HPC/Module naming scheme 2016 - Revision history

Stern: /* Test in a job file */

2016-11-30T22:29:52Z

Test in a job file

← Older revision		Revision as of 22:29, November 30, 2016
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	qstat ''jobnumber''		qstat ''jobnumber''
	…		…
	head modtest.[eo]~~1234~~*		head modtest.[eo0-9]*
	You should see something like:		You should see something like:
	'''vasp_gam is''' /opt/apps/vasp5/5.4.1.3-6-openmpi-1.10-intel-16/bin/vasp_gam		'''vasp_gam is''' /opt/apps/vasp5/5.4.1.3-6-openmpi-1.10-intel-16/bin/vasp_gam

Stern: /* Workflow to determine module names to load */

2016-11-21T18:55:12Z

Workflow to determine module names to load

← Older revision		Revision as of 18:55, November 21, 2016
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	# [[#Understanding dependency errors\|Determine a package's dependencies]].		# [[#Understanding dependency errors\|Determine a package's dependencies]].
	#: Inspect the output of <code>module show …</code>, look for any <code>prereq</code> statements, and load those on a previous line.		#: Inspect the output of <code>module show …</code>, look for any <code>prereq</code> statements, and load those on a previous line.
	~~Insist on a specific version and build only~~ if you require a build with a specific feature or behavior (such as to reproduce prior results with numeric consistency). To do so:		'''Only give full versions if:''' you require a build with a specific feature or behavior (such as to reproduce prior results with numeric consistency). To do so:
	:5. Append version and build specifications, as shown by the <code>module avail ''packagename''</code> command.		:5. Append version and build specifications, as shown by the <code>module avail ''packagename''</code> command.
	<!--		<!--
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	; Example:		; Example:
	:* Let's load a vasp5 module that uses the Intel-MPI flavor~~, named~~ "impi":		:* Let's load a vasp5 module that uses the Intel-MPI flavor ("impi"):
	$ '''module avail vasp5'''		$ '''module avail vasp5'''
	------------------------------------------------------------ /opt/apps/M/x86_64/EL ------------------------------------------------------------		------------------------------------------------------------ /opt/apps/M/x86_64/EL ------------------------------------------------------------

Stern: /* System-specific command files */

2016-11-18T22:46:34Z

System-specific command files

← Older revision		Revision as of 22:46, November 18, 2016
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	Specifically:		Specifically:
	* ~~Files~~ of the form <code>~/.modules-el''x''</code>, with ''x'' = 5,6,..., ~~trigger~~ the new naming scheme ~~and~~ will be loaded on the corresponding OS.		* The mere existence of files of the form <code>~/.modules-el''x''</code>, with ''x'' = 5,6,..., activates the new naming scheme. Subsequently, the file will be loaded and interpreed (in Tcl language) on the corresponding OS.
	* On CentOS-5 nodes, a file <code>~/.modules-el5-legacy</code> will trigger the legacy scheme, but only if <code>~/.modules-el5</code> is not present. In other words, a <code>~/.modules-el5</code> file has priority and causes <code>~/.modules-el5-legacy</code> to be ignored.		* On CentOS-5 nodes, a file <code>~/.modules-el5-legacy</code> will trigger the legacy scheme, but only if <code>~/.modules-el5</code> is not present. In other words, a <code>~/.modules-el5</code> file has priority and causes <code>~/.modules-el5-legacy</code> to be ignored.
	* Without any <code>~/.modules-*</code> files, CentOS-5 nodes will use the legacy scheme; CentOS-6 nodes always use the new scheme.		* Without any <code>~/.modules-*</code> files, CentOS-5 nodes will use the legacy scheme; CentOS-6 nodes always use the new scheme.

Stern: /* Module loading */

2016-11-18T22:42:37Z

Module loading

← Older revision		Revision as of 22:42, November 18, 2016
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	=== No pre-loading ===		=== No pre-loading ===
	No compiler or MPI modules are pre-loaded by the system.		No compiler or MPI modules are pre-loaded by the system.
	The system only loads the ("meta") module <code>profile/user</code> for you,		The system only loads the "meta" module <code>profile/user</code> for you,
	which merely ~~hands off to~~ your own <code>.module-*</code> files.		which merely looks for and loads your own <code>.module-*</code> files.

	=== No recursive loading ===		=== No recursive loading ===

Stern: /* Explicit module selections required */

2016-11-18T22:39:46Z

Explicit module selections required

← Older revision		Revision as of 22:39, November 18, 2016
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	; No recursive loading:		; No recursive loading:
	: A module under the new scheme does not implicitly load other modules that it might depend on, such as modules for compilers, an MPI flavor, or specialized libraries.		: A module under the new scheme does not implicitly load other modules that it might depend on, such as modules for compilers, an MPI flavor, or specialized libraries.
	: Previously, this was the case for some popular modules but with the system maturing and diversifying, unexpected consequences can occur easily.		: Previously, this was the case for some popular modules but with the system maturing and diversifying, unexpected consequences can occur too easily.

	<!-- See [[HPC/Modules Best Practices#Load dependent modules first]]. -->		<!-- See [[HPC/Modules Best Practices#Load dependent modules first]]. -->

Stern at 22:37, November 18, 2016

2016-11-18T22:37:57Z

← Older revision		Revision as of 22:37, November 18, 2016
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	== Explicit module selections required ==		== Explicit module selections required ==
	Under the new modules scheme, you must yourself load all desired modules~~, particularly '''compiler''' and '''MPI modules''',~~ in your shell setup files or in job files, in suitable order.		; Compiler and MPI modules are no longer pre-loaded.:
	Modules not depending on others must be loaded first.		: Previously, the Intel compilers, the Intel Math Kernel Library, and OpenMPI were loaded even when there were no <code>module load</code> commands in your dot-files.
			: Under the new modules scheme, you must yourself load all desired modules in your shell setup files or in job files, in suitable order. Modules not depending on others must be loaded first.
	: This is born of necessity because still useful older applications were compiled with older MPI flavors and versions (typically OpenMPI-1.4) which partially interfere with newer flavors (OpenMPI-1.8, 1.10, or Intel-MPI-5.x). In particular, each MPI flavor provides commands like <code>mpirun</code> and <code>mpifort</code>, and special care is needed to run the correct one if your chosen module set spans different MPI flavors.		: This is born of necessity because still useful older applications were compiled with older MPI flavors and versions (typically OpenMPI-1.4) which partially interfere with newer flavors (OpenMPI-1.8, 1.10, or Intel-MPI-5.x). In particular, each MPI flavor provides commands like <code>mpirun</code> and <code>mpifort</code>, and special care is needed to run the correct one if your chosen module set spans different MPI flavors.
	: While loading all desired modules explicitly may by a minor burden for you at first, your selections should become easier to understand now and easier to adapt later.		: While loading all desired modules explicitly may by a minor burden for you at first, your selections should become easier to understand now and easier to adapt later.

	~~; Compiler and MPI modules are no longer pre-loaded.:~~
	~~: Previously, the Intel compilers, the Intel Math Kernel Library, and OpenMPI were loaded even when there were no <code>module load</code> commands in your dot-files.~~

	; No recursive loading:		; No recursive loading:

Stern at 22:34, November 18, 2016

2016-11-18T22:34:34Z

← Older revision		Revision as of 22:34, November 18, 2016
Line 446:		Line 446:

	== Explicit module selections required ==		== Explicit module selections required ==
	Under the new modules scheme, you must yourself load all desired modules, particularly '''compiler''' and '''MPI modules''', in your shell setup files or in job files, in suitable order. Modules not depending on others must be loaded first.		Under the new modules scheme, you must yourself load all desired modules, particularly '''compiler''' and '''MPI modules''', in your shell setup files or in job files, in suitable order.
			Modules not depending on others must be loaded first.
	: This is born of necessity because still useful older applications were compiled with older MPI flavors and versions (typically OpenMPI-1.4) which partially interfere with newer flavors (OpenMPI-1.8, 1.10, or Intel-MPI-5.x). In particular, each MPI flavor provides commands like <code>mpirun</code> and <code>mpifort</code>, and special care is needed to run the correct one if your chosen module set spans different MPI flavors.		: This is born of necessity because still useful older applications were compiled with older MPI flavors and versions (typically OpenMPI-1.4) which partially interfere with newer flavors (OpenMPI-1.8, 1.10, or Intel-MPI-5.x). In particular, each MPI flavor provides commands like <code>mpirun</code> and <code>mpifort</code>, and special care is needed to run the correct one if your chosen module set spans different MPI flavors.
			: While loading all desired modules explicitly may by a minor burden for you at first, your selections should become easier to understand now and easier to adapt later.

	~~==== No modules are pre-loaded ====~~		; Compiler and MPI modules are no longer pre-loaded.:
	Compiler and MPI modules are no longer pre-loaded.
	: Previously, the Intel compilers, the Intel Math Kernel Library, and OpenMPI were loaded even when there were no <code>module load</code> commands in your dot-files.		: Previously, the Intel compilers, the Intel Math Kernel Library, and OpenMPI were loaded even when there were no <code>module load</code> commands in your dot-files.

	~~====~~ No recursive loading ~~====~~		; No recursive loading:
	A module under the new scheme does not implicitly load other modules that it might		: A module under the new scheme does not implicitly load other modules that it might depend on, such as modules for compilers, an MPI flavor, or specialized libraries.
	depend on, such as modules for compilers, an MPI flavor, or specialized		: Previously, this was the case for some popular modules but with the system maturing and diversifying, unexpected consequences can occur easily.
	libraries.
	Previously, this was the case for some popular modules but with the system
	maturing and diversifying, unexpected consequences can occur easily.

	~~You must load dependent modules yourself.~~
	~~While this may by a minor burden for you at first,~~
	~~your selections should become easier to understand now and easier to adapt later.~~
	<!-- See [[HPC/Modules Best Practices#Load dependent modules first]]. -->		<!-- See [[HPC/Modules Best Practices#Load dependent modules first]]. -->

Stern at 22:30, November 18, 2016

2016-11-18T22:30:58Z

Show changes

Stern: Stern moved page HPC/Module changes 2016 to HPC/Module naming scheme 2016

2016-11-17T18:18:10Z

Stern moved page HPC/Module changes 2016 to HPC/Module naming scheme 2016

← Older revision	Revision as of 18:18, November 17, 2016
(No difference)

Stern: /* Name changes for most modules */

2016-11-08T22:30:16Z

Name changes for most modules

← Older revision		Revision as of 22:30, November 8, 2016
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	fftw3/3.3/'''''intel'''''/3.3.2-1 # older serial version		fftw3/3.3/'''''intel'''''/3.3.2-1 # older serial version
	fftw3/3.3/'''''openmpi-1.10'''''/'''''intel-16'''''/3.3.4-11 # uses OpenMPI		fftw3/3.3/'''''openmpi-1.10'''''/'''''intel-16'''''/3.3.4-11 # uses OpenMPI
	fftw3/3.3/'''''openmpi-1.4'''''/'''''intel'''''/3.3.2-4 # older MPI version		fftw3/3.3/'''''openmpi-1.4'''''/'''''intel'''''/3.3.2-4 # older MPI version
	<span style="color:#777;">/usr/share/Modules/modulefiles:</span>		<span style="color:#777;">/usr/share/Modules/modulefiles:</span>
	<span style="color:#777;">/etc/modulefiles:</span>		<span style="color:#777;">/etc/modulefiles:</span>