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
