Hoffman2:FSL - Revision history

Hwang: /* Known Issue in Hoffman */

2026-05-05T18:15:48Z

Known Issue in Hoffman

← Older revision		Revision as of 18:15, 5 May 2026
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	This is because these versions of FSL overwrite the path to the dbus and noMachine cannot find the dbus in Hoffman.		This is because these versions of FSL overwrite the path to the dbus and noMachine cannot find the dbus in Hoffman.

	Normally dbus-launch should be under /usr/bin. If it's not, then it won't work.		Normally dbus-launch should be under /usr/bin. If it's not, then it won't work. By checking the dbu-launch path, it can be decided if it's the same issue or not.

	which dbus-launch		which dbus-launch

Hwang: /* Known Issue in Hoffman */

2026-05-05T18:14:04Z

Known Issue in Hoffman

← Older revision		Revision as of 18:14, 5 May 2026
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	== Known Issue in Hoffman==		== Known Issue in Hoffman==

	When using noMachine with newer version of FSL, user might get errors as the following		When using noMachine with newer version (6.0.7.x) of FSL, user might get errors as the following

	"Unable to contact" settings server : Failed to connect to socket /tmp/dbus-xxxxx: Connection refused		"Unable to contact" settings server : Failed to connect to socket /tmp/dbus-xxxxx: Connection refused

Hwang: /* Known Issue in Hoffman */

2026-05-05T18:10:51Z

Known Issue in Hoffman

← Older revision		Revision as of 18:10, 5 May 2026
Line 182:		Line 182:
	== Known Issue in Hoffman==		== Known Issue in Hoffman==

	When using noMachine + newer version of FSL, user might get errors as the following		When using noMachine with newer version of FSL, user might get errors as the following

	"Unable to contact" settings server : Failed to connect to socket /tmp/dbus-xxxxx: Connection refused		"Unable to contact" settings server : Failed to connect to socket /tmp/dbus-xxxxx: Connection refused

Hwang: /* FSL Known Issue in Hoffman */

2026-05-05T18:08:11Z

FSL Known Issue in Hoffman

← Older revision		Revision as of 18:08, 5 May 2026
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	# now run eddy_cuda9.1 or bedpostx_gpu		# now run eddy_cuda9.1 or bedpostx_gpu

	==~~FSL~~ Known Issue in Hoffman==		== Known Issue in Hoffman==

	When using noMachine + newer version of FSL, user might get errors as the following		When using noMachine + newer version of FSL, user might get errors as the following
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	3. In noMachine terminal, input "module load fsl/versionxxx". Then it should avoid the same error this time.		3. In noMachine terminal, input "module load fsl/versionxxx". Then it should avoid the same error this time.


	==External Links==		==External Links==
	* Official FSL website http://www.fmrib.ox.ac.uk/fsl/		* Official FSL website http://www.fmrib.ox.ac.uk/fsl/

Hwang at 18:06, 5 May 2026

2026-05-05T18:06:41Z

@@ Line 179: / Line 179: @@
   # now run eddy_cuda9.1 or bedpostx_gpu
 ==External Links==
 * Official FSL website http://www.fmrib.ox.ac.uk/fsl/

Jpdiaz: add fsl gpu example

2022-07-15T19:56:20Z

add fsl gpu example

← Older revision		Revision as of 19:56, 15 July 2022
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	\| Interactive display tool for 3D and 4D data.		\| Interactive display tool for 3D and 4D data.
	\|}		\|}


	==Cluster==		==Cluster==
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	See its documentation [[Hoffman2:Scripts:switch_fsl \| here]]. -->		See its documentation [[Hoffman2:Scripts:switch_fsl \| here]]. -->


	==NO_FSL_JOBS==		==NO_FSL_JOBS==
	Sometimes FSL doesn't know how to allocate enough resources for its jobs properly. Specifically we have found the FEAT tool often unable to do this for group analyses or other complex tasks. So we did some tinkering with FSL to allow you to override its job submission on Hoffman2 and run it like it was just on your laptop. '''The trick is to set <code>NO_FSL_JOBS=true</code> in your environment and FSL will not submit jobs.'''		Sometimes FSL doesn't know how to allocate enough resources for its jobs properly. Specifically we have found the FEAT tool often unable to do this for group analyses or other complex tasks. So we did some tinkering with FSL to allow you to override its job submission on Hoffman2 and run it like it was just on your laptop. '''The trick is to set <code>NO_FSL_JOBS=true</code> in your environment and FSL will not submit jobs.'''


	===Interactive Session===		===Interactive Session===
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			==FSL GPU==

			Some FSL tools, like ''eddy'' and ''bedpostx'', can utilize Hofmman's GPU architecture to speed up their processing times. Below is an example of how to request a CUDA 9.1-enabled GPU node.

			# request Tesla P4 GPU node
			qrsh -l gpu,P4,h_rt=5:00:00

			module load cuda/9.1
			module load fsl/6.0.4
			export NO_FSL_JOBS=true

			# now run eddy_cuda9.1 or bedpostx_gpu


	==External Links==		==External Links==
	* Official FSL website http://www.fmrib.ox.ac.uk/fsl/		* Official FSL website http://www.fmrib.ox.ac.uk/fsl/

Hwang: /* Interactive Session */

2020-02-06T23:49:15Z

Interactive Session

← Older revision		Revision as of 23:49, 6 February 2020
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	#[[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line\|SSH]] into the cluster		#[[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line\|SSH]] into the cluster
	#Check out an [[Hoffman2:Interactive_Sessions\|interactive node]] with the necessary time and memory		#Check out an [[Hoffman2:Interactive_Sessions\|interactive node]] with the necessary time and memory
	#*<code>qrsh -l i,h_rt=3:00:00,h_data=3G</code>		#*<code>qrsh -l h_rt=3:00:00,h_data=4G</code>
	#Set the environment variable		#Set the environment variable
	#*<code>export NO_FSL_JOBS=true</code>		#*<code>export NO_FSL_JOBS=true</code>
	#Run your FSL commands. '''This means not using qsub, or command files, but simply executing the FSL command'''		#Run your FSL commands. '''This means not using qsub, or command files, but simply executing the FSL command'''
	#The commands will just run and not submit any jobs.		#The commands will just run and not submit any jobs.


	===Submitting a Job===		===Submitting a Job===

Dmargolis at 14:07, 8 July 2017

2017-07-08T14:07:58Z

← Older revision		Revision as of 14:07, 8 July 2017
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	Multiple versions are maintained on the Hoffman2 cluster to allow researchers to be consistent in using the same version for data analysis within a single study. You can either:		Multiple versions are maintained on the Hoffman2 cluster to allow researchers to be consistent in using the same version for data analysis within a single study. You can either:
	* do nothing, and always use the "current" version of FSL on the cluster		* do nothing, and always use the "current" version of FSL on the cluster
	* [[Hoffman2:FSL~~#switch_fsl~~\|actively choose]] which version of FSL you would like to run		* [[Hoffman2:Modules#FSL\|actively choose]] which version of FSL you would like to run
	We recommend the latter for data integrity and reproducibility.		We recommend the latter for data integrity and reproducibility.

Dmargolis at 23:43, 22 May 2017

2017-05-22T23:43:42Z

← Older revision		Revision as of 23:43, 22 May 2017
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	# any other FSL commands you want		# any other FSL commands you want

	And make sure to run <code>chmod ~~755~~</code> to make the script executable		And make sure to run <code>chmod 750</code> to make the script executable
	chmod ~~755~~ myshellscript.sh		chmod 750 myshellscript.sh

	Submit the shell script [[Hoffman2:Submitting_Jobs\|as a job]] but with the adequate time and memory allocations		Submit the shell script [[Hoffman2:Submitting_Jobs\|as a job]] but with the adequate time and memory allocations

Dmargolis at 23:27, 22 May 2017

2017-05-22T23:27:25Z

← Older revision		Revision as of 23:27, 22 May 2017
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	#[[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line\|SSH]] into the cluster		#[[Hoffman2:Accessing_the_Cluster#SSH_-_Command_Line\|SSH]] into the cluster
	#Check out an [[Hoffman2:Interactive_Sessions\|interactive node]] with the necessary time and memory		#Check out an [[Hoffman2:Interactive_Sessions\|interactive node]] with the necessary time and memory
	#*<code>qrsh -l i,~~time~~=3:00:00,h_data=3G</code>		#*<code>qrsh -l i,h_rt=3:00:00,h_data=3G</code>
	#Set the environment variable		#Set the environment variable
	#*<code>export NO_FSL_JOBS=true</code>		#*<code>export NO_FSL_JOBS=true</code>
Line 162:		Line 162:

	Submit the shell script [[Hoffman2:Submitting_Jobs\|as a job]] but with the adequate time and memory allocations		Submit the shell script [[Hoffman2:Submitting_Jobs\|as a job]] but with the adequate time and memory allocations
	qsub -l ~~time~~=23:00:00,h_data=4G -V -m bea -cwd /path/to/myshellscript.sh		qsub -l h_rt=23:00:00,h_data=4G -V -m bea -cwd /path/to/myshellscript.sh

	And the FSL commands will be sent into the queue to run with your time and memory constraints rather than FSL's. This may take some playing with to get the time and memory allocations correct, but at least you have the ability to tweak them.		And the FSL commands will be sent into the queue to run with your time and memory constraints rather than FSL's. This may take some playing with to get the time and memory allocations correct, but at least you have the ability to tweak them.