VMD-L Mailing List

From: Romaric David (david_at_icps.u-strasbg.fr)
Date: Wed Jul 16 2003 - 08:22:29 CDT

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