HPC/Module Setup - Revision history

Stern: /* Module Conventions on Carbon */

2016-11-17T18:25:14Z

Module Conventions on Carbon

@@ Line 114: / Line 114: @@
 == Module Conventions on Carbon ==
+See [[HPC/Module naming scheme 2008]]
 [[Category:HPC]]

Stern: /* Shell Customizations */

2013-10-11T15:04:59Z

Shell Customizations

← Older revision		Revision as of 15:04, October 11, 2013
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	module load name1 name2 …		module load name1 name2 …
	module load name3/version		module load name3/version

	</syntaxhighlight>		</syntaxhighlight>

Stern: /* Shell Customizations */

2013-10-11T15:04:48Z

Shell Customizations

← Older revision		Revision as of 15:04, October 11, 2013
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	* For instance, to add binaries from a user's own compilation of <code>somepackage</code>, and load a couple of modules:		* For instance, to add binaries from a user's own compilation of <code>somepackage</code>, and load a couple of modules:
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">

	export PATH=$HOME/somepackage/bin:$HOME/bin:$PATH		export PATH=$HOME/somepackage/bin:$HOME/bin:$PATH

			# Load Carbon applications
	module load name1 name2 …		module load name1 name2 …
			module load name3/version

	</syntaxhighlight>		</syntaxhighlight>

Stern: /* Environment variable for package home directory */

2013-09-12T21:59:16Z

Environment variable for package home directory

← Older revision		Revision as of 21:59, September 12, 2013
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	$ '''module load quantum-espresso'''		$ '''module load quantum-espresso'''
	; ~~Package~~ binaries:		; Inspect package binaries:
	$ '''ls $QUANTUM_ESPRESSO_HOME/bin'''		$ '''ls $QUANTUM_ESPRESSO_HOME/bin'''
	average.x dos.x …		average.x dos.x …
Line 160:		Line 160:
	bands_FS.x ev.x …		bands_FS.x ev.x …
	…		…
	; ~~Package~~ documentation:		; Inspect package documentation:
	$ '''ls -F $QUANTUM_ESPRESSO_HOME/doc'''		$ '''ls -F $QUANTUM_ESPRESSO_HOME/doc'''
	Doc/ atomic_doc/ examples/		Doc/ atomic_doc/ examples/

	; ~~specifcy~~ link paths in makefiles:		; Specifcy link paths in makefiles:
	$ '''module load fftw3'''		$ '''module load fftw3'''
	$ cat Makefile		$ cat Makefile

Stern: /* Environment variable for package home directory */

2013-09-12T21:58:51Z

Environment variable for package home directory

← Older revision		Revision as of 21:58, September 12, 2013
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	Most modules will set a convenience variable <code>''' $''NAME''_HOME'''</code> which points to the package's toplevel directory.		Most modules will set a convenience variable <code>''' $''NAME''_HOME'''</code> which points to the package's toplevel directory.
	Dashes in the package name are converted to underscores in the environment variable.		Dashes in the package name are converted to underscores in the environment variable.
	This is a convention on Carbon.		This is a convention on Carbon and is useful to inspect binaries or documentation and auxiliary files of a package:

	~~This convention is mostly useful to inspect documentation and auxiliary files of a package:~~
	$ '''module load quantum-espresso'''		$ '''module load quantum-espresso'''
	~~<syntaxhighlight lang="bash">~~		; Package binaries:
	$ ls -F $QUANTUM_ESPRESSO_HOME/doc		$ '''ls $QUANTUM_ESPRESSO_HOME/bin'''
			average.x dos.x …
			band_plot.x dynmat.x …
			bands.x epsilon.x …
			bands_FS.x ev.x …
			…
			; Package documentation:
			$ '''ls -F $QUANTUM_ESPRESSO_HOME/doc'''
	Doc/ atomic_doc/ examples/		Doc/ atomic_doc/ examples/
	~~</syntaxhighlight>~~

	~~: … and to~~ specifcy link paths in makefiles:		; specifcy link paths in makefiles:
	$ '''module load fftw3'''		$ '''module load fftw3'''
			$ cat Makefile
	~~<syntaxhighlight lang="make">~~		…
	LDFLAGS += -L$(FFTW3_HOME)/lib		LDFLAGS += -L$(FFTW3_HOME)/lib
	~~</syntaxhighlight>~~		…

	=== Package-specific sample job ===		=== Package-specific sample job ===

Stern: /* Pick up newly added modules */

2013-09-12T21:53:29Z

Pick up newly added modules

← Older revision		Revision as of 21:53, September 12, 2013
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	* simply restart your shell in place:		* simply restart your shell in place:
	: <code>exec bash -l</code>		: <code>exec bash -l</code>
	:: ~~bash is followed by an option of~~ a lowercase letter "L".		:: Again, that's a lowercase letter "L".
	* Alternatively, log out and back in, which is a bit more involved.		* Alternatively, log out and back in, which is a bit more involved.

Stern: /* Test */

2013-09-12T21:52:39Z

Test

← Older revision		Revision as of 21:52, September 12, 2013
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	# run other shell commands		# run other shell commands
	...		...
	# ~~back~~ to the ~~original login~~ shell		# inspect nesting level, then return to the parent shell
	echo $SHLVL		echo $SHLVL
	exit		exit
	</syntaxhighlight>		</syntaxhighlight>
	* Make further corrections to ~/.bashrc as needed.		* Make further corrections to ~/.bashrc as needed.
	* You might get lost in multiple ''nested'' shell levels. To see the current nesting level, inspect the environment variable $SHLVL as shown above. A normal login shell runs at level '''1'''.		* You might get lost in multiple ''nested'' shell levels. To see the current nesting level, inspect the environment variable $SHLVL as shown above. A normal login shell runs at level '''1''', and the <code>exit</code> command in such a shell will log you out.

	=== Pick up newly added modules ===		=== Pick up newly added modules ===

Stern: /* Test */

2013-09-12T21:50:33Z

Test

← Older revision		Revision as of 21:50, September 12, 2013
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	To test the impact of any changes, temporarily run a new shell:		To test the impact of any changes, temporarily run a new shell:
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	~~echo $SHLVL~~
	bash -l # lowercase letter L		bash -l # lowercase letter L
	~~echo $SHLVL~~
	# run other shell commands		# run other shell commands
	...		...
	# back to the original login shell		# back to the original login shell
			echo $SHLVL
	exit		exit
	</syntaxhighlight>		</syntaxhighlight>
	* Make further corrections to ~/.bashrc as needed.		* Make further corrections to ~/.bashrc as needed.
	* You might get lost in multiple ''nested'' shell levels. To see the current nesting level, inspect the environment variable $SHLVL as shown above.		* You might get lost in multiple ''nested'' shell levels. To see the current nesting level, inspect the environment variable $SHLVL as shown above. A normal login shell runs at level '''1'''.

	=== Pick up newly added modules ===		=== Pick up newly added modules ===

Stern: /* Shell Customizations */

2013-09-12T21:49:51Z

Shell Customizations

← Older revision		Revision as of 21:49, September 12, 2013
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	</syntaxhighlight>		</syntaxhighlight>

	=== ~~Tests~~ ===		=== Test ===
	To test ~~major~~ changes, temporarily run a new shell~~. Inspect the environment variable $SHLVL to see the shell ''nesting'' level.~~		To test the impact of any changes, temporarily run a new shell:
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	echo $SHLVL		echo $SHLVL
	bash -l # lowercase letter L		bash -l # lowercase letter L
	echo $SHLVL		echo $SHLVL
	# run other ~~regular~~ commands		# run other shell commands
	...		...
	# back to the original login shell		# back to the original login shell
	exit		exit
	</syntaxhighlight>		</syntaxhighlight>
	When all looks good, either ~~log out and back in, or~~ simply restart your ~~login~~ shell ~~process~~ in place ~~(rather than as a child command)~~:		* Make further corrections to ~/.bashrc as needed.
	<~~syntaxhighlight lang="bash"~~>		* You might get lost in multiple ''nested'' shell levels. To see the current nesting level, inspect the environment variable $SHLVL as shown above.
	exec bash -l
	</~~syntaxhighlight~~>		=== Pick up newly added modules ===
			When all looks good, either:
			* simply restart your shell in place:
			: <code>exec bash -l</code>
			:: bash is followed by an option of a lowercase letter "L".
			* Alternatively, log out and back in, which is a bit more involved.

	=== Caveats ===		=== Caveats ===

Stern: /* Caveats */

2013-01-17T18:56:18Z

Caveats

← Older revision		Revision as of 18:56, January 17, 2013
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	** This will only work reliably for single-node jobs.		** This will only work reliably for single-node jobs.
	** It will generally ''fail for multi-node'' jobs (nodes > 1).		** It will generally ''fail for multi-node'' jobs (nodes > 1).
	**: Reason: The job script is only executed (by the <code>pbs_mom</code> daemon on your behalf) on the first core on the first node of your request. The environment of this process will be cloned for the other cores on the first node, but not for cores on other nodes. ~~There~~ are ~~flags for~~ <code>mpirun</code> or <code>mpiexec</code> to pass some or all environment variables to other MPI processes, but these flags are implementation-specific and may not work reliably.		**: Reason: The job script is only executed (by the <code>pbs_mom</code> daemon on your behalf) on the first core on the first node of your request. The environment of this process will be cloned for the other cores on the first node, but not for cores on other nodes. How remote environments are configured depends on the MPI implementation. The various <code>mpirun</code> or <code>mpiexec</code> offer flags to pass some or all environment variables to other MPI processes, but these flags are implementation-specific and may not work reliably.
	* The recommended way is as above, to place module commands in ~/.bashrc. This might preclude job-specific module sets for conflicting modules or tasks. I'm thinking about a proper solution for this. --[[User:Stern\|stern]]		* The most reliable and recommended way is as above, to place module commands in ~/.bashrc. This might preclude job-specific module sets for conflicting modules or tasks. I'm thinking about a proper solution for this. --[[User:Stern\|stern]]

	== Modules – General documentation ==		== Modules – General documentation ==