Microsoft Linux Cluster User Notes - Revision history

Admin: /* Launching it from Windows */

2017-10-10T11:06:01Z

Launching it from Windows

← Older revision		Revision as of 13:06, 10 October 2017
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	=== Launching it from Windows ===		=== Launching it from Windows ===
	* I'm going to write <code>\\fi--san03\homes\wrh1\testlinux\launch.bat</code> - which is a '''Windows''' batch file to launch the job.		* I'm going to write <code>\\fi--san03\homes\wrh1\testlinux\launch.bat</code> - which is a '''Windows''' batch file to launch the job.


	<pre>		<pre>
	job submit /scheduler:fi--didelxhn /jobtemplate:LinuxNodes ~/dide/home/testlinux/run.sh		job submit /scheduler:fi--didelxhn /jobtemplate:LinuxNodes ~/dide/home/testlinux/run.sh

Admin at 11:05, 10 October 2017

2017-10-10T11:05:49Z

← Older revision		Revision as of 13:05, 10 October 2017
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	* Obviously, replace <code><dide-username></code> with your username. So note here that <code>/homes/<dide-username></code> is what Linux refers to when you use <code>~</code>.		* Obviously, replace <code><dide-username></code> with your username. So note here that <code>/homes/<dide-username></code> is what Linux refers to when you use <code>~</code>.
	* The full path to your dide home directory, from a linux job, will therefore be: <code>/homes/<dide-username>/dide/home</code>.		* The full path to your dide home directory, from a linux job, will therefore be: <code>/homes/<dide-username>/dide/home</code>.

			== Running Something ==

			=== Hello World in C ===

			* We'll probably want the code to be compiled on the cluster, so here's a really simple example that compiles and runs something....
			* Here's my complicated simulation code, which I'm going to save as <code>\\fi--san03\homes\wrh1\testlinux\hw.c</code>.

			<pre>
			#include <stdio.h>
			int main() {
			printf("Hello World!\n");
			return 0;
			}
			</pre>

			* And now I'm going to write a script that compiles this code on Linux, and runs it collecting some results.
			* '''IMPORTANT:''' - this is going to be a <code>.sh</code> files, and must have Linux line-endings.

			<pre>
			cd ~/dide/home/testlinux
			gcc -o hw hw.c
			chmod 755 ./hw
			./hw > output.txt
			</pre>

			=== Launching it from Windows ===
			* I'm going to write <code>\\fi--san03\homes\wrh1\testlinux\launch.bat</code> - which is a '''Windows''' batch file to launch the job.


			<pre>
			job submit /scheduler:fi--didelxhn /jobtemplate:LinuxNodes ~/dide/home/testlinux/run.sh
			</pre>

			* This launch.bat can be anywhere on your local machine, but I've kept everything in the same place for simplicity.
			* Run the launch.bat on your Windows machine, and when the job runs, you'll see the <code>hw</code> executable file, and the <code>output.txt</code> file appear.

			=== Launching it from the Web Portal ===
			* If you're not on Windows (which may be one reason you want to run on a linux cluster...), then use the HPC Web Portal to launch the job.
			* Log into the portal - if you've got rights, you'll see <code>fi--didelxn</code> listed. (Otherwise, see the section at the top...!)
			* Submit Job on the <code>fi--didelxn</code>.
			* Paste <code>~/dide/home/testlinux/run.sh</code> in the main job window. Set other things if you like. And submit it.
			* Look for <code>hw</code> and <code>output.txt</code> to appear in the test folder.

Admin at 10:48, 10 October 2017

2017-10-10T10:48:25Z

@@ Line 1: / Line 1: @@
-The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (or when the cluster logs in as you), your DIDE home directory will be automatically mounted as ~/dide/home, (where ~ is automatically set to /homes/<dide-username> - which is cluster-node specific, hence different on every node. Don't save stuff there!). If you want access to other windows shares, then create a file in your DIDE home directory, called <code>.pam_mount.conf.xml</code> containing something like this, replacing <dide-username> with your username (mine would be wrh1):-
+== Using the Linux Cluster ==
 <pre>
@@ Line 11: / Line 19: @@
 </pam_mount>
 </pre>

Admin at 15:16, 4 October 2016

2016-10-04T15:16:26Z

← Older revision		Revision as of 17:16, 4 October 2016
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	==Mounting shares for cluster use==		==Mounting shares for cluster use==

	The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (or when the cluster logs in as you), your DIDE home directory will be automatically mounted as ~/dide/home. If you want access to other windows shares, then create a file in your DIDE home directory, called <code>.pam_mount.conf.xml</code> containing something like this, replacing <dide-username> with your username (mine would be wrh1):-		The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (or when the cluster logs in as you), your DIDE home directory will be automatically mounted as ~/dide/home, (where ~ is automatically set to /homes/<dide-username> - which is cluster-node specific, hence different on every node. Don't save stuff there!). If you want access to other windows shares, then create a file in your DIDE home directory, called <code>.pam_mount.conf.xml</code> containing something like this, replacing <dide-username> with your username (mine would be wrh1):-

	<pre>		<pre>

Admin at 15:14, 4 October 2016

2016-10-04T15:14:26Z

← Older revision		Revision as of 17:14, 4 October 2016
Line 1:		Line 1:
	==Mounting shares for cluster use==		==Mounting shares for cluster use==

	The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (or when the cluster logs in as you), your DIDE home directory will be automatically mounted as ~/dide/home ~~and the temp directory as ~/dide/temp~~. If you want access to other windows shares, then create a file in your DIDE home directory, called <code>.pam_mount.conf.xml</code> containing something like this:-		The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (or when the cluster logs in as you), your DIDE home directory will be automatically mounted as ~/dide/home. If you want access to other windows shares, then create a file in your DIDE home directory, called <code>.pam_mount.conf.xml</code> containing something like this, replacing <dide-username> with your username (mine would be wrh1):-

	<pre>		<pre>

Admin at 15:13, 4 October 2016

2016-10-04T15:13:26Z

← Older revision		Revision as of 17:13, 4 October 2016
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	<?xml version="1.0" encoding="utf-8" ?>		<?xml version="1.0" encoding="utf-8" ?>
	<pam_mount>		<pam_mount>
	<volume options="nodev,nosuid" user="*" mountpoint="/~~media~~/f2gsim" path="GlobalSim" server="fi--didef2.dide.ic.ac.uk" fstype="cifs" />		<volume options="vers=2.1,nodev,nosuid" user="*" mountpoint="/homes/<dide-username>/dide/tmp" path="Tmp" server="fi--didef2.dide.ic.ac.uk" fstype="cifs" />
	<volume options="vers=2.1,nodev,nosuid" user="*" mountpoint="/~~media~~/nas1gsim" path="Test" server="fi--didenas1.dide.ic.ac.uk" fstype="cifs" />		<volume options="vers=2.1,nodev,nosuid" user="*" mountpoint="/homes/<dide-username>/dide/f2gsim" path="GlobalSim" server="fi--didef2.dide.ic.ac.uk" fstype="cifs" />
			<volume options="vers=2.1,nodev,nosuid" user="*" mountpoint="/homes/<dide-username>/dide/nas1gsim" path="Test" server="fi--didenas1.dide.ic.ac.uk" fstype="cifs" />
	</pam_mount>		</pam_mount>
	</pre>		</pre>

	~~For some reason, NAS1 needs vers=2.1, whereas the other drives don't. No-one knows why.~~

Richfitz: Correct path that home is mounted to

2016-09-30T13:49:44Z

Correct path that home is mounted to

← Older revision		Revision as of 15:49, 30 September 2016
Line 1:		Line 1:
	==Mounting shares for cluster use==		==Mounting shares for cluster use==

	The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (or when the cluster logs in as you), your DIDE home directory will be automatically mounted as /~~media~~/home~~. The home shortcut "~~~~~" will also point to this~~. If you want access to other windows shares, then create a file in your DIDE home directory, called <code>.pam_mount.conf.xml</code> containing something like this:-		The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (or when the cluster logs in as you), your DIDE home directory will be automatically mounted as ~/dide/home and the temp directory as ~/dide/temp. If you want access to other windows shares, then create a file in your DIDE home directory, called <code>.pam_mount.conf.xml</code> containing something like this:-

	<pre>		<pre>

Admin at 12:17, 28 June 2016

2016-06-28T12:17:43Z

← Older revision		Revision as of 14:17, 28 June 2016
Line 1:		Line 1:
			==Mounting shares for cluster use==

	The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (or when the cluster logs in as you), your DIDE home directory will be automatically mounted as /media/home. The home shortcut "~" will also point to this. If you want access to other windows shares, then create a file in your DIDE home directory, called <code>.pam_mount.conf.xml</code> containing something like this:-		The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (or when the cluster logs in as you), your DIDE home directory will be automatically mounted as /media/home. The home shortcut "~" will also point to this. If you want access to other windows shares, then create a file in your DIDE home directory, called <code>.pam_mount.conf.xml</code> containing something like this:-

Admin: Created page with "The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (..."

2016-06-28T12:16:45Z

Created page with "The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (..."

New page

The only thing you really need to do before using the linux nodes on the fi--didelxhn cluster, is sort out any windows shares you're going to want access to. When you log in (or when the cluster logs in as you), your DIDE home directory will be automatically mounted as /media/home. The home shortcut "~" will also point to this. If you want access to other windows shares, then create a file in your DIDE home directory, called <code>.pam_mount.conf.xml</code> containing something like this:-

<pre>
<?xml version="1.0" encoding="utf-8" ?>
<pam_mount>
<volume options="nodev,nosuid" user="*" mountpoint="/media/f2gsim" path="GlobalSim" server="fi--didef2.dide.ic.ac.uk" fstype="cifs" />
<volume options="vers=2.1,nodev,nosuid" user="*" mountpoint="/media/nas1gsim" path="Test" server="fi--didenas1.dide.ic.ac.uk" fstype="cifs" />
</pam_mount>
</pre>

For some reason, NAS1 needs vers=2.1, whereas the other drives don't. No-one knows why.