Here is a summary for the archives. Thanks very much to all. I took the advice of Russ Hopson and did reviveccu from a shell as root. It worked like a charm.
Some advice from me: Don't let your batteries go beyond 5 years!
Bob Honeychuck
The original post:
----------------
A student was in TopSpin on my DPX 300 during a power failure. The console turned itself off. I replaced the battery pack on the 230 V UPS and turned the instrument back on. Now Linux is good, but TopSpin won't start. The Flexlm license seems to be OK. The internal boards are not damaged: fcutest, tcutest, and rcutest find no errors.
The error message mentions a read-only file system, but the permissions look OK in Konqueror.
Here is the error message on attempted startup by user chem. The 1.3 is correct. This is where our topspin resides.
-----
CPR : Path to prog : "/opt/topspin1.3/prog"
CPR : Path to exp : "/opt/topspin1.3/exp"
CPR : Path to conf : "/opt/topspin1.3/conf"
CPR : waiting for FLEXlm license
CPR : Your FLEXlm license is valid until 6-nov-2023
CPR : could not correct permissions of current data directory /opt/topspin1.3/prog/curdir/chem: Read-only file system
Program is exiting...
-----
Thank you very much.
Robert Honeychuck
Dept of Chemistry and Biochemistry
George Mason U
Fairfax VA 22030
rhoneych_at_gmu.edu<mailto:rhoneych_at_gmu.edu>
----------------
----------------
remove this curdir entry.
Rainer
----------------
Dear Robert, I would simple delete the /chem -directory in "curdir"
TopSpin will create it new.
Yours
Matthias Findeisen
----------------
could it be that the directory "chem" is not a local directory, but one that's remotely mounted ? And the mount procedure, for whatever reason, has decided to mount in read-only mode ?
Is it possible to access other files in other directories inside the /opt/topspin1.3 directory ?
Best wishes, Mike Engelhardt
----------------
Try renaming or deleting the offending directory. It will be recreated during start up
Clemens
----------------
I would suggest a quick reload of Topspin or just reload Diskless. This has worked for no good reason too many times. You might try changing the permissions as SU (root). I would start with the permissions and then diskless reload and then topspin reload.
Best regards,
Martha Morton
----------------
Long ago (uxnmr), there was a user file in curdir after a crash that would hang the system until you removed it...
Can you delete the file that was up during the outage?
Usually I go back to the nmrsu directory to see if it's just a user problem but this one may hang it up for everyone.
----------------
Try remounting the file system. That might usually solve the read-only file system errors
For eg, to mount the partition /dev/hda1 try the following
mount -o remount,rw /dev/hda1
-Ilango.
----------------
The read-only filesystem part is the part that I would pay attention to. You want to look in /etc/mtab to see what file systems are mounted which way. It is also possible that a bit in your root directory just got flipped (the one that allows write permission), which you may be able to fix with the chmod command in a shell (terminal window).
If you go to the root directory
cd /
and then
ls -l
you will see what is read-only versus read-write versus read-write-execute and you can run the chmod command to change it.
Jeff
----------------
Was Linux somehow damaged during the power failure? In other words did you have to rebuild it somehow?
I presume that you login to Linux with the userid: chem
Did you have to recreate the account at all as part of the Linux rebuild? My guess is that even though "userid = chem" is the same, the computer somehow believes it to be a different account, and therefore have different ownership.
Anyway, I think I have two ways to get you back in business. In both cases you will need to know the Linux root password.
Method 1: Make folder chem universally writable.
* Open a terminal window.
* su
* Enter the root password
* cd /opt/topspin1.3/prog/curdir
* cp -rp chem chem.one
* chmod -R 777 chem
* exit
* exit
What you have effectively done is make the chem folder "world writable" which is not an ideal solution, but it will at least get you back running TopSpin. The original chemfolder was copied to a folder called chem.one so you can go back if you don't like this solution.
Method 2: Delete the old chem folder; have TopSpin create a new one from scratch.
* Open a terminal window.
* su
* Enter the root password
* cd /opt/topspin1.3/prog/curdir
* cp -rp chem chem.ORIG
* rm -rf chem
* exit
* exit
What you have effectively done is copied the "original" chem folder to a new folder calledchem.ORIG
Then you deleted the original chem folder.
When you start TopSpin, it should create a "new" chem folder.
It will be as if this was the first time you started TopSpin.
Now, this could be a massive pain if you had lots of customizations with the TopSpin interface. But at least you should be back in business.
Good luck.
Bob.
----------------
Have you tried a different user?
Weixing Zhang
----------------
1) Something bad could have happened to the last data set. Topspin insists on opening the last data set looked at which is great unless the data is corrupted. To make it forget the last data set it looked at, open a terminal screen and start topspin with topspin -r
If that didn't work , try
shmrm
topspin-r
If still a problem:
2) Sometimes what the GUI says and what is real are two separate matters. Open a terminal screen, change to the directory in question:
cd /opt/topspin1.3/prog/curdir/chem
Check permissions with
ls -al
Directories should be rwxr-xr-x
(Or rwrwxr-x or rwxrwxrwx )
If permissions are not as above and you don't know what to do next, email me.
----------------
did you get the problem solved? the simplest thing to reboot the linux box and then because there was likely a file system corruption, it will run a fsck upon boot and will probably correct everything..
if it encounters issues that it cannot fix, you need to boot from the linux install disk into rescue mode and do an fsck from there. lf you need help, let me know…
john
----------------
We have a TS1.3 spectrometer, and I just looked at it. curdir/ is the folder where topspin logs various information for each user. Permissions on curdir for us are 777 or drwxrwxrwx under a ls -la (we run under CentOS, so would be different under windows). Same permissions for each user in curdir.
The read-only file system message, however, sounds like it might be an OS issue. Without knowing more about your computer system, hard to guess what might be wrong.
Hopefully someone else recognizes the specific problem, and provide an easy solution. Best of luck,
Charlie
----------------
This is true. There are likely all sorts of hung processes/sessions and locked user accounts because of the power failure while the software was in use. If they were running as nmrsu, as Daniel points out, that could lock it up for all users, until the hung processes and other communications glitches are cleared from both the computer and the console. Once cleared, a full restart on both should restore everything to working once again.
Kristie M. Adams
----------------
I would login to the host computer as ³root², and remove the directory
³chem² under /opt/topspin1.3/prog/curdir/. This will give the user ³chem²
a fresh start of the topspin program. You will need to reset all the
settings under ³setres², but it mostly likely will fix the problem.
Best,
Dee
----------------
Have you tried the 'reviveccu' command from the root terminal window? Instructions will pop up instructing you to turn off AQX rack and then reboot workstation. When workstation is back up to login screen, restart AQX. This has worked for me in the past.
Russ
----------------
It looks like the current user is "chem"?
Did you try a different user acct?
Does it gave the same error?
I would create a new acct from scratch and
do not copy anything from any old accts.
and then try to start TS again.
Best wishes,
Ben Ramirez
Received on Wed Sep 24 2014 - 12:33:37 MST