Run It - Revision history

Boerner at 07:47, 14 June 2021

2021-06-14T07:47:32Z

← Older revision		Revision as of 07:47, 14 June 2021
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	<li>OMP_DYNAMIC=FALSE</li>		<li>OMP_DYNAMIC=FALSE</li>
	<li>OMP_STACKSIZE='a reasonable value (i.e. 2000M)'</li>		<li>OMP_STACKSIZE='a reasonable value (i.e. 2000M)'</li>
	<li>~~OMP_NESTED~~=~~TRUE~~</li>		<li>OMP_PROC_BIND=true</li>
			<li>OMP_PLACES=cores</li>
			<li>OMP_MAX_ACTIVE_LEVELS=2147483647</li>
			<li>KMP_AFFINITY=granularity=core,scatter</li>
	</ul>		</ul>

Boerner: /* Run time environment */

2021-01-03T05:36:46Z

Run time environment

← Older revision		Revision as of 05:36, 3 January 2021
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	set the lmt threading behaviour via the two environment variables [https://www.openmp.org/spec-html/5.0/openmpse50.html OMP_NUM_THREADS]		set the lmt threading behaviour via the two environment variables [https://www.openmp.org/spec-html/5.0/openmpse50.html OMP_NUM_THREADS]
	and [https://software.intel.com/content/www/us/en/develop/documentation/onemkl-linux-developer-guide/top/managing-performance-and-memory/improving-performance-with-threading/using-additional-threading-control/setting-the-environment-variables-for-threading-control.html MKL_NUM_THREADS].		and [https://software.intel.com/content/www/us/en/develop/documentation/onemkl-linux-developer-guide/top/managing-performance-and-memory/improving-performance-with-threading/using-additional-threading-control/setting-the-environment-variables-for-threading-control.html MKL_NUM_THREADS].

			Alternatively, {{lmt}} can be obtained as a dedicated single core version using single-core third party libraries, or as a dedicated single-core version using threaded third party libraries.

	The performance of multi-threaded programs can also be heavily affected by [https://software.intel.com/content/www/us/en/develop/documentation/cpp-compiler-developer-guide-and-reference/top/optimization-and-programming-guide/openmp-support/openmp-library-support/thread-affinity-interface-linux-and-windows.html thread affinity] settings where the optimal settings must be found via trial and error. However,		The performance of multi-threaded programs can also be heavily affected by [https://software.intel.com/content/www/us/en/develop/documentation/cpp-compiler-developer-guide-and-reference/top/optimization-and-programming-guide/openmp-support/openmp-library-support/thread-affinity-interface-linux-and-windows.html thread affinity] settings where the optimal settings must be found via trial and error. However,

Boerner at 05:31, 3 January 2021

2021-01-03T05:31:34Z

← Older revision		Revision as of 05:31, 3 January 2021
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	Turns {{lmt}} into a pedigree analysis program. For a list of commandline arguments type @ped --help.		Turns {{lmt}} into a pedigree analysis program. For a list of commandline arguments type @ped --help.
	-->		-->

	== Run time environment ==		== Run time environment ==

Boerner: /* How to start */

2021-01-03T05:30:52Z

How to start

← Older revision		Revision as of 05:30, 3 January 2021
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	== How to start ==		== How to start ==

	{{lmt}} is always started from the Linux command line interface.		{{lmt}} is always started from the Linux command line interface. In default mode, {{lmt}} will search in the run time directory for a parameter file named {{cc\|para.xml}}. Alternatively the parameter file name can be provided via the command line option {{cc\| -f myfilename}}.

	<!-- == @<mode> and parameter file mode ==		<!-- == @<mode> and parameter file mode ==
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	Turns {{lmt}} into a pedigree analysis program. For a list of commandline arguments type @ped --help.		Turns {{lmt}} into a pedigree analysis program. For a list of commandline arguments type @ped --help.
	-->		-->

	== Run time environment ==		== Run time environment ==

Boerner: /* Run time environment */

2021-01-03T05:28:42Z

Run time environment

← Older revision		Revision as of 05:28, 3 January 2021
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	and [https://software.intel.com/content/www/us/en/develop/documentation/onemkl-linux-developer-guide/top/managing-performance-and-memory/improving-performance-with-threading/using-additional-threading-control/setting-the-environment-variables-for-threading-control.html MKL_NUM_THREADS].		and [https://software.intel.com/content/www/us/en/develop/documentation/onemkl-linux-developer-guide/top/managing-performance-and-memory/improving-performance-with-threading/using-additional-threading-control/setting-the-environment-variables-for-threading-control.html MKL_NUM_THREADS].

	The performance of multi-threaded programs can also be heavily affected by thread		The performance of multi-threaded programs can also be heavily affected by [https://software.intel.com/content/www/us/en/develop/documentation/cpp-compiler-developer-guide-and-reference/top/optimization-and-programming-guide/openmp-support/openmp-library-support/thread-affinity-interface-linux-and-windows.html thread affinity] settings where the optimal settings must be found via trial and error. However,
	affinity settings where the optimal settings must be found via trial and error. However,
	as a starting point, it is advisable to set the environment variable		as a starting point, it is advisable to set the environment variable
	<b>KMP_AFFINITY=granularity=core,scatter</b>.		<b>KMP_AFFINITY=granularity=core,scatter</b>.

Boerner at 05:20, 3 January 2021

2021-01-03T05:20:33Z

← Older revision		Revision as of 05:20, 3 January 2021
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	small data sets resulting in an increased run time. What "medium to small" means depends on the actual computer and must therefore be determined by the user. The user can		small data sets resulting in an increased run time. What "medium to small" means depends on the actual computer and must therefore be determined by the user. The user can
	set the lmt threading behaviour via the two environment variables [https://www.openmp.org/spec-html/5.0/openmpse50.html OMP_NUM_THREADS]		set the lmt threading behaviour via the two environment variables [https://www.openmp.org/spec-html/5.0/openmpse50.html OMP_NUM_THREADS]
	and [https://software.intel.com/content/www/us/en/develop/documentation/onemkl-linux-developer-guide/top/managing-performance-and-memory/improving-performance-with-threading/using-additional-threading-control/~~onemkl~~-~~specific~~-environment-variables-for~~-openmp~~-threading-control.html~~#onemkl-specific-environment-variables-for-openmp-threading-control~~ MKL_NUM_THREADS].		and [https://software.intel.com/content/www/us/en/develop/documentation/onemkl-linux-developer-guide/top/managing-performance-and-memory/improving-performance-with-threading/using-additional-threading-control/setting-the-environment-variables-for-threading-control.html MKL_NUM_THREADS].

	The performance of multi-threaded programs can also be heavily affected by thread		The performance of multi-threaded programs can also be heavily affected by thread

Boerner: /* Run time environment */

2021-01-03T05:18:09Z

Run time environment

← Older revision		Revision as of 05:18, 3 January 2021
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	<b>lmt</b> is highly threaded and will try to use all available computing resources. Will this is		<b>lmt</b> is highly threaded and will try to use all available computing resources. Will this is
	desirable for very large models it can hamper performance when crunching medium to		desirable for very large models it can hamper performance when crunching medium to
	small data sets resulting in an increased run time. What "medium to small" means ~~de-~~		small data sets resulting in an increased run time. What "medium to small" means depends on the actual computer and must therefore be determined by the user. The user can
	~~pends~~ on the actual computer and must therefore be determined by the user. The user can		set the lmt threading behaviour via the two environment variables [https://www.openmp.org/spec-html/5.0/openmpse50.html OMP_NUM_THREADS]
	set the lmt threading behaviour via the two environment variables ~~<b>~~OMP_NUM_THREADS</b>		and [https://software.intel.com/content/www/us/en/develop/documentation/onemkl-linux-developer-guide/top/managing-performance-and-memory/improving-performance-with-threading/using-additional-threading-control/onemkl-specific-environment-variables-for-openmp-threading-control.html#onemkl-specific-environment-variables-for-openmp-threading-control MKL_NUM_THREADS].
	and ~~<b>~~MKL_NUM_THREADS~~</b>~~.

	The performance of multi-threaded programs can also be heavily affected by thread		The performance of multi-threaded programs can also be heavily affected by thread

Boerner at 05:11, 3 January 2021

2021-01-03T05:11:26Z

← Older revision		Revision as of 05:11, 3 January 2021
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	experience a severe drop in performance of each of the runs. This is usually caused		experience a severe drop in performance of each of the runs. This is usually caused
	by competition for resources and therefore parallel runs of several lmt instances should		by competition for resources and therefore parallel runs of several lmt instances should
	be avoided. However, using the ~~<b>~~numactl~~</b>~~ environment may provide an option to avoid		be avoided. However, using the [https://linux.die.net/man/8/numactl numactl] environment to encapsulate {{lmt}} instances may provide an option to avoid performance drops.
	performance drops~~. Please check out <b>numactl --help</b> for further reading~~.

Boerner at 05:06, 3 January 2021

2021-01-03T05:06:50Z

← Older revision		Revision as of 05:06, 3 January 2021
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	{{lmt}} is always started from the Linux command line interface.		{{lmt}} is always started from the Linux command line interface.

	== @<mode> and parameter file mode ==		<!-- == @<mode> and parameter file mode ==

	{{lmt}} can run on various task. Some tasks may be readily described via a bunch of		{{lmt}} can run on various task. Some tasks may be readily described via a bunch of
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	Turns {{lmt}} into a pedigree analysis program. For a list of commandline arguments type @ped --help.		Turns {{lmt}} into a pedigree analysis program. For a list of commandline arguments type @ped --help.
			-->
	== Run time environment ==		== Run time environment ==

Boerner: /* Supported analysis types in parameter file mode */

2021-01-03T04:27:57Z

Supported analysis types in parameter file mode

← Older revision		Revision as of 04:27, 3 January 2021
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	Turns {{lmt}} into a pedigree analysis program. For a list of commandline arguments type @ped --help.		Turns {{lmt}} into a pedigree analysis program. For a list of commandline arguments type @ped --help.

	~~=== Supported analysis types in parameter file mode ===~~

	~~==== solve ====~~

	~~Large scale linear mixed model solving conditional on supplied co-variances~~

	~~==== sample ====~~

	~~Large scale single pass and blocked Gibbs sampling of Gaussian linear mixed model variance components.~~

	~~==== mmme ====~~

	~~Construction of large scale linear mixed model coefficient matrices.~~

	~~==== yhat ====~~

	~~Calculation of <math>\hat{y}=Xb + .... +</math> from the solutions of a linear mixed model.~~


	== Run time environment ==		== Run time environment ==