch: /* How to run MCNP5/MCNPX */

2014-07-06T19:33:36Z

How to run MCNP5/MCNPX

Ondrejch: /* How to run MCNP5/MCNPX */

2013-08-16T20:29:00Z

How to run MCNP5/MCNPX

WikiSysop: /* How to run MCNP5/MCNPX */

2013-02-26T20:38:46Z

How to run MCNP5/MCNPX

WikiSysop at 15:08, 6 July 2012

2012-07-06T15:08:01Z

WikiSysop at 03:09, 4 November 2011

2011-11-04T03:09:38Z

WikiSysop at 03:04, 4 November 2011

2011-11-04T03:04:44Z

WikiSysop at 03:01, 4 November 2011

2011-11-04T03:01:37Z

WikiSysop: Created page with "== How to run MCNP5/MCNPX == The first step is to ensure that you have permission to use MCNP5/X from [http://rsicc.ornl.gov/Default.aspx RSICC]. Once you have permission, let…"

2011-11-03T23:06:42Z

Created page with "== How to run MCNP5/MCNPX == The first step is to ensure that you have permission to use MCNP5/X from [http://rsicc.ornl.gov/Default.aspx RSICC]. Once you have permission, let…"

New page

== How to run MCNP5/MCNPX ==

The first step is to ensure that you have permission to use MCNP5/X from [http://rsicc.ornl.gov/Default.aspx RSICC]. Once you have permission, let me know so I can add you to the ''mcnp5'' group on the cluster. This will set up your shell environment automatically so you can run MCNP5/X with ease!

@@ Line 13: / Line 13: @@
 Running MCNP5 in it's most basic form involves calling the MCNP5 executable with several arguments.  As an example, you can run MCNP5 with the input file called ''mcnp_input'' as such:
-<code>'''user@node:~/$''' mcnp5.mpi name=''mcnp_input''</code>
+<code>'''user@node:~/$''' mcnp5 name=''mcnp_input''</code>
 This will run your input using one thread on the node you're running on.
@@ Line 21: / Line 21: @@
 MCNP5 supports OpenMP so that you can run using multiple threads on your selected node.  Since none of the cluster nodes have only one core it is very advantageous to use this option to obtain an almost linear increase in speed as threads are added.  Remember to check [http://necluster.engr.utk.edu/ganglia/ Ganglia] to see how many cores the node you want to run on has.  Running MCNP5 in this fashion is almost as easy as running just one thread, so there's no reason not to do it!:
-<code>'''user@node:~/$''' mcnp5.mpi TASKS ''n'' name=''mcnp_input''</code>
+<code>'''user@node:~/$''' mcnp5 TASKS ''n'' name=''mcnp_input''</code>
 For this, ''n'' is the number of threads you want to run.

← Older revision		Revision as of 21:47, 27 August 2014
Line 65:		Line 65:
	== Common Problems ==		== Common Problems ==

−	~~COMING LESS SOON!~~	+	See the common problems section of [[TORQUE/Maui]].

← Older revision		Revision as of 19:33, 6 July 2014
Line 4:		Line 4:

	'''THIS INFORMATION HAS BEEN LARGELY SUPERSEDED BY THE [[TORQUE/Maui]] AND [[Beginners Guide to MCNP with Torque]] PAGES! IT IS KEPT FOR LEGACY REASONS.'''		'''THIS INFORMATION HAS BEEN LARGELY SUPERSEDED BY THE [[TORQUE/Maui]] AND [[Beginners Guide to MCNP with Torque]] PAGES! IT IS KEPT FOR LEGACY REASONS.'''
		+
		+	'''Please DELETE runtape files if you don't need them!'''

	=== Running MCNP5 ===		=== Running MCNP5 ===

@@ Line 3: / Line 3: @@
 The first step is to ensure that you have permission to use MCNP5/X from [http://rsicc.ornl.gov/Default.aspx RSICC].  Once you have permission, let me know so I can add you to the ''mcnp5'' group on the cluster.  You can then load the MCNP5 or MCNPX module with <code>module load MCNP5</code> or <code>module load MCNPX</code> respectively.
-'''THIS INFORMATION HAS BEEN LARGELY SUPERSEDED BY THE [[TORQUE/Maui]] PAGE!  IT IS KEPT FOR LEGACY REASONS.'''
+'''THIS INFORMATION HAS BEEN LARGELY SUPERSEDED BY THE [[TORQUE/Maui]] AND [[Beginners Guide to MCNP with Torque]] PAGES!  IT IS KEPT FOR LEGACY REASONS.'''
 === Running MCNP5 ===

← Older revision		Revision as of 20:38, 26 February 2013
Line 2:		Line 2:

	The first step is to ensure that you have permission to use MCNP5/X from [http://rsicc.ornl.gov/Default.aspx RSICC]. Once you have permission, let me know so I can add you to the ''mcnp5'' group on the cluster. You can then load the MCNP5 or MCNPX module with <code>module load MCNP5</code> or <code>module load MCNPX</code> respectively.		The first step is to ensure that you have permission to use MCNP5/X from [http://rsicc.ornl.gov/Default.aspx RSICC]. Once you have permission, let me know so I can add you to the ''mcnp5'' group on the cluster. You can then load the MCNP5 or MCNPX module with <code>module load MCNP5</code> or <code>module load MCNPX</code> respectively.
		+
		+	'''THIS INFORMATION HAS BEEN LARGELY SUPERSEDED BY THE [[TORQUE/Maui]] PAGE! IT IS KEPT FOR LEGACY REASONS.'''

	=== Running MCNP5 ===		=== Running MCNP5 ===

@@ Line 1: / Line 1: @@
 == How to run MCNP5/MCNPX ==
-The first step is to ensure that you have permission to use MCNP5/X from [http://rsicc.ornl.gov/Default.aspx RSICC].  Once you have permission, let me know so I can add you to the ''mcnp5'' group on the cluster.  This will set up your shell environment automatically so you can run MCNP5/X with ease!
+The first step is to ensure that you have permission to use MCNP5/X from [http://rsicc.ornl.gov/Default.aspx RSICC].  Once you have permission, let me know so I can add you to the ''mcnp5'' group on the cluster.  You can then load the MCNP5 or MCNPX module with <code>module load MCNP5</code> or <code>module load MCNPX</code> respectively.
 === Running MCNP5 ===
@@ Line 9: / Line 9: @@
 Running MCNP5 in it's most basic form involves calling the MCNP5 executable with several arguments.  As an example, you can run MCNP5 with the input file called ''mcnp_input'' as such:
-<code>'''user@node:~/$''' mcnp5.both name=''mcnp_input''</code>
+<code>'''user@node:~/$''' mcnp5.mpi name=''mcnp_input''</code>
 This will run your input using one thread on the node you're running on.
@@ Line 17: / Line 17: @@
 MCNP5 supports OpenMP so that you can run using multiple threads on your selected node.  Since none of the cluster nodes have only one core it is very advantageous to use this option to obtain an almost linear increase in speed as threads are added.  Remember to check [http://necluster.engr.utk.edu/ganglia/ Ganglia] to see how many cores the node you want to run on has.  Running MCNP5 in this fashion is almost as easy as running just one thread, so there's no reason not to do it!:
-<code>'''user@node:~/$''' mcnp5.both TASKS ''n'' name=''mcnp_input''</code>
+<code>'''user@node:~/$''' mcnp5.mpi TASKS ''n'' name=''mcnp_input''</code>
 For this, ''n'' is the number of threads you want to run.
@@ Line 26: / Line 26: @@
 * '''Machine File'''
-<code> '''user@node:~/$''' /opt/openmpi-1.4.3/bin/mpirun -np ''#'' -machinefile ''machine_file'' /opt/MCNP5-1.60/bin/linux/mcnp5.both TASKS ''n'' name=''mcnp_input'' balance</code>
+<code> '''user@node:~/$''' mpirun -np ''#'' -machinefile ''machine_file'' mcnp5.mpi TASKS ''n'' name=''mcnp_input''</code>
 Where ''#'' is the number of nodes you want to run on and ''machine_file'' is a text file containing a list of nodes that you want to run out.  Note that ''#'' has to be less than or equal to the number of nodes you list in your ''machine_file''.
@@ Line 43: / Line 43: @@
 * '''Command Line''':
-<code>'''user@node:~/$''' /opt/openmpi-1.4.3/bin/mpirun -np ''#'' -host ''<host1,host2,...,hostn>'' /opt/MCNP5-1.60/bin/linux/mcnp5.both TASKS ''n'' name=''mcnp_input'' balance</code>
+<code>'''user@node:~/$''' mpirun -np ''#'' -host ''<host1,host2,...,hostn>'' mcnp5.mpi TASKS ''n'' name=''mcnp_input''</code>
 In this method, you just list your hosts in a comma separated block.  Continuing with the example from the previous section (running on 4 nodes):
-<code>'''user@node:~/$''' /opt/openmpi-1.4.3/bin/mpirun -np 4 -host node2,node3,node4,node5 /opt/MCNP5-1.60/bin/linux/mcnp5.both TASKS ''n'' name=''mcnp_input'' balance</code>
+<code>'''user@node:~/$''' mpirun -np 4 -host node2,node3,node4,node5 mcnp5.mpi TASKS ''n'' name=''mcnp_input''</code>
 The same caveat regarding the master node applies.
@@ Line 53: / Line 53: @@
 === Running MCNPX ===
-COMING SOON!
+MCNPX is run in a similar way to MCNP5.  There are two differences:
 == Common Problems ==
 COMING LESS SOON!

@@ Line 28: / Line 28: @@
 <code> '''user@node:~/$''' /opt/openmpi-1.4.3/bin/mpirun -np ''#'' -machinefile ''machine_file'' /opt/MCNP5-1.60/bin/linux/mcnp5.both TASKS ''n'' name=''mcnp_input'' balance</code>
-Where ''#'' is the number of nodes you want to run on and ''machine_file'' is a text file containing a list of nodes that you want to run out.  Note that ''#'' has to be less to or equal than the number of nodes you list in your ''machine_file''.
+Where ''#'' is the number of nodes you want to run on and ''machine_file'' is a text file containing a list of nodes that you want to run out.  Note that ''#'' has to be less than or equal to the number of nodes you list in your ''machine_file''.
 A typical ''machine_file'' would be something like this:

@@ Line 41: / Line 41: @@
 '''Note:''' MCNP requires one node to be the ''master node''.  This node will be the first node that you list in the machine file.  Thus, if you run MCNP5 like the above example, MCNP will tell you that it is only running on 3 nodes.  The number of threads on the master node will always be 1, regardless of what you set ''n'' to in the ''TASKS'' argument.  If, in our example we say ''TASKS 4'', MCNP will use 13 threads total: 1 on node2 (master node), and 4 on node3, node4, and node5.
-* Command Line:
+* '''Command Line''':
 <code>'''user@node:~/$''' /opt/openmpi-1.4.3/bin/mpirun -np ''#'' -host ''<host1,host2,...,hostn>'' /opt/MCNP5-1.60/bin/linux/mcnp5.both TASKS ''n'' name=''mcnp_input'' balance</code>

← Older revision		Revision as of 03:01, 4 November 2011
Line 1:		Line 1:
	== How to run MCNP5/MCNPX ==		== How to run MCNP5/MCNPX ==

		+	The first step is to ensure that you have permission to use MCNP5/X from [http://rsicc.ornl.gov/Default.aspx RSICC]. Once you have permission, let me know so I can add you to the ''mcnp5'' group on the cluster. This will set up your shell environment automatically so you can run MCNP5/X with ease!
		+
		+	=== Running MCNP5 ===
		+
		+	==== Basic Run ====
		+
		+	Running MCNP5 in it's most basic form involves calling the MCNP5 executable with several arguments. As an example, you can run MCNP5 with the input file called ''mcnp_input'' as such:
		+
		+	<code>'''user@node:~/$''' mcnp5.both name=''mcnp_input''</code>
		+
		+	This will run your input using one thread on the node you're running on.
		+
		+	==== OpenMP Run ====
		+
		+	MCNP5 supports OpenMP so that you can run using multiple threads on your selected node. Since none of the cluster nodes have only one core it is very advantageous to use this option to obtain an almost linear increase in speed as threads are added. Remember to check [http://necluster.engr.utk.edu/ganglia/ Ganglia] to see how many cores the node you want to run on has. Running MCNP5 in this fashion is almost as easy as running just one thread, so there's no reason not to do it!:
		+
		+	<code>'''user@node:~/$''' mcnp5.both TASKS ''n'' name=''mcnp_input''</code>
		+
		+	For this, ''n'' is the number of threads you want to run.

−	~~The first step~~ is ~~to ensure that~~ you have ~~permission~~ to use ~~MCNP5~~/~~X from [http:~~//~~rsicc~~.~~ornl~~.~~gov~~/~~Default~~.~~aspx RSICC]~~. ~~Once~~ you ~~have permission, let me know so I can add~~ you to the ''~~mcnp5~~'' ~~group on~~ the ~~cluster~~. This will ~~set up your shell environment automatically so~~ you ~~can~~ run MCNP5/X with ~~ease~~!	+	==== MPI Run ====
		+
		+	For the ultimate in speed you can use OpenMPI to run your case on multiple nodes at the same time. You can combine MPI with OpenMP to run multiple threads on multiple nodes. Running with MPI is slightly more involved since you have to remember the use absolute paths to make sure everything is picked up. Also, you need to specify which nodes to run on. There are two ways to do this: 1) Using a machine file, 2) From the command line.
		+
		+	* '''Machine File'''
		+	<code> '''user@node:~/$''' /opt/openmpi-1.4.3/bin/mpirun -np ''#'' -machinefile ''machine_file'' /opt/MCNP5-1.60/bin/linux/mcnp5.both TASKS ''n'' name=''mcnp_input'' balance</code>
		+
		+	Where ''#'' is the number of nodes you want to run on and ''machine_file'' is a text file containing a list of nodes that you want to run out. Note that ''#'' has to be less to or equal than the number of nodes you list in your ''machine_file''.
		+
		+	A typical ''machine_file'' would be something like this:
		+
		+	<pre>node2
		+	node3
		+	node4
		+	node5</pre>
		+
		+	For this example ''#'' would be 4.
		+
		+	'''Note:''' MCNP requires one node to be the ''master node''. This node will be the first node that you list in the machine file. Thus, if you run MCNP5 like the above example, MCNP will tell you that it is only running on 3 nodes. The number of threads on the master node will always be 1, regardless of what you set ''n'' to in the ''TASKS'' argument. If, in our example we say ''TASKS 4'', MCNP will use 13 threads total: 1 on node2 (master node), and 4 on node3, node4, and node5.
		+
		+	* Command Line:
		+
		+	<code>'''user@node:~/$''' /opt/openmpi-1.4.3/bin/mpirun -np ''#'' -host ''<host1,host2,...,hostn>'' /opt/MCNP5-1.60/bin/linux/mcnp5.both TASKS ''n'' name=''mcnp_input'' balance</code>
		+
		+	In this method, you just list your hosts in a comma separated block. Continuing with the example from the previous section (running on 4 nodes):
		+
		+	<code>'''user@node:~/$''' /opt/openmpi-1.4.3/bin/mpirun -np 4 -host node2,node3,node4,node5 /opt/MCNP5-1.60/bin/linux/mcnp5.both TASKS ''n'' name=''mcnp_input'' balance</code>
		+
		+	The same caveat regarding the master node applies.
		+
		+	=== Running MCNPX ===
		+
		+	COMING SOON!
		+
		+	== Common Problems ==
		+
		+	COMING LESS SOON!