VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 01 2015 - 11:51:58 CDT
- Next message: Burlen Loring: "Re: segv in vmd upon opening a file"
- Previous message: Axel Kohlmeyer: "Re: segv in vmd upon opening a file"
- In reply to: Axel Kohlmeyer: "Re: segv in vmd upon opening a file"
- Next in thread: Burlen Loring: "Re: segv in vmd upon opening a file"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
We've got CentOS 5.5 machines that report the same basic gdb version
Burlen has, but they don't exhibit the problem he has, so his OS rev
must be older yet:
% head -1 /etc/issue
CentOS release 5.5 (Final)
% gdb
GNU gdb (GDB) Red Hat Enterprise Linux (7.0.1-23.el5)
% uname -a
Linux xxxxx.ks.uiuc.edu 2.6.18-194.el5 #1 SMP Fri Apr 2 14:58:14 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
Cheers,
John
On Wed, Apr 01, 2015 at 12:29:34PM -0400, Axel Kohlmeyer wrote:
> On Wed, Apr 1, 2015 at 12:25 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > Axel,
> > Yes, I completely agree.
> > That's why I've asked him to report the OS version...
>
> it has to be a rather old RHEL 5.x version. check out the debugger
> version string that was quoted in the first e-mail:
>
> GNU gdb (GDB) Red Hat Enterprise Linux (7.0.1-23.el5_5.1)
>
> that looks like RHEL 5.1. debugger/compiler are usually updated
> between RHEL updates, IIRC
>
> axel.
>
> >
> > Since he sees the problem when running in text mode, I think that the most
> > likely possibility is then a problem with their pthreads implementation,
> > particularly since he experienced the same problem with a version compiled
> > from source.
> >
> > I just wanted to first eliminate broken OpenGL from the equation since
> > I've seen bad GL drivers corrupt memory and cause all kinds of side effects.
> >
> > Cheers,
> > John
> >
> > On Wed, Apr 01, 2015 at 11:51:25AM -0400, Axel Kohlmeyer wrote:
> >> john,
> >>
> >> this looks similar to the threading bug that was in the Linux kernel
> >> on early RHEL 4.x versions.
> >> note that the program dies on joining the threads after the gridsearch
> >> for bonds. so i would doubt it is related to X11 or OpenGL.
> >>
> >> axel.
> >>
> >> On Wed, Apr 1, 2015 at 10:51 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >> > Burlen,
> >> > This is helpful. What version of Linux is on the system you're using,
> >> > and which of the 64-bit VMD Linux packages did you install? I'm particularly
> >> > interested in the output of these commands:
> >> > uname -a
> >> > cat /etc/issue
> >> >
> >> > Cheers,
> >> > John
> >> >
> >> > On Wed, Apr 01, 2015 at 01:23:28AM -0700, Burlen Loring wrote:
> >> >> Hi John,
> >> >>
> >> >> Thanks for the help! So I tried text mode as you suggest but the
> >> >> crash is the same (output below).
> >> >>
> >> >> Although the OpenGL window pops up and I can interact with it there
> >> >> may be some OpenGL issue. I'll have to inquire as to the hardware
> >> >> etc. glxinfo command is not installed. This is a cluster, the login
> >> >> nodes may have some crappy graphics cards, folks are using it with
> >> >> NX, and I think this is the source of GLX Indirect. I'm pretty sure
> >> >> that vmd was running here at some point in the past. Again I'll have
> >> >> to ask the guy I'm taking over for ;-)
> >> >>
> >> >> Burlen
> >> >>
> >> >> $vmd -dispdev text
> >> >> Info) VMD for LINUXAMD64, version 1.9.2 (February 19, 2015)
> >> >> Info) http://www.ks.uiuc.edu/Research/vmd/
> >> >> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> >> >> Info) Please include this reference in published work using VMD:
> >> >> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> >> >> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> >> >> Info) -------------------------------------------------------------
> >> >> Info) Multithreading available, 8 CPUs detected.
> >> >> Info) Free system memory: 38998MB (80%)
> >> >>
> >> >> vmd > mol new 1ubq.pdb
> >> >> Info) Using plugin pdb for structure file 1ubq.pdb
> >> >> Info) Using plugin pdb for coordinates from file 1ubq.pdb
> >> >> Info) Determining bond structure from distance search ...
> >> >> Segmentation fault
> >> >>
> >> >> On 3/31/2015 5:56 PM, John Stone wrote:
> >> >> >Hi,
> >> >> > From the logs you sent, I noticed this, which is a bit of a red flag:
> >> >> >Info) OpenGL renderer: Mesa GLX Indirect
> >> >> >What graphics hardware do you have in this machine?
> >> >> >
> >> >> >If you run VMD in text mode, and load the same file, do you have
> >> >> >the same seg fault? Run VMD in text mode like this:
> >> >> > vmd -dispdev text
> >> >> >
> >> >> >If you do NOT have the seg fault in this case, then I am assuming
> >> >> >problems with the OpenGL graphics configuration. On the other hand,
> >> >> >if you do encounter a seg fault here when running in text mode, then
> >> >> >we will need to dig into this in much more detail.
> >> >> >
> >> >> >If you can run the text mode test and get back to me, that'd be great.
> >> >> >
> >> >> >Cheers,
> >> >> > John Stone
> >> >> > vmd_at_ks.uiuc.edu
> >> >> >
> >> >> >
> >> >> >On Tue, Mar 31, 2015 at 02:20:44PM -0700, Burlen Loring wrote:
> >> >> >>Hi ,
> >> >> >>
> >> >> >>I am having some issue with vmd 1.9.2. As soon as I open a file (the
> >> >> >>first example in the tutorial) there is a crash. I am pasting a
> >> >> >>stack trace and the output below when running: vmd -debug. First I
> >> >> >>tried the binary from the vmd site, then I tried building form
> >> >> >>source, but the crash is the same. Any idea what is going wrong
> >> >> >>here?
> >> >> >>
> >> >> >>Thanks
> >> >> >>Burlen
> >> >> >>
> >> >> >>$vmd -debug
> >> >> >>***
> >> >> >>*** Running VMD in debugger, type 'run' at debugger prompt
> >> >> >>***
> >> >> >>GNU gdb (GDB) Red Hat Enterprise Linux (7.0.1-23.el5_5.1)
> >> >> >>Copyright (C) 2009 Free Software Foundation, Inc.
> >> >> >>License GPLv3+: GNU GPL version 3 or later
> >> >> >><http://gnu.org/licenses/gpl.html>
> >> >> >>This is free software: you are free to change and redistribute it.
> >> >> >>There is NO WARRANTY, to the extent permitted by law. Type "show copying"
> >> >> >>and "show warranty" for details.
> >> >> >>This GDB was configured as "x86_64-redhat-linux-gnu".
> >> >> >>For bug reporting instructions, please see:
> >> >> >><http://www.gnu.org/software/gdb/bugs/>...
> >> >> >>Reading symbols from /global/common/carver/graphics/vmd/1.9.2/lib/vmd/vmd_LINUXAMD64...done.
> >> >> >>(gdb) run
> >> >> >>Starting program:
> >> >> >>/global/common/carver/graphics/vmd/1.9.2/lib/vmd/vmd_LINUXAMD64
> >> >> >>[Thread debugging using libthread_db enabled]
> >> >> >>[New Thread 0x50000940 (LWP 26008)]
> >> >> >>Info) VMD for LINUXAMD64, version 1.9.2 (February 19, 2015)
> >> >> >>Info) http://www.ks.uiuc.edu/Research/vmd/
> >> >> >>Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> >> >> >>Info) Please include this reference in published work using VMD:
> >> >> >>Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> >> >> >>Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> >> >> >>Info) -------------------------------------------------------------
> >> >> >>Info) Multithreading available, 8 CPUs detected.
> >> >> >>Info) Free system memory: 38022MB (78%)
> >> >> >>Info) OpenGL renderer: Mesa GLX Indirect
> >> >> >>Info) Features: STENCIL MDE MTX PP PS
> >> >> >>Info) GLSL rendering mode is NOT available.
> >> >> >>Info) Textures: 2-D (2048x2048), Multitexture (8)
> >> >> >>vmd > Info) Using plugin pdb for structure file
> >> >> >>/global/common/carver/graphics/vmd/tutorial/1ubq.pdb
> >> >> >>Info) Using plugin pdb for coordinates from file
> >> >> >>/global/common/carver/graphics/vmd/tutorial/1ubq.pdb
> >> >> >>Info) Determining bond structure from distance search ...
> >> >> >>[New Thread 0x60001940 (LWP 26018)]
> >> >> >>[New Thread 0x70002940 (LWP 26019)]
> >> >> >>[Thread 0x70002940 (LWP 26019) exited]
> >> >> >>[New Thread 0x7fffe2fc4940 (LWP 26020)]
> >> >> >>[Thread 0x60001940 (LWP 26018) exited]
> >> >> >>[Thread 0x7fffe2fc4940 (LWP 26020) exited]
> >> >> >>[New Thread 0x7fffd2fc3940 (LWP 26021)]
> >> >> >>[Thread 0x7fffd2fc3940 (LWP 26021) exited]
> >> >> >>[New Thread 0x7fffc2fc2940 (LWP 26022)]
> >> >> >>[New Thread 0x7fffb2fc1940 (LWP 26023)]
> >> >> >>[Thread 0x7fffc2fc2940 (LWP 26022) exited]
> >> >> >>[Thread 0x7fffb2fc1940 (LWP 26023) exited]
> >> >> >>
> >> >> >>Program received signal SIGSEGV, Segmentation fault.
> >> >> >>0x00007fffef3c8a38 in pthread_join () from /lib64/libpthread.so.0
> >> >> >>(gdb) where
> >> >> >>#0 0x00007fffef3c8a38 in pthread_join () from /lib64/libpthread.so.0
> >> >> >>#1 0x00000000004c2a18 in vmd_bondsearch_thr(float const*, float
> >> >> >>const*, GridSearchPairlist*, int, int**, int*, int**, int, float) ()
> >> >> >>#2 0x000000004011eb85 in ?? ()
> >> >> >>#3 0x0000000000000000 in ?? ()
> >> >> >>(gdb)
> >> >
> >> > --
> >> > NIH Center for Macromolecular Modeling and Bioinformatics
> >> > Beckman Institute for Advanced Science and Technology
> >> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> >> > http://www.ks.uiuc.edu/Research/vmd/
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> College of Science & Technology, Temple University, Philadelphia PA, USA
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/
- Next message: Burlen Loring: "Re: segv in vmd upon opening a file"
- Previous message: Axel Kohlmeyer: "Re: segv in vmd upon opening a file"
- In reply to: Axel Kohlmeyer: "Re: segv in vmd upon opening a file"
- Next in thread: Burlen Loring: "Re: segv in vmd upon opening a file"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]