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.imgswapswapdefaults0 0
#hippocampus-nfs:/data/datanfsdefaults0 2
#hippocampus-nfs:/home/BCBL/home/BCBLnfsdefaults0 2
ltm.bcbl.local:/root_vdm_1/home/bcbl/homenfs4defaults0 0
ltm.bcbl.local:/root_vdm_1/data/bcbl/data nfs4defaults0 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
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The information in this e-mail is intended only for the person to
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contains patient information, please contact the Partners
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you in error
but does not contain patient information, please contact the
sender and properly
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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
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