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Hi!I'am a student of medicine in Foggia,Italy.To elaborate a single .nii file for a single subjects i use "recon-all -i (name of .nii file) -s (name of subjects) -all -openmp 8(i have 8 core)"and to finish the work is necessary 8 hours.
Now i want elaborate 10 .nii file for 10 subjects(a file for each subject).Is better to open 10 terminal and use the command recon-all in each terminal without -openmp,or with -openmp?Or to use this,Now i open 10 terminal BUT for every terminal i use the command Taskset to assign every terminal to a core of my cpus(2 core is busy with 2 recon-all....)
Wich is the best way to finish the work more rapidly?
Sorry for my bad english and i hope for a reply.Thanks
Morciano Ottavio
MD.Student
If you have 10 processors and enough memory, then you should run 10 simultaneously (ie, without using -openmp).
On 06/25/2018 05:34 PM, Ottavio Morciano wrote:
Hi!I'am a student of medicine in Foggia,Italy.To elaborate a single .nii file for a single subjects i use "recon-all -i (name of .nii file) -s (name of subjects) -all -openmp 8(i have 8 core)"and to finish the work is necessary 8 hours.
Now i want elaborate 10 .nii file for 10 subjects(a file for each subject).Is better to open 10 terminal and use the command recon-all in each terminal without -openmp,or with -openmp?Or to use this,Now i open 10 terminal BUT for every terminal i use the command Taskset to assign every terminal to a core of my cpus(2 core is busy with 2 recon-all....)
Wich is the best way to finish the work more rapidly?
Sorry for my bad english and i hope for a reply.Thanks
Morciano Ottavio
MD.Student
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Without taskset ? Just open terminal and type recon-all -i x -s y -all for each subjects?
Il lun 25 giu 2018, 23:43 Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
If you have 10 processors and enough memory, then you should run 10 simultaneously (ie, without using -openmp).
On 06/25/2018 05:34 PM, Ottavio Morciano wrote:
Hi!I'am a student of medicine in Foggia,Italy.To elaborate a single .nii file for a single subjects i use "recon-all -i (name of .nii file) -s (name of subjects) -all -openmp 8(i have 8 core)"and to finish the work is necessary 8 hours.
Now i want elaborate 10 .nii file for 10 subjects(a file for each subject).Is better to open 10 terminal and use the command recon-all in each terminal without -openmp,or with -openmp?Or to use this,Now i open 10 terminal BUT for every terminal i use the command Taskset to assign every terminal to a core of my cpus(2 core is busy with 2 recon-all....)
Wich is the best way to finish the work more rapidly?
Sorry for my bad english and i hope for a reply.Thanks
Morciano Ottavio
MD.Student
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Ottavio,
you can also install gnu parallel (https://www.gnu.org/software/parallel/) and run in parallel on all your cpus with just one parallel command line:
export SUBJECTS_DIR=/home/my/study/fs60/MRIstudy/sMRI/native
cd /home/my/MRIdata/sMRI/native
ls *.nii | parallel --jobs 8 recon-all -all -s {.} -i {}
cheers,
Giuseppe
On 25/06/2018 23:49, Ottavio Morciano wrote:
External Email - Use Caution
Without taskset ? Just open terminal and type recon-all -i x -s y -all for each subjects?
Il lun 25 giu 2018, 23:43 Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> ha scritto:
If you have 10 processors and enough memory, then you should run 10 simultaneously (ie, without using -openmp). On 06/25/2018 05:34 PM, Ottavio Morciano wrote: > > > Hi!I'am a student of medicine in Foggia,Italy.To elaborate a single > .nii file for a single subjects i use "recon-all -i (name of .nii > file) -s (name of subjects) -all -openmp 8(i have 8 core)"and to > finish the work is necessary 8 hours. > > Now i want elaborate 10 .nii file for 10 subjects(a file for each > subject).Is better to open 10 terminal and use the command recon-all > in each terminal without -openmp,or with -openmp?Or to use this,Now i > open 10 terminal BUT for every terminal i use the command Taskset to > assign every terminal to a core of my cpus(2 core is busy with 2 > recon-all....) > > Wich is the best way to finish the work more rapidly? > > Sorry for my bad english and i hope for a reply.Thanks > > Morciano Ottavio > > MD.Student > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
External Email - Use Caution
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Thanks Sir
2018-06-26 9:33 GMT+02:00 Giuseppe Cabras giuseppe.cabras@uniud.it:
Hi Ottavio,
you can also install gnu parallel (https://www.gnu.org/software/parallel/) and run in parallel on all your cpus with just one parallel command line:
export SUBJECTS_DIR=/home/my/study/fs60/MRIstudy/sMRI/native
cd /home/my/MRIdata/sMRI/native
ls *.nii | parallel --jobs 8 recon-all -all -s {.} -i {}
cheers,
Giuseppe
On 25/06/2018 23:49, Ottavio Morciano wrote:
External Email - Use CautionWithout taskset ? Just open terminal and type recon-all -i x -s y -all for each subjects?
Il lun 25 giu 2018, 23:43 Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
If you have 10 processors and enough memory, then you should run 10 simultaneously (ie, without using -openmp).
On 06/25/2018 05:34 PM, Ottavio Morciano wrote:
Hi!I'am a student of medicine in Foggia,Italy.To elaborate a single .nii file for a single subjects i use "recon-all -i (name of .nii file) -s (name of subjects) -all -openmp 8(i have 8 core)"and to finish the work is necessary 8 hours.
Now i want elaborate 10 .nii file for 10 subjects(a file for each subject).Is better to open 10 terminal and use the command recon-all in each terminal without -openmp,or with -openmp?Or to use this,Now i open 10 terminal BUT for every terminal i use the command Taskset to assign every terminal to a core of my cpus(2 core is busy with 2 recon-all....)
Wich is the best way to finish the work more rapidly?
Sorry for my bad english and i hope for a reply.Thanks
Morciano Ottavio
MD.Student
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
External Email - Use Caution
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Ottavio Morciano