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.Watson@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 < nicks@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 garikoitz@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 listFreesurfer@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.