[Freesurfer] FW: FW: problem with hard coded directory (/scratch)
Hi FS's experts, I sent out a couple of emails to seek for help on an error from running recon-all using freesurfer 6.0 beta. Could anyone help with the question? Thank you! - Fengji From: Fengji Geng Sent: Thursday, January 07, 2016 8:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know. we ran recon-all -all -s -hippocampal-subfields-T1T2 . We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch. I can also send you the strace output if needed. Thank you! - Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Can you give us specific examples of problem programs? On 01/04/2016 09:54 AM, Fengji Geng wrote: > Hello Bruce, > > Happy New Year! > > After we reported the error related to '/scratch' several weeks ago > (see the email attached below), we tested the newest version of > freesurfer 6.0 recently, it looks likes that a lot of "if (-e > /scratch)" have been changed to "if (-dw /scratch)". However, there > are still a lot of binaries in the bin directory that match the string > "scratch", which cause the same error that I encountered before. I am > wondering if it is possible for you to fix '/scratch' in the bin > directory. > > Thank you! - Fengji ___ 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.
Re: [Freesurfer] FW: FW: problem with hard coded directory (/scratch)
Hi Fengji, Sorry for the late reply; I was on vacation and totally missed your question. The hippocampal subfield module uses /scratch to create temporary files if available. If not, it creates a directory under the tmp directory inside the subject directory. It was coded this way because in our system, because of the way the cluster is setup, writing to /scratch is way more efficient. For now, the only thing you can do is to enable writing permissions on /scratch, or deleting /scratch. For the future: maybe we should remove the /scratch check and go to the subject's tmp directory directly (Zeke, Nick, what do you think?) Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Fengji Geng" <ge...@umd.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, January 14, 2016 7:46:44 PM Subject: [Freesurfer] FW: FW: problem with hard coded directory (/scratch) Hi FS's experts, I sent out a couple of emails to seek for help on an error from running recon-all using freesurfer 6.0 beta. Could anyone help with the question? Thank you! - Fengji From: Fengji Geng Sent: Thursday, January 07, 2016 8:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know. we ran recon-all -all -s -hippocampal-subfields-T1T2 . We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch. I can also send you the strace output if needed. Thank you! - Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Can you give us specific examples of problem programs? On 01/04/2016 09:54 AM, Fengji Geng wrote: > Hello Bruce, > > Happy New Year! > > After we reported the error related to '/scratch' several weeks ago > (see the email attached below), we tested the newest version of > freesurfer 6.0 recently, it looks likes that a lot of "if (-e > /scratch)" have been changed to "if (-dw /scratch)". However, there > are still a lot of binaries in the bin directory that match the string > "scratch", which cause the same error that I encountered before. I am > wondering if it is possible for you to fix '/scratch' in the bin > directory. > > Thank you! - Fengji ___ 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 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.
Re: [Freesurfer] FW: FW: problem with hard coded directory (/scratch)
Hi Fengji, you have sent several emails. I keep asking you to give us a specific binary that has the problem, but you seem to ignore my request, wait a couple of weeks, then post the question back to the list. I'm happy to take look, but please send me something more specific! thanks doug On 01/14/2016 01:46 PM, Fengji Geng wrote: > Hi FS's experts, > I sent out a couple of emails to seek for help on an error from > running recon-all using freesurfer 6.0 beta. Could anyone help with > the question? > Thank you! > > > > - > Fengji > > > *From:* Fengji Geng > *Sent:* Thursday, January 07, 2016 8:15 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] FW: problem with hard coded directory > (/scratch) > > Hi Douglas, > You asked us to give you an example of the problem program. I will try > to do it here, but if it is not what you want, please let me know. > > we ran recon-all -all -s -hippocampal-subfields-T1T2 > . We saw the program tried > to create /scratch/$subject_hippoSF_T1_v10_right directory > and failing with (Read-only file system) because the user does not > have permission to write to /scratch. > > I can also send you the strace output if needed. > > Thank you! > > - > Message: 4 > Date: Mon, 4 Jan 2016 13:37:48 -0500 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] FW: problem with hard coded directory > (/scratch) > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Can you give us specific examples of problem programs? > > On 01/04/2016 09:54 AM, Fengji Geng wrote: > > Hello Bruce, > > > > Happy New Year! > > > > After we reported the error related to '/scratch' several weeks ago > > (see the email attached below), we tested the newest version of > > freesurfer 6.0 recently, it looks likes that a lot of "if (-e > > /scratch)" have been changed to "if (-dw /scratch)". However, there > > are still a lot of binaries in the bin directory that match the string > > "scratch", which cause the same error that I encountered before. I am > > wondering if it is possible for you to fix '/scratch' in the bin > > directory. > > > > Thank you! > > - > Fengji > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
