Hello list, we found the problem, symbolic links: /home/glerma/ is the home of the app server where fs is installed. /home/glerma/glerma/freesurfer/subjects was the SUBJECTS_DIR, but it has a sym link, since: glerma -> /bcbl/home/home_g-m/glerma so changing SUBJECTS_DIR to: /bcbl/home/home_g-m/glerma/freesurfer/subjects solved the problem.
Do you think this is a problem with fs resolving sym links? We haven't found any problem with matlab or fsl. thanks again! Gari On Sat, May 11, 2013 at 12:46 AM, Garikoitz Lerma-Usabiaga < gariko...@gmail.com> wrote: > Yes, > first two lines for example in SUBJECTS_DIR (I had to change SUBJECTS_DIR > since now I have it in the app server, as said before): > drwxr-xr-x 77 glerma domain users 4096 Dec 20 17:25 BERTSO > drwxr-xr-x 10 glerma domain users 2048 Feb 14 16:27 BERTSO_MRI > > and for the parent directory: > drwxr-xr-x 8 glerma domain users 1024 Mar 14 12:37 OSIRIX > drwxr-xr-x 8 glerma domain users 1024 Mar 8 08:59 OsiriX Data > drwxr-xr-x 26 glerma domain users 2048 May 7 17:55 subjects > > > thanks! > Gari > > > > On Sat, May 11, 2013 at 12:37 AM, Chris Watson < > christopher.wat...@childrens.harvard.edu> wrote: > >> Can you paste the output of "ls -l $SUBJECTS_DIR", so we can see what >> the permissions are? You may also want to paste the output of the parent >> directory as well. >> >> On 05/10/2013 06:18 PM, Garikoitz Lerma-Usabiaga wrote: >> >> Thanks Chris, >> > ls -l $SUBJECTS_DIR: it works >> > This is the output of the command (I cannot make sense out of it): >> >> [glerma@cajal ~]$ cat /etc/fstab >> /dev/VolGroup00/LogVol00 / ext3 defaults >> 1 1 >> LABEL=/boot /boot ext3 defaults 1 >> 2 >> tmpfs /dev/shm tmpfs defaults 0 >> 0 >> devpts /dev/pts devpts gid=5,mode=620 0 >> 0 >> sysfs /sys sysfs defaults 0 >> 0 >> proc /proc proc defaults 0 >> 0 >> /dev/VolGroup00/LogVol01 swap swap defaults >> 0 0 >> /var/lib/swap/swap_cajal.img swap swap defaults 0 0 >> #hippocampus-nfs:/data /data nfs defaults 0 2 >> #hippocampus-nfs:/home/BCBL /home/BCBL nfs defaults 0 2 >> ltm.bcbl.local:/root_vdm_1/home /bcbl/home nfs4 defaults 0 0 >> ltm.bcbl.local:/root_vdm_1/data /bcbl/data nfs4 defaults 0 0 >> >> #hippocampus-nfs:/home/BCBL /home/BCBL nfs >> rw,bg,intr,hard,timeo=600,wsize=32768,rsize=32768,nfsvers=3,tcp,noacl 0 2 >> >> >> (this is in the old app server, which worked before the migration to >> the new file system) >> >> thanks again! >> Gari >> >> >> On Sat, May 11, 2013 at 12:07 AM, Chris Watson < >> christopher.wat...@childrens.harvard.edu> wrote: >> >>> Can you check that the UID and GID both match on the client and server >>> sides? Is it the same user that is able to use other programs, yet unable >>> to write via Freesurfer? Is your user an NIS account? >>> >>> Can you output >>> # ls -l $SUBJECTS_DIR >>> >>> I assume that since you say other programs can write to the filesystem, >>> it is mounted properly, but can you show what is in /etc/fstab? i.e. make >>> sure you see "rw" instead of "ro". >>> >>> >>> On 05/10/2013 05:55 PM, Garikoitz Lerma-Usabiaga wrote: >>> >>> Thanks for the answers. >>> I am not the sys admin, but I think I can answer both questions: >>> > I assume the system is in read-write mode since the rest of the >>> programs (i.e. Matlab) are working. >>> > The SUBJECT_DIR is in each personal space, I mean: >>> --- FS is installed in a Linux CentOS 5 machine, I have an account in >>> that machine (and I can work normally if my SUBJECTS_DIR is in that machine) >>> --- I have a personal drive space in the NFS 4, and I used to have my >>> SUBJECTS_DIR in that drive, but after they upgraded it to NFS 4, it didn't >>> work again. >>> > We have a new cluster now, they are testing it, it has Red Hat >>> installed, with FS 5.2, and I've been told that it cannot write (same >>> problem). >>> >>> The strange thing is that other programs work fine with this setup. >>> >>> Do you think the problem is in the file system config (it seems so) or >>> in FS config to be able to work with NFS 4? >>> >>> I have asked the sys admin for the output of the system-config-nfs, I >>> don't have admin privileges to run it. >>> >>> thanks again! >>> Gari >>> >>> >>> >>> On Fri, May 10, 2013 at 11:46 PM, Nick Schmansky < >>> ni...@nmr.mgh.harvard.edu> wrote: >>> >>>> Gari, >>>> >>>> At the NMR Center we use NFS v4 without problems with freesurfer. Is >>>> the >>>> SUBJECTS_DIR writable? Note that in the default freesurfer >>>> distribution, >>>> the freesurfer/subjects directory is not writable (contains sample and >>>> template subjects). >>>> >>>> Nick >>>> >>>> >>>> > Hi, >>>> > Has anybody got problems using FS with NFS v4? >>>> > We cannot write subjects if the SUBJECTS_DIR is in a NFS v4 system. >>>> > >>>> > Many thanks, >>>> > Gari >>>> > >>>> > ---------- Forwarded message ---------- >>>> > From: Garikoitz Lerma-Usabiaga <gariko...@gmail.com> >>>> > Date: Tue, May 7, 2013 at 5:25 PM >>>> > Subject: NFS v4 on CentOS 5.4 or Red Hat 6.2 >>>> > To: Freesurfer <freesurfer@nmr.mgh.harvard.edu> >>>> > >>>> > >>>> > Hi FS experts, >>>> > we have changed our file systems to NFS v4 and we found that FS cannot >>>> > write to it (I mean, FS installed in an app server and subjects in the >>>> > file >>>> > system is not working). >>>> > Last new I have is that FS in CentOS could read but not write and in >>>> Red >>>> > Hat could not write or read. >>>> > >>>> > Is it a known problem? Is it something going on with FS or the >>>> problem is >>>> > in our end? (the rest of the programs are working fine: FSL, >>>> Matlab...) >>>> > >>>> > >>>> > Many thanks, >>>> > Gari >>>> > _______________________________________________ >>>> > 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 >>> listfreesur...@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. >>> >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >> >> >
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