Analysis with Nipype - Revision history

Jstout: /* Running Pipeline */

2020-02-07T15:22:21Z

Running Pipeline

← Older revision		Revision as of 11:22, 7 February 2020
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	===Running Pipeline===		===Running Pipeline===
	Login to biowulf		Login to biowulf
			# --cpus-per-task=Multithreading amount
			# --ntasks=Number of Parrallel tasks
			# Total CPU count = (cpus-per-task * ntasks) - Most nodes support 56 max CPUs
	sinteractive --exclusive --cpus-per-task=8 --mem-per-cpu=2g --ntasks=6		sinteractive --exclusive --cpus-per-task=8 --mem-per-cpu=2g --ntasks=6
	#sinteractive --cpus-per-task=12 --mem=48g ## I will check on these
	export OMP_NUM_THREADS=4 #Otherwise these tasks will try to use all of the cores		export OMP_NUM_THREADS=4 #Otherwise these tasks will try to use all of the cores
	module load afni		module load afni

2020-02-07T14:48:22Z

Running Pipeline

← Older revision		Revision as of 10:48, 7 February 2020
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	===Running Pipeline===		===Running Pipeline===
	Login to biowulf		Login to biowulf
	sinteractive --exclusive -~~-num~~-cpus-per-task=8 --mem-per-cpu=2g --ntasks=6		sinteractive --exclusive --cpus-per-task=8 --mem-per-cpu=2g --ntasks=6
	#sinteractive --cpus-per-task=12 --mem=48g ## I will check on these		#sinteractive --cpus-per-task=12 --mem=48g ## I will check on these
	export OMP_NUM_THREADS=4 #Otherwise these tasks will try to use all of the cores		export OMP_NUM_THREADS=4 #Otherwise these tasks will try to use all of the cores

2020-02-07T14:47:52Z

Running Pipeline

← Older revision		Revision as of 10:47, 7 February 2020
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	===Running Pipeline===		===Running Pipeline===
	Login to biowulf		Login to biowulf
	sinteractive --cpus-per-task=12 --mem=~~48g~~ ~~## I will check on these~~		sinteractive --exclusive --num-cpus-per-task=8 --mem-per-cpu=2g --ntasks=6
			#sinteractive --cpus-per-task=12 --mem=48g ## I will check on these
	export OMP_NUM_THREADS=4 #Otherwise these tasks will try to use all of the cores		export OMP_NUM_THREADS=4 #Otherwise these tasks will try to use all of the cores
	module load afni		module load afni

2020-02-05T14:48:09Z

Running Pipeline

← Older revision		Revision as of 10:48, 5 February 2020
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	===Running Pipeline===		===Running Pipeline===
	Login to biowulf		Login to biowulf
	sinteractive --cpus-per-task=12 --~~meg~~=48g ## I will check on these		sinteractive --cpus-per-task=12 --mem=48g ## I will check on these
	export OMP_NUM_THREADS=4 #Otherwise these tasks will try to use all of the cores		export OMP_NUM_THREADS=4 #Otherwise these tasks will try to use all of the cores
	module load afni		module load afni

2020-01-28T19:13:46Z

Running Pipeline

← Older revision		Revision as of 15:13, 28 January 2020
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	Login to biowulf		Login to biowulf
	sinteractive --cpus-per-task=12 --meg=48g ## I will check on these		sinteractive --cpus-per-task=12 --meg=48g ## I will check on these
			export OMP_NUM_THREADS=4 #Otherwise these tasks will try to use all of the cores
	module load afni		module load afni
	module load ctf		module load ctf

2020-01-24T22:32:05Z

← Older revision		Revision as of 18:32, 24 January 2020
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	*Add environment information to miniconda ##Need to provide environment.yml		*Add environment information to miniconda ##Need to provide environment.yml
	*Add pyctf, SAMsrc, and megblocks to the miniconda environment ## TODO < provide a way to do this. Add the paths to miniconda/env......pth file		*Add pyctf, SAMsrc, and megblocks to the miniconda environment ## TODO < provide a way to do this. Add the paths to miniconda/env......pth file


			===Running Pipeline===
			Login to biowulf
			sinteractive --cpus-per-task=12 --meg=48g ## I will check on these
			module load afni
			module load ctf
			conda activate mne #This is whatever environment configured for nipype
			~/

2020-01-24T19:52:30Z

← Older revision		Revision as of 15:52, 24 January 2020
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	===Nipype configuration for Biowulf===		===Nipype configuration for Biowulf===
	pull pyctf <br>		pull pyctf <br>
	module load fftw..... # ~~first~~ do a ~~module~~ ~~spide~~ ~~fftw~~ ~~and~~ ~~find~~ ~~one~~ to ~~use~~		module load fftw/3.3.8/openmpi-4.0.0/gcc-7.3.0 ## it is possible to use another version - do 'module spider fftw'
	~~Navigate~~ to ~~top~~ ~~folder~~ ~~(with~~ Makefile)		cd $PYCTF_DIR #Folde will have the Makefile
	~~Make~~ clean		make clean
	~~Make~~		make
	~~Make~~ install		make install
	~~Make~~ usersite (will add a link so package is seen in conda)		make usersite (will add a link so package is seen in conda)
	pull SAMsrcV5 <br>		pull SAMsrcV5 <br>
			For installation instructions read the INSTALL text file - somewhat summarized below
			cd $SAMSRCV5_DIR
			make
			cd config
			make symlinks

	pull megblocks <br>		pull megblocks <br>
	install miniconda (or Anaconda) <br>		install miniconda (or Anaconda) <br>
			https://hpc.nih.gov/apps/python.html#envs << Go to the Creating Python Environments Section to configure
	*Add environment information to miniconda ##Need to provide environment.yml		*Add environment information to miniconda ##Need to provide environment.yml
	*Add pyctf, SAMsrc, and megblocks to the miniconda environment ## TODO < provide a way to do this. Add the paths to miniconda/env......pth file		*Add pyctf, SAMsrc, and megblocks to the miniconda environment ## TODO < provide a way to do this. Add the paths to miniconda/env......pth file

2020-01-24T15:29:57Z

← Older revision		Revision as of 11:29, 24 January 2020
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	[[Image:Nipype meg.png \| 800px]]		[[Image:Nipype meg.png \| 800px]]
			===Nipype Resources===
			https://nipype.readthedocs.io/en/latest/ <br>
			https://miykael.github.io/nipype_tutorial/ <br>

	===Nipype configuration for Biowulf===		===Nipype configuration for Biowulf===

2020-01-24T15:27:39Z

← Older revision		Revision as of 11:27, 24 January 2020
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	Nipye controls the flow of data and automatically determines dependencies to create filenames and folders'''<br>		Nipye controls the flow of data and automatically determines dependencies to create filenames and folders'''<br>

	[[Image:Nipype meg.png]]		[[Image:Nipype meg.png \| 800px]]

	===Nipype configuration for Biowulf===		===Nipype configuration for Biowulf===

2020-01-24T15:25:10Z

← Older revision		Revision as of 11:25, 24 January 2020
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	[[Image:Nipype meg.png]]		[[Image:Nipype meg.png]]

	~~'''~~Nipype configuration for Biowulf~~''' <br>~~		===Nipype configuration for Biowulf===
	pull pyctf <br>		pull pyctf <br>
			module load fftw..... # first do a module spide fftw and find one to use
	*Navigate to top folder (with Makefile)		Navigate to top folder (with Makefile)
	*Make clean
	*Make		Make clean
			Make
	*Make install		Make install
	*Make usersite (will add a link so package is seen in conda)		Make usersite (will add a link so package is seen in conda)
	pull SAMsrcV5 <br>		pull SAMsrcV5 <br>
	pull megblocks <br>		pull megblocks <br>