VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 16 2003 - 16:34:45 CDT

Hi,
  Thanks for the output, I'll see about giving you a different
binary to test in the next few days.. Its not surprising that you
don't see the shared memory region via the 'ipcs' command since the
CAVE library (and FreeVR as well as many other programs) uses other
methods to acquire shared memory. On the SGI there are special arena-based
memory management routines one can use, as well as the more portable
mmap() methods for getting shared memory. The 'ipcs' command normally
only reports information about SysV style shared memory segments, semaphores,
and message queues. POSIX semaphores, message queues, etc will not show up
in the output of 'ipcs'.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 16, 2003 at 03:22:29PM +0200, Romaric David wrote:
> John Stone wrote:
> > build you a binary that has more aggressive OpenGL debugging enabled
> > and we can figure out why your display gets the funny initialization
> > problem sometimes:
> > ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd/alpha/
> >
> Hello,
>
> I tried this version, but the console output is not that different when everyting works OK
> and when the problem occurs.
>
> I noticed that a message Info) Attempting to get 256MB of CAVE Shared Memory
> is printed, but I can't see the corresponding memory area using "ipcs".
>
> I noticed too that you use cave 2.6. Would you be interested in compiling it
> against Cave 3.0 ? In this case, I could open you an account on our machine
> to give it a try.
>
> I attached the two outputs, when first the colours were B&W, and the second one (really
> second try this case, I was lucky) when colours were everywhere.
>
> Romaric
>
> --
> --------------------------------------
> R. David - david_at_icps.u-strasbg.fr
> Tel. : 03 90 24 45 48 (Fax 45 47)
> --------------------------------------
> Info) VMD for IRIX6, version 1.8.2a4 (July 9, 2003)
> 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, 52 CPUs detected.
> Info) Attempting to get 256MB of CAVE Shared Memory
> Info) Created arena.
> CAVE Library Version 2.6g (w/ more NCSA Ext) (OGL) - Compiled Sep 2 1999 on IRIX interocitor 6.2
> CAVE: **** Overall Default file ****
> CAVE: Reading configuration file /usr/local/O2/CAVE/etc/cave.config
> CAVE: **** Machine Default file ****
> CAVE: Reading configuration file /usr/local/O2/CAVE/etc/seven.config
> CAVE: **** ~/.caverc ****
> CAVE: Reading configuration file /home/icps/david/.caverc
> CAVE: **** ./.caverc ****
> ****************************************************************
> CAVE Configuration (brief):
> Display Type ..................... sim (123)
> Active walls ...................... 2
> screen0 [1380x1035+0+0] "DISPLAY=:0.0" sync=1 both eye(s)
> screen1 [1380x1035+0+1035] "DISPLAY=:0.1" sync=1 both eye(s)
> Display mode ...................... stereo
> Blanktime ......................... y
> Tracker type ...................... daemon
> Wand .............................. daemon
> Network ........................... none
> Distribution ...................... none
> App Distribution .................. none
> Scramnet .......................... n
> ****************************************************************
> Info) Creating R/W lock for shared mem access sync.
> Info) Cave shared memory scene created.
> CAVE pipe #0 (screen0) started: PID=13097272
> CAVE wall 0 started: PID=13097272
> CAVE pipe #1 (screen1) started: PID=13155070
> CAVE wall 0 started: PID=13155070
> CAVE Warning: Failed to get requested visual; reducing number of samples to 4
> CAVE main process: PID=13112636
> CAVE Initialization successful ....
> CAVE Warning: Failed to get requested visual; reducing number of samples to 4
> CAVE Warning: Failed to get requested visual; reducing number of samples to 2
> CAVE Warning: Failed to get requested visual; reducing number of samples to 1
> CAVE Warning: Failed to get requested visual; reducing number of samples to 0
> CAVE Warning: Failed to get requested visual; removing multisampling
> Info) CAVE Initialized
> Info) Started 2 slave rendering processes.
> Info) Using plugin pdb for structure file 1pit.pdb
> Info) Using plugin pdb for coordinates from file 1pit.pdb
> Info) Using plugin pdb for coordinates from file 1pit.pdb
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 1024
> Info) Residues: 58
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 1 Protein: 1 Nucleic: 0
> Info) OpenGL renderer: IRLP/S/1/64/4
> Info) OpenGL renderer: IRLP/S/1/64/4
> Info) Features:
> Info) Features:
> Info) Textures: 2-D (2048x2048)
> Info) Features:
> Info) Textures: 2-D (2048x2048)
> Info) Finished with coordinate file 1pit.pdb.
> vmd >
> IPC status from /dev/kmem as of Wed Jul 16 15:09:23 2003
>
> Message Queues:
> T ID KEY MODE OWNER GROUP
>
> Shared Memory:
> m 9575 0x0000101e --rw-rw-rw- root sys
> m 9576 0x0000101f --rw-rw-rw- root sys
> m 9657 0x00000000 --rw-r--r-- larue maitrise
> m 9658 0x00000000 --rw-r--r-- larue maitrise
>
> Semaphores:

> Info) VMD for IRIX6, version 1.8.2a4 (July 9, 2003)
> 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, 52 CPUs detected.
> Info) Attempting to get 256MB of CAVE Shared Memory
> Info) Created arena.
> CAVE Library Version 2.6g (w/ more NCSA Ext) (OGL) - Compiled Sep 2 1999 on IRIX interocitor 6.2
> CAVE: **** Overall Default file ****
> CAVE: Reading configuration file /usr/local/O2/CAVE/etc/cave.config
> CAVE: **** Machine Default file ****
> CAVE: Reading configuration file /usr/local/O2/CAVE/etc/seven.config
> CAVE: **** ~/.caverc ****
> CAVE: Reading configuration file /home/icps/david/.caverc
> CAVE: **** ./.caverc ****
> ****************************************************************
> CAVE Configuration (brief):
> Display Type ..................... sim (123)
> Active walls ...................... 2
> screen0 [1380x1035+0+0] "DISPLAY=:0.0" sync=1 both eye(s)
> screen1 [1380x1035+0+1035] "DISPLAY=:0.1" sync=1 both eye(s)
> Display mode ...................... stereo
> Blanktime ......................... y
> Tracker type ...................... daemon
> Wand .............................. daemon
> Network ........................... none
> Distribution ...................... none
> App Distribution .................. none
> Scramnet .......................... n
> ****************************************************************
> Info) Creating R/W lock for shared mem access sync.
> Info) Cave shared memory scene created.
> CAVE pipe #0 (screen0) started: PID=13191000
> CAVE wall 0 started: PID=13191000
> CAVE pipe #1 (screen1) started: PID=13110920
> CAVE wall 0 started: PID=13110920
> CAVE Warning: Failed to get requested visual; reducing number of samples to 4
> CAVE Warning: Failed to get requested visual; reducing number of samples to 2
> CAVE Warning: Failed to get requested visual; reducing number of samples to 1
> CAVE Warning: Failed to get requested visual; reducing number of samples to 0
> CAVE Warning: Failed to get requested visual; removing multisampling
> CAVE main process: PID=13144261
> CAVE Initialization successful ....
> CAVE Warning: Failed to get requested visual; reducing number of samples to 4
> CAVE Warning: Failed to get requested visual; reducing number of samples to 2
> CAVE Warning: Failed to get requested visual; reducing number of samples to 1
> CAVE Warning: Failed to get requested visual; reducing number of samples to 0
> CAVE Warning: Failed to get requested visual; removing multisampling
> Info) CAVE Initialized
> Info) Started 2 slave rendering processes.
> Info) Using plugin pdb for structure file 1pit.pdb
> Info) Using plugin pdb for coordinates from file 1pit.pdb
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 1024
> Info) Residues: 58
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 1 Protein: 1 Nucleic: 0
> Info) OpenGL renderer: IRLP/S/1/64/4
> Info) OpenGL renderer: IRLP/S/1/64/4
> Info) Features:
> Info) Textures: 2-D (2048x2048)
> Info) Features:
> Info) Textures: 2-D (2048x2048)
> Info) Finished with coordinate file 1pit.pdb.
> IPC status from /dev/kmem as of Wed Jul 16 15:13:22 2003
>
> Message Queues:
> T ID KEY MODE OWNER GROUP CREATOR CGROUP CBYTES QNUM QBYTES LSPID LRPID STIME RTIME CTIME
>
> Shared Memory:
> T ID KEY MODE OWNER GROUP CREATOR CGROUP NATTCH SEGSZ CPID LPID ATIME DTIME CTIME
> m 9575 0x0000101e --rw-rw-rw- root sys root sys 4 1308 13047247 13149633 15:11:04 15:10:46 15:51:30
> m 9576 0x0000101f --rw-rw-rw- root sys root sys 4 296 13047247 13149633 15:11:04 no-entry 15:51:30
>
> Semaphores:
> T ID KEY MODE OWNER GROUP CREATOR CGROUP NSEMS OTIME CTIME 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078