Running With Slurm - Revision history

Oborn at 22:26, 2 August 2010

2010-08-02T22:26:50Z

Oborn at 23:09, 14 April 2010

2010-04-14T23:09:56Z

Oborn at 23:09, 14 April 2010

2010-04-14T23:09:20Z

Oborn at 22:43, 9 April 2010

2010-04-09T22:43:09Z

Oborn at 22:19, 1 April 2010

2010-04-01T22:19:07Z

Oborn at 01:42, 1 April 2010

2010-04-01T01:42:26Z

Oborn at 01:42, 1 April 2010

2010-04-01T01:42:05Z

Oborn: Created page with '[Slurm https://computing.llnl.gov/linux/slurm/] is the queuing system used on Brems. It allows multiple users to put jobs into a queue and the system to negotiate running them op...'

2010-04-01T01:21:38Z

Created page with '[Slurm https://computing.llnl.gov/linux/slurm/] is the queuing system used on Brems. It allows multiple users to put jobs into a queue and the system to negotiate running them op...'

New page

[Slurm https://computing.llnl.gov/linux/slurm/] is the queuing system used on Brems. It allows multiple users to put jobs into a queue and the system to negotiate running them optimally. To use slurm with MCNPX do the following: '''(beta instructions)'''

Create a script file like this one, substituting your MCNPX parameters:
brian@brems:~/work/maxwell/run15$ cat runmcnpx
#!/bin/bash
#number of processes to run:
#SBATCH -n 8
DATAPATH=/opt/mcnpx/data/
srun /opt/mcnpx/v27b_64_mpi_i8_slurm/bin/mcnpx i=14MeV.i

Add your run to the queue:
brian@brems:~/work/maxwell/run15$ sbatch ./runmcnpx
sbatch: Submitted batch job 3

Verify that your run is in the queue:
brian@brems:~/work/maxwell/run15$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
3 brems runmcnpx brian PD 0:00 1 (Resources)
2 brems runmcnpx brian R 11:54 1 brems

You can check the output of your run:
brian@brems:~/work/maxwell/run15$ cat slurm-3.out
mcnpx ver=27b ld=Tue Aug 18 08:00:00 MST 2009 03/31/10 19:03:50

*************************************************************
* *
* MCNPX *
* *
* Copyright 2007. Los Alamos National Security, LLC. *
* All rights reserved. *
* *
* This material was produced under U.S. Government contract *

← Older revision		Revision as of 22:26, 2 August 2010
Line 1:		Line 1:
−	[Slurm https://computing.llnl.gov/linux/slurm/] is the queuing system used on Brems. It allows multiple users to put jobs into a queue and the system to negotiate running them optimally. ~~To use slurm with MCNPX do the~~ following~~: '''(beta~~ instructions~~)'''~~	+	[Slurm https://computing.llnl.gov/linux/slurm/] is the queuing system used on Brems. It allows multiple users to put jobs into a queue and the system to negotiate running them optimally.
		+
		+	The following instructions are for running MCNPX on Brems.

	==Adding you run to the queue==		==Adding you run to the queue==

@@ Line 31: / Line 31: @@
   sbatch: Submitted batch job 3
-====Checking runs currently in the queue====
+==Checking runs currently in the queue==
   brian@brems:~/work$ squeue
    JOBID PARTITION     NAME     USER  ST       TIME  NODES NODELIST(REASON)
@@ Line 40: / Line 40: @@
      brems    1.0mm     neba   R    1:01:30      1 brems
-====Check the output of your run====
+==Check the output of your run==
 Replace 33 with the '''JOBID''' of your run:
   brian@brems:~/work$ less slurm-33.out
@@ Line 53: / Line 53: @@
   * This material was produced under U.S. Government contract *
-====Cancel a queued or running job====
+==Cancel a queued or running job==
 Use the '''scancel''' command, replacing 33 with your '''JOBID'''
   brian@brems:~/work$ scancel 33
-====Attach to a currently running job====
+==Attach to a currently running job==
 Use the '''sattach''' command, replacing 33 with your '''JOBID''', but making sure to retain the .0
   brian@brems:~/work$ sattach 106.0

@@ Line 1: / Line 1: @@
 [Slurm https://computing.llnl.gov/linux/slurm/] is the queuing system used on Brems. It allows multiple users to put jobs into a queue and the system to negotiate running them optimally. To use slurm with MCNPX do the following: '''(beta instructions)'''
 Create a script file like this one, substituting your MCNPX parameters at the end of the last line:
   #!/bin/bash
@@ Line 6: / Line 25: @@
   #SBATCH -n 8
   export DATAPATH=/opt/mcnpx/data/
-  srun /opt/mcnpx/v27b_64_mpi_i8_slurm/bin/mcnpx n=14MeV.i
+  srun /opt/mcnpx/v27b_64_mpi_i8_slurm/bin/mcnpx i=14MeV.i o=14MeV.o
-Add your run to the queue:
+Add your run to the queue using '''sbatch'''. The -J is optional and allows you to specify a name for your job so you can keep track on them in the queue better.
-  brian@brems:~/work/maxwell/run15$ sbatch ./runmcnpx
+  brian@brems:~/work$ sbatch ./runmcnpx -J myjobname
   sbatch: Submitted batch job 3
-Verify that your run is in the queue:
+====Checking runs currently in the queue====
-  brian@brems:~/work/maxwell/run15$ squeue
+  brian@brems:~/work$ squeue
    JOBID PARTITION     NAME     USER  ST       TIME  NODES NODELIST(REASON)
-    brems runmcnpx    brian  PD       0:00      1 (Resources)
+     brems  14MeV.i    brian  PD       0:00      1 (Resources)
-    brems runmcnpx    brian   R      11:54      1 brems
+    brems  18MeV.i    brian  PD       0:00      1 (Resources)
-You can check the output of your run:
+====Check the output of your run====
-  brian@brems:~/work/maxwell/run15$ cat slurm-3.out
+Replace 33 with the '''JOBID''' of your run:
   mcnpx    ver=27b   ld=Tue Aug 18 08:00:00 MST 2009   03/31/10 19:03:50
   *************************************************************
   *                                                           *
@@ Line 31: / Line 53: @@
   * This material was produced under U.S. Government contract *
-To cancel a queued or running job use scancel:
+====Cancel a queued or running job====
-  brian@brems:~$ scancel 3
+Use the '''scancel''' command, replacing 33 with your '''JOBID'''
-  brian@brems:~$ squeue
+  brian@brems:~/work$ scancel 33
-   JOBID PARTITION     NAME     USER  ST       TIME  NODES NODELIST(REASON)
-     brems runmcnpx    brian  PD       0:00      1 (Resources)
-     brems runmcnpx    brian   R      33:02      1 brems
+====Attach to a currently running job====

@@ Line 36: / Line 36: @@
   brian@brems:~$ squeue
    JOBID PARTITION     NAME     USER  ST       TIME  NODES NODELIST(REASON)
-     brems runmcnpx makavakh  PD       0:00      1 (Resources)
+     brems runmcnpx    brian  PD       0:00      1 (Resources)
      brems runmcnpx    brian   R      33:02      1 brems

← Older revision		Revision as of 01:42, 1 April 2010
Line 31:		Line 31:
	* *		* *
	* This material was produced under U.S. Government contract *		* This material was produced under U.S. Government contract *
		+
		+	To cancel a queued or running job use scancel:
		+	brian@brems:~$ scancel 3
		+	brian@brems:~$ squeue
		+	JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
		+	4 brems runmcnpx makavakh PD 0:00 1 (Resources)
		+	2 brems runmcnpx brian R 33:02 1 brems