No idea, I think the sysadmins set up that way after the file system change, but I couldn't tell... at least it is working now, many thanks for your help! Gari
On Sat, Jun 1, 2013 at 11:28 PM, Watson, Christopher < christopher.wat...@childrens.harvard.edu> wrote: > I've never had any problems with sym links, but what you have is > definitely confusing! Is there any reason you have it that way? As a rule > of thumb, i'd keep things as simple as possible. > ________________________________________ > From: Garikoitz Lerma-Usabiaga [gariko...@gmail.com] > Sent: Saturday, June 01, 2013 4:21 PM > To: Watson, Christopher > Cc: Freesurfer > Subject: Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2 > > 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<mailto: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<mailto: > 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<mailto: > 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<mailto: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<mailto: > 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<mailto: > 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<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. > > > > > > _______________________________________________ > 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. > > > > _______________________________________________ > 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. > > > > > >
_______________________________________________ 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.
