Using environment modules - Revision history

Dawes0011 at 08:59, 16 June 2023

2023-06-16T08:59:02Z

← Older revision		Revision as of 10:59, 16 June 2023
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	-bash-4.1$ module avail		-bash-4.1$ module avail

	---------------------------- ~~/cm~~/shared/modulefiles ----------------------------		---------------------------- /shared/modulefiles ----------------------------
	acml/gcc/64/5.3.1 netcdf/gcc/64/4.1.3		acml/gcc/64/5.3.1 netcdf/gcc/64/4.1.3
	acml/gcc/fma4/5.3.1 netcdf/gcc/64/4.3.0		acml/gcc/fma4/5.3.1 netcdf/gcc/64/4.3.0
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	-bash-4.1$ module avail python		-bash-4.1$ module avail python

	---------------------------- ~~/cm~~/shared/modulefiles ----------------------------		---------------------------- /shared/modulefiles ----------------------------
	python/2.7.6 python/3.3.3 python/3.4.2		python/2.7.6 python/3.3.3 python/3.4.2
	</source>		</source>

Haars001 at 14:18, 10 July 2020

2020-07-10T14:18:09Z

← Older revision		Revision as of 16:18, 10 July 2020
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	== External links ==		== External links ==
	* http://modules.sourceforge.net		* http://modules.sourceforge.net
			* https://modules.readthedocs.io/en/latest/ (documentation)
	* http://www.admin-magazine.com/HPC/Articles/Environment-Modules		* http://www.admin-magazine.com/HPC/Articles/Environment-Modules

Dawes001 at 13:55, 19 March 2019

2019-03-19T13:55:46Z

← Older revision		Revision as of 15:55, 19 March 2019
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	== See also ==		== See also ==
	* [[B4F_cluster \| B4F Cluster]]
	* [[Lx6_and_Lx7_compute_nodes \| Lx6 and Lx7 compute nodes]]
	* [[Environment_Modules \| Environment Modules]]		* [[Environment_Modules \| Environment Modules]]
	* [[Control_R_environment_using_modules \| Control R environment using modules]]		* [[Control_R_environment_using_modules \| Control R environment using modules]]

Vaend001 at 18:56, 19 February 2019

2019-02-19T18:56:50Z

← Older revision		Revision as of 20:56, 19 February 2019
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	== Viewing Modules ==		== Viewing Modules ==
	Upon logging in to ~~the HPC~~, you should find that when you do:		Upon logging in to Anunna, you should find that when you do:
	module list		module list

Line 16:		Line 16:
	module available		module available

	And this will show you the (very exhaustive) list of modules on ~~the HPC~~:		And this will show you the (very exhaustive) list of modules on Anunna:

	<source lang='bash'>		<source lang='bash'>

Dawes001 at 13:32, 4 September 2015

2015-09-04T13:32:13Z

← Older revision		Revision as of 15:32, 4 September 2015
Line 65:		Line 65:

	This script will not run at all in the default 2.4 version of Python on the cluster. In order for this script to run you must use Python3. To do this, first list all versions of Python:		This script will not run at all in the default 2.4 version of Python on the cluster. In order for this script to run you must use Python3. To do this, first list all versions of Python:
	<source>		<source lang='bash'>
	-bash-4.1$ module avail python		-bash-4.1$ module avail python

Dawes001 at 13:31, 4 September 2015

2015-09-04T13:31:26Z

← Older revision		Revision as of 15:31, 4 September 2015
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			=== Environment Modules ===
	[http://modules.sourceforge.net/ Environment modules] are a simple way to allow multiple potentially clashing programs to coexist on a large shared machine such as an HPC. It allows a user to specify exactly which programs are loaded, and even which version of each program, whilst simultaneously allowing the administrator the ability to automatically configure the appropriate environment variables for the system itself.		[http://modules.sourceforge.net/ Environment modules] are a simple way to allow multiple potentially clashing programs to coexist on a large shared machine such as an HPC. It allows a user to specify exactly which programs are loaded, and even which version of each program, whilst simultaneously allowing the administrator the ability to automatically configure the appropriate environment variables for the system itself.

			== Viewing Modules ==
	Upon logging in to the HPC, you should find that when you do:		Upon logging in to the HPC, you should find that when you do:
	module list		module list
Line 36:		Line 38:
	And the complete list of versions will be shown.		And the complete list of versions will be shown.

			== Loading Modules ==
	To load a module, simply		To load a module, simply
	module load foo		module load foo
Line 45:		Line 47:
	Will load foo version 1, compiled with gcc. Be advised that this may not always work, as some modules are not compatible with each other, but a message will be shown if this is the case. Additionally, some modules will automatically load other modules with them for them to operate.		Will load foo version 1, compiled with gcc. Be advised that this may not always work, as some modules are not compatible with each other, but a message will be shown if this is the case. Additionally, some modules will automatically load other modules with them for them to operate.

			== Unloading Modules ==
	If you want to remove a module that you've loaded, then		If you want to remove a module that you've loaded, then
	module unload foo		module unload foo
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	=== Example ===		== Example ==
	Consider this simple python3 script that should calculate Pi to 1 million digits:		Consider this simple python3 script that should calculate Pi to 1 million digits:
	<source lang='python'>		<source lang='python'>
Line 62:		Line 64:
	</source>		</source>

	~~=== Loading modules ===~~
	This script will not run at all in the default 2.4 version of Python on the cluster. In order for this script to run you must use Python3. To do this, first list all versions of Python:		This script will not run at all in the default 2.4 version of Python on the cluster. In order for this script to run you must use Python3. To do this, first list all versions of Python:
	<source>		<source>

Dawes001 at 13:29, 4 September 2015

2015-09-04T13:29:20Z

← Older revision		Revision as of 15:29, 4 September 2015
Line 1:		Line 1:
	~~<-- this is only preliminary text; this article needs more work -->~~		[http://modules.sourceforge.net/ Environment modules] are a simple way to allow multiple potentially clashing programs to coexist on a large shared machine such as an HPC. It allows a user to specify exactly which programs are loaded, and even which version of each program, whilst simultaneously allowing the administrator the ability to automatically configure the appropriate environment variables for the system itself.
	[http://modules.sourceforge.net/\|Environment modules] are a simple way to allow multiple potentially clashing programs to coexist on a large shared machine such as an HPC. It allows a user to specify exactly which programs are loaded, and even which version of each program, whilst simultaneously allowing the administrator the ability to automatically configure the appropriate environment variables for the system itself.

	Upon logging in to the HPC, you should find that when you do:		Upon logging in to the HPC, you should find that when you do:

Dawes001: Rewrite!

2015-09-04T13:28:11Z

Rewrite!

@@ Line 1: / Line 1: @@
 <-- this is only preliminary text; this article needs more work -->
 === Example ===
@@ Line 12: / Line 64: @@
 === Loading modules ===
-In order for this script to run, the first thing that is needed is that Python3, which is not the default Python version on the cluster, is load into your environment. Availability of (different versions of) software can be checked by the following command:
+This script will not run at all in the default 2.4 version of Python on the cluster. In order for this script to run you must use Python3. To do this, first list all versions of Python:
-  module avail
+<source>
-In the list you should note that python3 is indeed available to be loaded, which then can be loaded with the following command:
+Then you can load the specific version you need:
    module load python/3.3.3
 == See also ==

Megen002 at 23:35, 10 December 2013

2013-12-10T23:35:43Z

← Older revision		Revision as of 01:35, 11 December 2013
Line 17:		Line 17:
	In the list you should note that python3 is indeed available to be loaded, which then can be loaded with the following command:		In the list you should note that python3 is indeed available to be loaded, which then can be loaded with the following command:
	module load python/3.3.3		module load python/3.3.3

			== See also ==
			* [[B4F_cluster \| B4F Cluster]]
			* [[Lx6_and_Lx7_compute_nodes \| Lx6 and Lx7 compute nodes]]
			* [[Environment_Modules \| Environment Modules]]
			* [[Control_R_environment_using_modules \| Control R environment using modules]]
			* [[Create_shortcut_log-in_command \| Create a shortcut for the ssh log-in command]]
			* [[Installing_R_packages_locally \| Installing R packages locally]]

			== External links ==
			* http://modules.sourceforge.net
			* http://www.admin-magazine.com/HPC/Articles/Environment-Modules

Megen002: Created page with "<-- this is only preliminary text; this article needs more work --> === Example === Consider this simple python3 script that should calculate Pi to 1 million digits:
2013-12-10T23:31:58Z

Created page with "<-- this is only preliminary text; this article needs more work --> === Example === Consider this simple python3 script that should calculate Pi to 1 million digits: <source ..."

New page
<-- this is only preliminary text; this article needs more work -->

=== Example ===
Consider this simple python3 script that should calculate Pi to 1 million digits:
<source lang='python'>
from decimal import *
D=Decimal
getcontext().prec=10000000
p=sum(D(1)/16**k(D(4)/(8k+1)-D(2)/(8k+4)-D(1)/(8k+5)-D(1)/(8*k+6))for k in range(411))
print(str(p)[:10000002])
</source>

=== Loading modules ===
In order for this script to run, the first thing that is needed is that Python3, which is not the default Python version on the cluster, is load into your environment. Availability of (different versions of) software can be checked by the following command:
module avail

In the list you should note that python3 is indeed available to be loaded, which then can be loaded with the following command:
module load python/3.3.3