Segmentation Fault

nonfcomm · Post by **nonfcomm** » Wed Feb 08, 2006 7:34 pm

I am running Neuron on 64-bit Linux. Whenever I open a new program window during a simulation I get this output:

/usr/local/nrn/x86_64/bin/nrniv: Segmentation violation See $NEURONHOME/lib/help/oc.help
in xrecord.hoc near line 32
^
doNotify()
screen_update()
continuerun(11000)
run()
and others

Up until this point, this has not been a general problem as I just didn't open any new programs during a simulation. Unfortunately, my simulation times have grown dramatically (now on the order of days instead of hours--brute force parameter search) the inability to access any programs that have not been open constantly since the beginning of the simulation has become rather arduous.

I had hoped that running Neuron without the GUI would be a solution. To the best of my knowledge, there is no GUI code in the model (i.e. when I load it with the nrngui command only the file menu comes up). When I tried the nrniv command, it would not load any of my mechanisms built in NMODL. When I tried the sparc/special init.hoc (init.hoc is my initial hoc file), it didn't recognize the init() or run() commands.

What would be your recommendations?

Post by **hines** » Thu Feb 09, 2006 1:28 pm

Try launching with the -nogui option. That will avoid any graphical use of the screen. When you say a "new program window" do you mean a completely separate program that is not NEURON? The only thing I can imagine
that would cause such an error is if you are trying to open a new NEURON tool window from the NEURONMainMenu while NEURON is simulating. Under no circumstances should NEURON fail when you are working outside its process space (other terminals and other programs). If there are such circumstances then NEURON or the OS or the window manager has a bug and needs to be fixed or worked around by upgrading. In that case, please let me know how to reproduce the problem. Also mention the NEURON version you are using.

nonfcomm · Post by **nonfcomm** » Thu Feb 09, 2006 3:56 pm

I am using the most recent release of Neuron (5.8.88). In order to reproduce the problem, you need a simulation running and then open any new (non-neuron) program or even some new windows. Things that have caused this problem:

Starting Firefox
Starting Evolution (Suse email client)
Opening new mail window in Evolution
Starting gaim
Opening any OpenOffice program

There are probably others, but I do not remember them at this time. My linux is Suse 10 64bit which is completely up to date.

nonfcomm · Post by **nonfcomm** » Thu Feb 09, 2006 4:02 pm

The -nogui option did eliminate this problem.

Post by **hines** » Thu Feb 09, 2006 6:09 pm

I am afraid I do not have access to an x86_64 linux machine running an xserver. The most I can do is login through an intermediate machine and run a sim with X11 tunneling and open an xterm while the sim is active. Under those circumstances I do not see a problem. Your original message mentioning the screen_update was reminiscent of a problem that occurred on mswin machines when NEURON tried to draw to the screen after the machine had gone into screen saver mode. Anyway, since the segmentation violation was on an x86_64/nrniv I know you must have built from the sources and are not using the rpm. So I can't blame that. If you are willing, you might try installing the most recent alpha version of the tar.gz file from
http://www.neuron.yale.edu/ftp/neuron/versions/alpha/
and see if the problem goes away.

nonfcomm · Post by **nonfcomm** » Sat Mar 18, 2006 4:05 am

I don't know if anything has changed, but when I did a reinstall (I reinstalled the OS) today the gui did not work whatsoever for either v. 5.8.88 or the CVS. I get this:

smithd@linux:/home/smithd> nrngui
Xlib: connection to ":0.0" refused by server
Xlib: No protocol specified

can't open DISPLAY

???

Post by **hines** » Sat Mar 18, 2006 7:09 am

Before typing "nrngui" check your DISPLAY environment variable with

Code: Select all

echo $DISPLAY

and see what it says. If there is no DISPLAY then you need to set it. If there is, then does it still work with the --nogui option? If you have been using the CVS archive for some time then the most recent changes and switch to the experimental 5.9.x version and also a minor change to the InterViews sources may cause a problem which is most easily overcome by doing a "make clean" in both packages, doing a "cvs update -d" to make sure you have all directories, and a fresh build all the way from "sh build.sh", "configure", "make", and "make install" for both packages.

nonfcomm · Post by **nonfcomm** » Fri Nov 17, 2006 8:58 pm

Apologies for not testing this earlier. The problem has gone away with the newest install (5.9.0 11-01-06).