VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 18 2004 - 11:23:11 CDT

David,
  Its likely that we're going to have to trace this using
a debugger given the strace() output you've sent. By the way,
what CAVE software are you linking VMD against? I have not tested
the current VMD code with the Linux versions of the CAVE library
produced by VRCO, as we don't have that software available to us, so
it is quite possible that this is something fundamental about the
way the Linux version of the CAVE lib works. My suggestion is to
recompile VMD again with '-g' so you get debugging symbols, and
try running it with gdb. The easiest way of doing that is like this:
  source /usr/local/bin/vmd (to get env variables set, then immediately quit)
  cd ~/my/project/area/vmd/LINUX
  gdb vmd_LINUX (commands that follow would be typed into 'gdb')
    run (wait until you get to the spot where VMD hangs, then press ctrl-c
           to break it so you can to a backtrace..)
    where (shows what function you were in when you broke out of the program)

You can send further follow-up messages to vmd_at_ks.uiuc.edu since this is
probably of relatively low interest to most VMD-L readers given that
CAVEs are fairly scarce still.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 18, 2004 at 09:13:23AM +0200, Romaric David wrote:
> John Stone wrote:
> >
> > Hi,
> > What do you get if you run that VMD from 'strace' like this?
> > strace -F vmd -dispdev text
> >
> > We're interested in the "open" and "select" calls that
> > reference the same file handles, so we can figure out why the heck
> > VMD would be getting stuck on a select call.
> >
> > Did you compile this VMD binary yourself, or is it one of our binaries?
> >
> Hello,
>
> I had to compile VMD myself : I need cave support on Linux and I couldn't find a pre-compiled
> binary.
>
> Here is the part of the strace output of vmd_LINUX (the binary) where things start to go wrong :
>
>
> -- brk(0x8279000) = 0x8279000
> open(".vmdrc", O_RDONLY) = -1 ENOENT (No such file or directory)
> open("/home/icps/david/.vmdrc", O_RDONLY) = -1 ENOENT (No such file or directory)
> open("/usr/local/O2/Visualiation/Vmd/lib/vmd/.vmdrc", O_RDONLY) = -1 ENOENT (No such file or directory)
> select(0, NULL, NULL, NULL, {0, 1000}) = 0 (Timeout)
> select(0, NULL, NULL, NULL, {0, 1000}) = 0 (Timeout)
> select(0, NULL, NULL, NULL, {0, 1000}) = 0 (Timeout)
> select(0, NULL, NULL, NULL, {0, 1000}) = 0 (Timeout)
> select(0, NULL, NULL, NULL, {0, 1000}) = 0 (Timeout)
> select(0, NULL, NULL, NULL, {0, 1000}) = 0 (Timeout)
> select(0, NULL, NULL, NULL, {0, 1000}) = 0 (Timeout)
> select(0, NULL, NULL, NULL, {0, 1000}) = 0 (Timeout)
>
>
> The strace -F output of the vmd script goes like this :
>
> rt_sigprocmask(SIG_SETMASK, [INT], [INT], 8) = 0
> rt_sigprocmask(SIG_BLOCK, [CHLD], [INT], 8) = 0
> fork() = 5855
> gettimeofday({1087542582, 35618}, NULL) = 0
> rt_sigprocmask(SIG_SETMASK, [INT], [INT CHLD], 8) = 0
> rt_sigprocmask(SIG_BLOCK, [CHLD], [INT], 8) = 0
> rt_sigprocmask(SIG_SETMASK, [INT], [INT CHLD], 8) = 0
> rt_sigprocmask(SIG_BLOCK, [CHLD], [INT], 8) = 0
> rt_sigsuspend([INT 34]/home/icps/david/tardists/vmd-1.8.1/LINUX/vmd_LINUX: /home/icps/david/tardists/Mesa-6.0.1/lib/libGL.so.1: no version information
> available (required by /home/icps/david/tardists/vmd-1.8.1/LINUX/vmd_LINUX)
>
> and stays stuck here...
>
> I cand send you the entire traces if you fell they would be of any help,
>
> Romaric
>
> --------------------------------------
> R. David - david_at_icps.u-strasbg.fr
> Tel. : 03 90 24 45 48 (Fax 45 47)
> -------------------------------------- 

-- 
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