From: chris.harwell_at_pharma.novartis.com
Date: Fri Dec 17 2004 - 15:27:21 CST

Hi,

I am having some trouble with displaying and running VMD 1.8.2 on Linux
 (redhat-release-9-3) with the ATI FireGL X1-256p graphics card using
ATI's fglrx-4.3.0-3.14.6 driver (3.14.6) with my monitor setup in
1280 x 1024 @ 100Hz mode with Stereo enabled and OpenGLOverlay off.
This seems to work for software like Sybyl or Maestro, but vmd is dumping
core on me. I fear this is yet another ATI issue.

Does anyone on this list have a similar setup working?

If so, would you be willing to share your configuration?

TIA,
chris harwell
 
[harwech1_at_mmlnxviz vmd]$ fglrxinfo
display: :0.0 screen: 0
OpenGL vendor string: ATI Technologies Inc.
OpenGL renderer string: Fire GL X1 Pentium 4 (SSE2) (FireGL) (GNU_ICD)
OpenGL version string: 1.3.4641 (X4.3.0-3.14.6)

[harwech1_at_mmlnxviz vmd]$ rpm -q fglrx
fglrx-4.3.0-3.14.6
[harwech1_at_mmlnxviz vmd]$ head README
                        README file for VMD 1.8.2
---------------------------------------------------------------------------

What is VMD? See also http://www.ks.uiuc.edu/Research/vmd/
---------------------------------------------------------------------
  VMD is designed for the visualization and analysis of biological
systems such as proteins, nucleic acids, lipid bilayer assemblies,
etc. It may be used to view more general molecules, as VMD can read
standard Protein Data Bank (PDB) files and display the contained
structure. VMD provides a wide variety of methods for rendering and
[harwech1_at_mmlnxviz vmd]$ file ~/core.*
/nas/people/camm/harwech1/core.6364: ELF 32-bit LSB core file Intel 80386,
version 1 (SYSV), SVR4-style, from 'fgl_glxgears'
/nas/people/camm/harwech1/core.7350: ELF 32-bit LSB core file Intel 80386,
version 1 (SYSV), SVR4-style, from 'fgl_glxgears'
/nas/people/camm/harwech1/core.7389: ELF 32-bit LSB core file Intel 80386,
version 1 (SYSV), SVR4-style, from 'vmd_LINUX'
/nas/people/camm/harwech1/core.7429: ELF 32-bit LSB core file Intel 80386,
version 1 (SYSV), SVR4-style, from 'vmd_LINUX'
/nas/people/camm/harwech1/core.7474: ELF 32-bit LSB core file Intel 80386,
version 1 (SYSV), SVR4-style, from 'vmd_LINUX'
/nas/people/camm/harwech1/core.7685: ELF 32-bit LSB core file Intel 80386,
version 1 (SYSV), SVR4-style, from 'vmd_LINUX'
/nas/people/camm/harwech1/core.8457: ELF 32-bit LSB core file Intel 80386,
version 1 (SYSV), SVR4-style, from 'vmd_LINUX'
/nas/people/camm/harwech1/core.8805: ELF 32-bit LSB core file Intel 80386,
version 1 (SYSV), SVR4-style, from 'vmd_LINUX'

xvidtune
Vendor: , Model:
Num hsync: 1, Num vsync: 1
hsync range 0: 31.50 - 108.50
vsync range 0: 60.00 - 100.00
from show:
"1280x1024" 190.96 1280 1376 1520 1760 1024 1025 1028 1085 +hsync
+vsync

# File: XF86Config-4
# File generated by fglrxconfig (C) ATI Research, a substitute for
xf86config.

# Note by ATI: the below copyright notice is there for servicing possibly
# pending third party rights on the file format and the instance of this
file.
#
# Copyright (c) 1999 by The XFree86 Project, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the
"Software"),
# to deal in the Software without restriction, including without
limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included
in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE XFREE86 PROJECT BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
# WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT
OF
# OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
# Except as contained in this notice, the name of the XFree86 Project
shall
# not be used in advertising or otherwise to promote the sale, use or
other
# dealings in this Software without prior written authorization from the
# XFree86 Project.
#

# **********************************************************************
# Refer to the XF86Config(4/5) man page for details about the format of
# this file.
# **********************************************************************

# **********************************************************************
# DRI Section
# **********************************************************************
Section "dri"
# Access to OpenGL ICD is allowed for all users:
    Mode 0666
# Access to OpenGL ICD is restricted to a specific user group:
# Group 100 # users
# Mode 0660
EndSection

# **********************************************************************
# Module section -- this section is used to specify
# which dynamically loadable modules to load.
# **********************************************************************
#
Section "Module"

# This loads the DBE extension module.

    Load "dbe" # Double buffer extension

# This loads the miscellaneous extensions module, and disables
# initialisation of the XFree86-DGA extension within that module.
    SubSection "extmod"
      Option "omit xfree86-dga" # don't initialise the DGA extension
    EndSubSection

# This loads the Type1 and FreeType font modules
    Load "type1"
    Load "freetype"

# This loads the GLX module
    Load "glx" # libglx.a
    Load "dri" # libdri.a

EndSection

# **********************************************************************
# Files section. This allows default font and rgb paths to be set
# **********************************************************************

Section "Files"

# The location of the RGB database. Note, this is the name of the
# file minus the extension (like ".txt" or ".db"). There is normally
# no need to change the default.

    RgbPath "/usr/X11R6/lib/X11/rgb"

# Multiple FontPath entries are allowed (which are concatenated together),
# as well as specifying multiple comma-separated entries in one FontPath
# command (or a combination of both methods)
#
# If you don't have a floating point coprocessor and emacs, Mosaic or
other
# programs take long to start up, try moving the Type1 and Speedo
directory
# to the end of this list (or comment them out).
#

    FontPath "/usr/X11R6/lib/X11/fonts/local/"
    FontPath "/usr/X11R6/lib/X11/fonts/misc/"
    FontPath "/usr/X11R6/lib/X11/fonts/75dpi/:unscaled"
    FontPath "/usr/X11R6/lib/X11/fonts/100dpi/:unscaled"
    FontPath "/usr/X11R6/lib/X11/fonts/Type1/"
    FontPath "/usr/X11R6/lib/X11/fonts/Speedo/"
    FontPath "/usr/X11R6/lib/X11/fonts/75dpi/"
    FontPath "/usr/X11R6/lib/X11/fonts/100dpi/"

# The module search path. The default path is shown here.

# ModulePath "/usr/X11R6/lib/modules"

EndSection

# **********************************************************************
# Server flags section.
# **********************************************************************

Section "ServerFlags"

# Uncomment this to cause a core dump at the spot where a signal is
# received. This may leave the console in an unusable state, but may
# provide a better stack trace in the core dump to aid in debugging

# Option "NoTrapSignals"

# Uncomment this to disable the <Crtl><Alt><BS> server abort sequence
# This allows clients to receive this key event.

# Option "DontZap"

# Uncomment this to disable the <Crtl><Alt><KP_+>/<KP_-> mode switching
# sequences. This allows clients to receive these key events.

# Option "Dont Zoom"

# Uncomment this to disable tuning with the xvidtune client. With
# it the client can still run and fetch card and monitor attributes,
# but it will not be allowed to change them. If it tries it will
# receive a protocol error.

# Option "DisableVidModeExtension"

# Uncomment this to enable the use of a non-local xvidtune client.

# Option "AllowNonLocalXvidtune"

# Uncomment this to disable dynamically modifying the input device
# (mouse and keyboard) settings.

# Option "DisableModInDev"

# Uncomment this to enable the use of a non-local client to
# change the keyboard or mouse settings (currently only xset).

# Option "AllowNonLocalModInDev"

EndSection

# **********************************************************************
# Input devices
# **********************************************************************

# **********************************************************************
# Core keyboard's InputDevice section
# **********************************************************************

Section "InputDevice"

    Identifier "Keyboard1"
    Driver "Keyboard"
# For most OSs the protocol can be omitted (it defaults to "Standard").
# When using XQUEUE (only for SVR3 and SVR4, but not Solaris),
# uncomment the following line.

# Option "Protocol" "Xqueue"

    Option "AutoRepeat" "500 30"

# Specify which keyboard LEDs can be user-controlled (eg, with xset(1))
# Option "Xleds" "1 2 3"

# Option "LeftAlt" "Meta"
# Option "RightAlt" "ModeShift"

# To customise the XKB settings to suit your keyboard, modify the
# lines below (which are the defaults). For example, for a non-U.S.
# keyboard, you will probably want to use:
# Option "XkbModel" "pc102"
# If you have a US Microsoft Natural keyboard, you can use:
# Option "XkbModel" "microsoft"
#
# Then to change the language, change the Layout setting.
# For example, a german layout can be obtained with:
# Option "XkbLayout" "de"
# or:
# Option "XkbLayout" "de"
# Option "XkbVariant" "nodeadkeys"
#
# If you'd like to switch the positions of your capslock and
# control keys, use:
# Option "XkbOptions" "ctrl:swapcaps"

# These are the default XKB settings for XFree86
# Option "XkbRules" "xfree86"
# Option "XkbModel" "pc101"
# Option "XkbLayout" "us"
# Option "XkbVariant" ""
# Option "XkbOptions" ""

# Option "XkbDisable"

    Option "XkbRules" "xfree86"
    Option "XkbModel" "pc104"
    Option "XkbLayout" "us"

EndSection

# **********************************************************************
# Core Pointer's InputDevice section
# **********************************************************************

Section "InputDevice"

# Identifier and driver

    Identifier "Mouse1"
    Driver "mouse"
    Option "Protocol" "PS/2"
    Option "Device" "/dev/mouse"

# When using XQUEUE, comment out the above two lines, and uncomment
# the following line.

# Option "Protocol" "Xqueue"

# Baudrate and SampleRate are only for some Logitech mice. In
# almost every case these lines should be omitted.

# Option "BaudRate" "9600"
# Option "SampleRate" "150"

# Emulate3Buttons is an option for 2-button Microsoft mice
# Emulate3Timeout is the timeout in milliseconds (default is 50ms)

# Option "Emulate3Buttons"
# Option "Emulate3Timeout" "50"

# ChordMiddle is an option for some 3-button Logitech mice

# Option "ChordMiddle"

EndSection

# **********************************************************************
# Other input device sections
# this is optional and is required only if you
# are using extended input devices. This is for example only. Refer
# to the XF86Config man page for a description of the options.
# **********************************************************************
#
# Section "InputDevice"
# Identifier "Mouse2"
# Driver "mouse"
# Option "Protocol" "MouseMan"
# Option "Device" "/dev/mouse2"
# EndSection
#
# Section "InputDevice"
# Identifier "spaceball"
# Driver "magellan"
# Option "Device" "/dev/cua0"
# EndSection
#
# Section "InputDevice"
# Identifier "spaceball2"
# Driver "spaceorb"
# Option "Device" "/dev/cua0"
# EndSection
#
# Section "InputDevice"
# Identifier "touchscreen0"
# Driver "microtouch"
# Option "Device" "/dev/ttyS0"
# Option "MinX" "1412"
# Option "MaxX" "15184"
# Option "MinY" "15372"
# Option "MaxY" "1230"
# Option "ScreenNumber" "0"
# Option "ReportingMode" "Scaled"
# Option "ButtonNumber" "1"
# Option "SendCoreEvents"
# EndSection
#
# Section "InputDevice"
# Identifier "touchscreen1"
# Driver "elo2300"
# Option "Device" "/dev/ttyS0"
# Option "MinX" "231"
# Option "MaxX" "3868"
# Option "MinY" "3858"
# Option "MaxY" "272"
# Option "ScreenNumber" "0"
# Option "ReportingMode" "Scaled"
# Option "ButtonThreshold" "17"
# Option "ButtonNumber" "1"
# Option "SendCoreEvents"
# EndSection

# **********************************************************************
# Monitor section
# **********************************************************************

# Any number of monitor sections may be present

Section "Monitor"
    Identifier "Monitor0"
    HorizSync 31.5 - 108.5
    VertRefresh 60-100
    Option "DPMS"

# === Active Stereo mode lines based on GTF ===
# XVGA @ 100Hz
Modeline "1024x768_at_100" 113.309 1024 1096 1208 1392 768 769 772 814 +hsync
+vsync
# XVGA @ 120Hz
Modeline "1024x768_at_120" 139.054 1024 1104 1216 1408 768 769 772 823 +hsync
+vsync
# SXGA @ 100Hz
Modeline "1280x1024_at_100" 190.960 1280 1376 1520 1760 1024 1025 1028 1085
+hsync +vsync
# SXGA @ 120Hz
Modeline "1280x1024_at_120" 233.793 1280 1384 1528 1776 1024 1025 1028 1097
+hsync +vsync

EndSection

# **********************************************************************
# Graphics device section
# **********************************************************************

# Any number of graphics device sections may be present

# Standard VGA Device:

Section "Device"
    Identifier "Standard VGA"
    VendorName "Unknown"
    BoardName "Unknown"

# The chipset line is optional in most cases. It can be used to override
# the driver's chipset detection, and should not normally be specified.

# Chipset "generic"

# The Driver line must be present. When using run-time loadable driver
# modules, this line instructs the server to load the specified driver
# module. Even when not using loadable driver modules, this line
# indicates which driver should interpret the information in this section.

    Driver "vga"
# The BusID line is used to specify which of possibly multiple devices
# this section is intended for. When this line isn't present, a device
# section can only match up with the primary video device. For PCI
# devices a line like the following could be used. This line should not
# normally be included unless there is more than one video device
# installed.

# BusID "PCI:0:10:0"

# VideoRam 256

# Clocks 25.2 28.3

EndSection

# === ATI device section ===

Section "Device"
    Identifier "ATI Graphics Adapter"
    Driver "fglrx"
# ### generic DRI settings ###
# === disable PnP Monitor ===
    #Option "NoDDC"
# === disable/enable XAA/DRI ===
    Option "no_accel" "no"
    Option "no_dri" "no"
# === misc DRI settings ===
    Option "mtrr" "off" # disable DRI mtrr mapper,
driver has its own code for mtrr
# ### FireGL DDX driver module specific settings ###
# === Screen Management ===
    Option "DesktopSetup" "0x00000000"
    Option "MonitorLayout" "CRT, CRT"
    Option "IgnoreEDID" "on"
    Option "HSync2" "unspecified"
    Option "VRefresh2" "unspecified"
    Option "ScreenOverlap" "0"
# === TV-out Management ===
    Option "NoTV" "yes"
    Option "TVStandard" "NTSC-M"
    Option "TVHSizeAdj" "0"
    Option "TVVSizeAdj" "0"
    Option "TVHPosAdj" "0"
    Option "TVVPosAdj" "0"
    Option "TVHStartAdj" "0"
    Option "TVColorAdj" "0"
    Option "GammaCorrectionI" "0x00000000"
    Option "GammaCorrectionII" "0x00000000"
# === OpenGL specific profiles/settings ===
    Option "Capabilities" "0x00000000"
# === Video Overlay for the Xv extension ===
    Option "VideoOverlay" "off"
# === OpenGL Overlay ===
# Note: When OpenGL Overlay is enabled, Video Overlay
# will be disabled automatically
    Option "OpenGLOverlay" "off"
        # CRH Note w/ OpenGLOverlay set to on - glxgears and fgl_glxgears
        # work, but then in SYBYL the hardware stereo option is greyed out
        # ugh
        # either way vmd seems to be dying now (new ATI version)
# === Center Mode (Laptops only) ===
    Option "CenterMode" "off"
# === Pseudo Color Visuals (8-bit visuals) ===
    Option "PseudoColorVisuals" "off"
# === QBS Management ===
    Option "Stereo" "on"
    Option "StereoSyncEnable" "1"
# === FSAA Management ===
    Option "FSAAEnable" "no"
    Option "FSAAScale" "1"
    Option "FSAADisableGamma" "no"
    Option "FSAACustomizeMSPos" "no"
    Option "FSAAMSPosX0" "0.000000"
    Option "FSAAMSPosY0" "0.000000"
    Option "FSAAMSPosX1" "0.000000"
    Option "FSAAMSPosY1" "0.000000"
    Option "FSAAMSPosX2" "0.000000"
    Option "FSAAMSPosY2" "0.000000"
    Option "FSAAMSPosX3" "0.000000"
    Option "FSAAMSPosY3" "0.000000"
    Option "FSAAMSPosX4" "0.000000"
    Option "FSAAMSPosY4" "0.000000"
    Option "FSAAMSPosX5" "0.000000"
    Option "FSAAMSPosY5" "0.000000"
# === Misc Options ===
    Option "UseFastTLS" "0"
    Option "BlockSignalsOnLock" "on"
    Option "UseInternalAGPGART" "yes"
    Option "ForceGenericCPU" "no"
    BusID "PCI:1:0:0" # vendor=1002, device=4e47
    Screen 0
EndSection

# **********************************************************************
# Screen sections
# **********************************************************************

# Any number of screen sections may be present. Each describes
# the configuration of a single screen. A single specific screen section
# may be specified from the X server command line with the "-screen"
# option.
Section "Screen"
    Identifier "Screen0"
    Device "ATI Graphics Adapter"
    Monitor "Monitor0"
    DefaultDepth 24
    #Option "backingstore"

    Subsection "Display"
        Depth 24
        Modes "1280x1024_at_100"
        ViewPort 0 0 # initial origin if mode is smaller than desktop
# Virtual 1280 1024
    EndSubsection
EndSection

# **********************************************************************
# ServerLayout sections.
# **********************************************************************

# Any number of ServerLayout sections may be present. Each describes
# the way multiple screens are organised. A specific ServerLayout
# section may be specified from the X server command line with the
# "-layout" option. In the absence of this, the first section is used.
# When now ServerLayout section is present, the first Screen section
# is used alone.

Section "ServerLayout"

# The Identifier line must be present
    Identifier "Server Layout"

# Each Screen line specifies a Screen section name, and optionally
# the relative position of other screens. The four names after
# primary screen name are the screens to the top, bottom, left and right
# of the primary screen.

    Screen "Screen0"

# Each InputDevice line specifies an InputDevice section name and
# optionally some options to specify the way the device is to be
# used. Those options include "CorePointer", "CoreKeyboard" and
# "SendCoreEvents".

    InputDevice "Mouse1" "CorePointer"
    InputDevice "Keyboard1" "CoreKeyboard"

EndSection

### EOF ###