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 <subject_name> -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>. We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch.
I can also send you the strace output if needed.
Thank you!
--------------------------------------------------------------------------------- Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: 568ABBFC.5000702@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed
Can you give us specific examples of problem programs?
On 01/04/2016 09:54 AM, Fengji Geng wrote:
Hello Bruce,
Happy New Year!
After we reported the error related to '/scratch' several weeks ago (see the email attached below), we tested the newest version of freesurfer 6.0 recently, it looks likes that a lot of "if (-e /scratch)" have been changed to "if (-dw /scratch)". However, there are still a lot of binaries in the bin directory that match the string "scratch", which cause the same error that I encountered before. I am wondering if it is possible for you to fix '/scratch' in the bin directory.
Thank you!
----- Fengji
can you be more specific? Which program failed? Also, please send us the recon-all.log file so we have the information we need to help you.
cheers Bruce On Thu, 7 Jan 2016, Fengji Geng wrote:
Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know.
we ran recon-all -all -s <subject_name> -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>. We saw the program tried to create /scratch/$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 greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: 568ABBFC.5000702@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
Do you have the problem if you do not include the hippo subfields?
On 01/07/2016 08:15 AM, Fengji Geng wrote:
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 <subject_name> -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>. We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch.
I can also send you the strace output if needed.
Thank you!
Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: 568ABBFC.5000702@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed
Can you give us specific examples of problem programs?
On 01/04/2016 09:54 AM, Fengji Geng wrote:
Hello Bruce,
Happy New Year!
After we reported the error related to '/scratch' several weeks ago (see the email attached below), we tested the newest version of freesurfer 6.0 recently, it looks likes that a lot of "if (-e /scratch)" have been changed to "if (-dw /scratch)". However, there are still a lot of binaries in the bin directory that match the string "scratch", which cause the same error that I encountered before. I am wondering if it is possible for you to fix '/scratch' in the bin directory.
Thank you!
Fengji
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi FS's experts, I sent out a couple of emails to seek for help on an error from running recon-all using freesurfer 6.0 beta. Could anyone help with the question? Thank you!
----- Fengji
________________________________ From: Fengji Geng Sent: Thursday, January 07, 2016 8:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch)
Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know.
we ran recon-all -all -s <subject_name> -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>. We saw the program tried to create /scratch/$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 greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: 568ABBFC.5000702@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
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" gengf@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 <subject_name> -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>. 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 greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: 568ABBFC.5000702@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
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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 <subject_name> -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>. 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 greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: 568ABBFC.5000702@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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Eugenio Iglesias -
Fengji Geng