 | There are a handful of 'features' that look like bugs,
but cannot be fixed without a severe impact on performance or other important factors:
- If you resize the YASARA window, it may jump to a different location. This behavior
is required by YASARA's graphics engine. If you are using two monitors,
look here for more details.
- If you put a window that is always on top (e.g. the Windows task manager) in front of
the YASARA window, activate a YASARA menu entry, and move the other window away,
a copy of this window may remain visible until you leave the YASARA menus.
It depends on your OpenGL driver whether or not this behavior can be observed.
- If your keyboard contains special characters (German 'Umlaute', French characters with accents etc.),
these keys will not work. The main reason is that using these characters would render
your macros or movies unusable for people with a different operating system, creating
a chain of troubles, which we decided to break in the beginning. Also YASARA's vector fonts
usually do not contain these characters, so they could not be displayed anyway.
- When using semi-transparent surfaces combined with YASARA's built in antialiasing,
there may be thin borders around some atoms. This is normal OpenGL behavior.
The only workaround is to disable YASARA's antialiasing and activate OpenGL
hardware antialiasing in the settings of your video card.
|
| This problem was observed in (K)Ubuntu AMD64 and is caused by their aim to squeeze the entire system on a single CD,
at the cost of dropping backwards compatibility. You need to install the missing packages with this command:
sudo aptitude install ia32-libs
If this fails, for example because you do not have a direct internet connection,
then surf to packages.ubuntu.com, scroll down to
'Search' and download the following packages manually:
libc6-i386
lib32gcc1
lib32stdc++6
lib32z1
ia32-libs
For each of these packages, type
sudo dpkg install NameOfThePackageWithAllExtensions
|
|
This can happen under Linux, when you mounted the CD with the wrong flags. You then get a
'Permission denied' error message. To solve the problem, open the file /etc/fstab and search for a line like the following:
/dev/cdrom /mnt/cdrom iso9660 ro,user,exec,noatime 0 0
Now make sure that you have the exec and noatime
flags set, then remount the CD. The most likely reason is that you do not have enough memory: Your computer needs to have a total of
128 MB physical memory installed for the normal YASARA and 512 MB for the Twinset YASARA,
as well as twice this amount of swap space (256 MB for YASARA and 1 GB for the Twinset).
Another rare cause for this problem was reported by users who had anti-virus software like TrendMicro2005 activated with maximum security settings. These programs may silently prevent you from running any software that has been downloaded from the web. Temporarily deactivate the tool,
then run YASARA again. If YASARA does not start, but a message like
Error: Could not open /dev/nvidiactl because the permissions
are too restrictive. Please see the FREQUENTLY ASKED QUESTIONS
section of /usr/share/doc/NVIDIA_GLX-1.0/README for steps
to correct.
appears, become root and run the following commands:
chmod 0666 /dev/nvidia*
chown root /dev/nvidia*
To prevent the problem from reappearing, it may help to reconfigure the security module of the PAM system.
In most cases this security system works, but it can get confused. Different Linux distributions have different files to control this; please consult with your distributor for the correct method of disabling this security feature.
As an example, if your system has the file /etc/security/console.perms then you should edit the file and remove the line that starts with
' dri' (we have also received reports that additional references to
dri in console.perms must be removed). If instead your system has the file
/etc/logindevperms then you should edit the file and remove the line that lists
/dev/nvidiactl. The above steps will prevent the PAM security system from modifying the permissions on the NVIDIA device files.
This message indicates that the operating system decided to kill YASARA instead of running it. The most likely reason is that you do not have enough RAM to run YASARA without exhausting your swap space and freezing your system. Your computer needs to have
128 MB physical memory installed for the normal YASARA and 512 MB for the Twinset YASARA,
as well as twice this amount of swap space (256 MB for YASARA and 1 GB for the Twinset).
To check your configuration, open a terminal and type
free
The output should look roughly like this one:
total used free shared buffers cached
Mem: 255240(a) 239944 15296 0 11332 112944
-/+ buffers/cache: 115668 139572
Swap: 522072(b) 252 521820
To run YASARA, the number marked (a) should be >120000,
while (b) should be >250000. For the Twinset, (a) should be >500000 and (b) should be
>1000000. If you meet these requirements and still get killed,
edit the file yasara.ini and change the 'Memory' field like that:
Memory 48
If that works, you can subsequently assign larger amounts of memory to YASARA. If it still does not work, type and check that all memory options are set to 'unlimited':
max locked memory (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
virtual memory (kbytes, -v) unlimited
If this is not the case, set them to unlimited:
ulimit -l unlimited
ulimit -m unlimited
ulimit -v unlimited
Some of this changes may only be made by user 'root'. To make them permanent,
you have to edit the file /etc/security/limits.conf and add the lines
* hard memlock unlimited
* soft memlock unlimited
* hard rss unlimited
* soft rss unlimited
* hard data unlimited
* soft data unlimited
And afterwards reboot the machine. To make the YASARA executable small, it is dynamically linked to a number of libraries that are normally installed in every Linux distribution since
2000. If you encounter the problem, please contact support@yasara.org and provide details about your Linux distribution,
as well as the output of this command: We will then quickly send you a new download link that solves the problem.
Alternatively, you can install the missing library yourself,
assuming that you know the root password on your machine or your system administrator allows
'sudo' access to package installation. A special case are
64bit Linux distributions (AMD64): especially (K)Ubuntu normally comes without backwards compatible support for
32bit applications, look here for a solution
. One possible explanation is that YASARA tried to enter
fullscreen mode using an extremely high resolution screen
(or two screens combined with TwinView etc.). In this case just delete the file yasara/yasara.ini and restart. If this does not help, open a terminal, type glxinfo and check the output for available visuals. It should look a bit like that:
visual x bf lv rg d st colorbuffer ax dp st accumbuffer ms cav
id dep cl sp sz l ci b ro r g b a bf th cl r g b a ns b eat
----------------------------------------------------------------------
0x21 16 tc 0 16 0 r y . 5 6 5 0 0 16 0 16 16 16 16 0 0 None
0x22 16 dc 0 16 0 r y . 5 6 5 0 0 16 0 16 16 16 16 0 0 None
0x23 16 tc 0 16 0 r . . 5 6 5 0 0 16 0 16 16 16 16 0 0 None
0x24 16 tc 0 16 0 r y . 5 6 5 0 0 0 0 16 16 16 16 0 0 None
0x25 16 tc 0 16 0 r . . 5 6 5 0 0 0 0 16 16 16 16 0 0 None
0x26 16 dc 0 16 0 r . . 5 6 5 0 0 16 0 16 16 16 16 0 0 None
0x27 16 dc 0 16 0 r y . 5 6 5 0 0 0 0 16 16 16 16 0 0 None
0x28 16 dc 0 16 0 r . . 5 6 5 0 0 0 0 16 16 16 16 0 0 None
If you get nothing comparable, you need to install OpenGL drivers for your video card. Contact your system administrator if you do not have the root password,
otherwise visit www.nvidia.com or www.ati.com
for more details. There are two reasons for this error message:
- When downloading YASARA, you selected a different CPU than the one in your computer.
Go to www.yasara.org/update, input the serial number that is listed in our mail with
the initial download link, and choose 'Many different, I want to install on multiple PCs'
as your CPU.
- When downloading YASARA, you did not select a specific CPU. In this case, the processor
in your PC is either many many years too old for molecular modeling (Pentium MMX, Pentium II,
AMD K6 etc.) or a rather exotic model that is incompatible with the current mainstream CPUs.
You can unfortunately not run YASARA on this PC.
- If you have been able to start YASARA in the past, then the reason for this error
is most likely the one described in the error box. Restart YASARA, and if this does
not help, delete the file yasara.ini to set the window size back to the default.
- If this is the first time you try to run YASARA, then the reason for this error
is almost certainly a bug or incomplete functionality in your OpenGL graphics driver.
The following hardware configurations have been reported to occasionally cause this
problem:
- Windows with some exotic, not entirely OpenGL compliant integrated graphics chipsets
like the SiS Mirage 2 (SiS760GX chipset, version 3.75). Please notify us if a newer
driver version solves the problem.
This problem was observed in Fedora Core 6 as soon as
3D desktop effects were activated. Updating the X-server to the latest version (1.1.1-47.7.fc6) solved the issue.
|
| This warning appears when you switch between the MacBook TrackPad and an external mouse with scroll wheel. The message is caused by a chain of design bugs in MacOSX,
and can safely be ignored. When you start YASARA under Linux and get the message
Disabled smooth atom colors because OpenGL extension XY is not supported
then your OpenGL driver is either very old or not installed properly. YASARA still runs,
but it can display only the following atom colors: blue, magenta, red, yellow, green,
cyan and gray, e.g. smooth color gradients will only be visible in ribbons and ray-traced output,
but not in the individual atoms on screen. If the message 'Loading required GL library
/usr/X11R6/lib/libGL.so.1.2 disabling TCL support' appears in the terminal, this indicates that your OpenGL driver is not installed properly. This was reported for the default installation of some ATI Radeon cards,
and YASARA may subsequently hang in the startup screen. Click here for instructions how to install proper Radeon drivers
. This warning may appear on some Redhat Linux distributions and is normally harmless. To get rid of the message,
install the compat-glibc RPM, for example compat-glibc-7.x-2.2.4.32.6.i386.rpm.
In another case where this error message was not harmless but prevented YASARA from running,
it turned out that the reason was third party software that changed environment variables to replace system libraries. Removing these changes solved the problem.
This warning is not related to YASARA and affects all OpenGL applications. Rumours are that it is caused by a Linux kernel problem,
occurs in all distributions with certain video chips (e.g. Intel) and will be resolved in kernel
2.6.20. Fortunately YASARA runs correctly, the message can thus be ignored.
This bug was observed with Radeon 9600 cards in Linux,
it has been reported to freedesktop.org Click View > Lighting and set 'Ambient influence' and
'Shadow density' to 0 as a workaround. When you start YASARA under Linux and get the message
Xlib: extension "XFree86-DRI" missing on display ":0.0"
this indicates that your OpenGL driver is not installed properly. This happens for example when installing an old nVIDIA driver on a new Linux distribution with Kernel
2.6, e.g. Fedora Core 1. Do not ignore the message, you may encounter serious graphics problems and system hangs. Instead update to the latest driver. |
If YASARA displays the startup screen with the message 'Initializing graphics engine...' at the bottom,
but nothing else happens, this can have a number of reasons:
- Your OpenGL driver may have a serious performance problem. This is the case
with Matrox G400-G550 cards, that need three minutes to get past the startup screen.
Go for a cup of coffee, this happens only the first time and when you try to resize
the window. Anyway, the three spare minutes are probably a good time to get a new graphics
card.
- While the startup screen is displayed, YASARA runs extensive OpenGL calibration
algorithms, which may cause broken OpenGL drivers to hang. Most of the time, this
happens in Linux and indicates that you need to install a new OpenGL driver.
Click here for more details.
All these warnings are non-fatal, YASARA will run normally. If it does not,
the reason lies somewhere else. | YASARA plugins use the Python scripting language. If Python is not installed,
these plugins will not be loaded and some convenient options will be missing in the menus
(e.g. to get PDB files from the web). Just click Help > Install program > Python to install it,
or alternatively download Python from www.python.org
. You need to restart YASARA afterwards. An alterative explanation is that your computer is running short of swap space and YASARA cannot run Python.
Look here for more details. In order to display graphics smoothly,
YASARA should redraw the screen synchronously with your monitor, otherwise you may encounter so called
'tearing effects'. Not all graphics cards allow you to activate this option.
In Windows try to go to Control Panel > Display > Settings
> Advanced > OpenGL and see if there (or close by) is an option called 'Activate Sync to VBlank'.
In Linux, it depends on your graphics card. nVIDIA cards should be handled automatically by YASARA. Until
2006, ATI Radeon drivers allowed you to activate this option during the installation. Nowadays you can simply run as root
'aticonfig --sync-vsync=on' and then restart the X-server. Unfortunately this does not always work.
In MacOSX, YASARA normally activates the synchronization automatically. If you nevertheless get the warning,
it points towards an internal MacOSX problem. |
This problem was reported for some S3 graphics chips and is caused by a bug in their driver. Updating the S3 graphics driver
( www.s3graphics.com) to at least version
139412 solves the issue. If you do not know which graphics chip you have, look here. When you click on an entry in the top menu line or bring up a context menu,
some things can go wrong. | This behaviour was confirmed for two graphics chips:
- NVIDIA Riva TNT2 with very old, broken OpenGL drivers (e.g. version .1200).
Download the latest drivers from www.nvidia.com to solve this problem.
Version .5216 was confirmed to work perfectly.
- S3 Twister chips that are sometimes found in notebooks:
Crashes were observed with rather old, broken OpenGL drivers. Get the latest one
and notify us if this solves the problem.
A trivial first solution is to disable window animations: click on Window
> Animation > Off. If you are using old drivers for ATI Radeon and Matrox G400-G550 cards,
it may take half a second for the menu to appear. Owners of a Radeon 8500 card and above can simply update the driver,
this will solve the problem. For cards older than the Radeon 8500, this may help as well,
please report your experience. For Matrox owners, updating the driver can even make things worse,
and it's probably best to just get a new graphics card. This only happens with Radeon
8500 cards and is a bug in ATI's driver. The problem has been reported, and solved by ATI in the Catalyst driver
3.4 and later. As a work-around, you can also go to Control panel > Display > Settings and set the screen color depth to
'32 bit true color'. You can also try to edit yasara.ini and set VisualQual to 0.
YASARA uses plugins written in Python, that add their own menu entries. If Python is not installed or broken,
these menu entries will not appear. Look here for more details
.
This can happen if you installed a 'fancy mouse pointer'-tool,
that shows very colorful pointers. If these pointers cannot be displayed as a hardware cursor by your graphics card,
the operating system has to copy the mouse pointer pixel by pixel into the video ram,
which often does not work with OpenGL windows. Switch back to a simple mouse pointer to solve this issue.
(Under Linux, that's often an option in /etc/X11/XF86Config or /etc/X11/xorg.conf,
e.g. for NVIDIA cards, you must set hwcursor to "1"). The usual reason is that another application has registered certain keyboard-shortcuts as hot-keys,
which then do not reach YASARA anymore. Exit YASARA and press the problematic key or combination of keys to see what happens and find the application in charge. Then change the hot-key settings there.
The Spaceball from 3DConnexion is currently only supported in Linux. YASARA has been tested with the Spaceball
3003FLX, but also the later models should be compatible. Before you start YASARA,
make sure that the Spaceball driver is running: If you do not see output except one line with grep, start the xdriver manually
(you can find the program on the Spaceball CD in the unix/linux directory).
Click 'Automatic search' to locate the Spaceball. If it cannot be found,
follow the hints displayed and also run the xdriver program as root. As soon as the Spaceball has been detected, choose the Application 'X Window Driver
2.0/3.0' and click 'Install', then 'Exit'. Now you can start YASARA and configure your Spaceball by clicking on Window
> Spaceball. More details can be found at the SpaceballPar
and SpaceballButton commands. |
If YASARA responds very slowly, this can have a couple of different reasons. A trivial cause may be that your
'FramesPerSecond' setting is too low: Click Window > Update frequency and set it to a high number,
e.g. 75. |
If you are running Windows 95 to XP, click on Start > Control Panel
> Display > Settings > Advanced > maybe 'Adapter' or 'Options', depends on your card. In Windows NT,
the usual location is Start > Settings > Control Panel > Display > Settings
> Display type. Somewhere around there, you should find the name of your graphics card and the driver version
(e.g. a list of *.dll files). In Windows Vista,
click Start > Control panel > Classic View > Device Manager > Display adapters. Double-click on your display adapter,
then click 'Driver'. In Linux, open a terminal and type
glxinfo
to display information about your OpenGL driver. If you purchased your graphics card before
2000, it may be a problem to run YASARA at a usable speed. The reason is usually not that the graphics card is too weak,
but that there is not enough video memory and the driver switches back to software rendering. Nevertheless,
YASARA runs OK on a Matrox G400 with 16MB ram. First edit the file yasara.ini and set VisualQual to
0, then reduce your screen color depth to 16 bits (65536 colors), and the screen resolution to
<=1024x768. If this helps, try subsequently higher resolutions. If you have less than
16MB ram on your video card, it's probably best to just get a new one. Examples of cards that are just too old for YASARA:
- ATI Mach, Rage IIC, Rage XL, Rage XC
- All 3DFX Voodoo cards
- Matrox Mystique
Microsoft unfortunately ships graphics drivers with reduced functionality,
which support only very slow OpenGL software rendering and leave the power of your graphics card unused,
except for the transparent Aero glass windows and video games. Click Start > Control panel > Classic View > Device Manager > Display adapters to determine the manufacturer of your graphics chip. Double-click on your display adapter,
then click 'Driver' to find your graphics driver version. Known issues:
- nVIDIA drivers 7.14.10.9677 and older are known not to accelerate graphics, downloading
the latest Windows Vista driver from www.nvidia.com solves the problem.
The new driver version should be 9.6.8.5 or higher.
- Windows Vista is currently (2006/12/01) not well suited for running graphics intensive
scientific applications like YASARA. Even with the latest nVIDIA drivers, the performance
is only ~30% of what you get in Linux or Windows XP on the same machine.
Try to avoid Windows Vista until Microsoft has solved the technical problems.
In this case it is most likely a driver issue
. During the development of YASARA, we found lots of bugs in OpenGL graphics drivers,
which we reported to the respective companies (e.g. ATI, nVIDIA, Matrox). These bugs were fixed in subsequent driver releases,
so most of the time you can solve the issue by just installing the latest drivers.
To determine your OpenGL driver version, click on Start > Control Panel
> Display > Settings > Advanced > Adapter. You will somewhere find a list of files with version numbers like..
nvopengl.dll 4.13.01.3082
In this nVIDIA example, 3082 is the driver version.
- The original Microsoft drivers shipping with Windows XP are bugged and can
cause YASARA to crash. Please download the latest driver from www.nvidia.com.
- nVIDIA Geforce driver versions 3082 and earlier cannot run YASARA properly,
installing new drivers (at least version 4523) solves the problem.
- nVIDIA Quadro drivers around version 6693 have a bug that makes the YASARA
console at the bottom of the window invisible. Updating to at least version
7184 solves the problem.
In this case it is most likely a driver issue. During the development of YASARA,
we found lots of bugs in OpenGL graphics drivers, which we reported to the respective companies
(e.g. ATI, nVIDIA, Matrox). These bugs were fixed in subsequent driver releases,
so most of the time you can solve the issue by just installing the latest drivers.
To determine your OpenGL driver version, click on Start > Control Panel
> Display > Settings > Advanced > Adapter. You will somewhere find a list of files with version numbers.
- ATI driver version 6.14.10.6542 from 2005 was reported to show completely corrupted
graphics on a dual core machine with an ATI Radeon X600 PRO card.
Updating the Radeon driver to Catalyst 6.6 solved the problem.
- ATI Catalyst 6.11 from 2006 with OpenGL driver 6.14.10.5819 was reported to show colorless
ribbons and cartoons or even crash on an ATI Radeon 7000 card with 32MB video ram
and two connected monitors. Closer inspection showed that the driver couldn't cope
with the exhausted video ram. The problem could be solved by not expanding the
desktop over both monitors.
nVIDIA does not allow Linux distributors to include their Geforce drivers. So a freshly installed Linux will run terribly slow with OpenGL applications,
including YASARA. (Non-OpenGL programs like Rasmol will work fine however, that's why you may not have noticed it.)
Open a terminal and type If the output does not show 'nVIDIA corporation' but
'SGI' and 'www.mesa3d.org', you DO NOT have an accelerated OpenGL installation and cannot use the power of your Geforce card.
To best way to install the required drivers depends on your Linux distribution. It is likely that your distribution offers prebuilt packages,
which you can simply install with your package manager. For
(K)Ubuntu, the usual sequence of commands (after enabling the universe and multiverse repositories) is:
sudo apt-get update
sudo apt-get install nvidia-glx
sudo dpkg-reconfigure xserver.org (select 'nvidia' from the list)
Edit the file /etc/X11/xorg.conf, and follow the instructions below regarding dri and nvidia. The press
<Ctrl>+<Alt>+<Backspace> to restart the X-server. If 'glxinfo
| grep vendor' now displays nVIDIA, you are ready to go.
Fedora Core 5 is broken with respect to the official nVIDIA drivers. A solution is provided at
http://www.fedorafaq.org/#nvidia. Even with this recipe,
we got one or two reports of unexpected nVIDIA problems on Fedora Core 5.
If there are no prebuilt packages for your distribution
, go to www.nvidia.com and download their latest Linux driver. They also provide detailed installation instructions. Note that you need the root password to install.
The probably most important thing when installing is that your X-server is not running. Press
<Ctrl>+<Alt>+<F2> to switch to a text screen, log in as root and type
/sbin/init 3
Usually you type
sh ./NVIDIA-Linux-x86-1.0-[DriverVersion].run
to install (for SuSE Linux, add the parameter -q). If this fails,
you have to look in the file /var/log/nvidia-installer.log After installing,
you can find detailed instructions on how to proceed in the file
/usr/share/doc/NVIDIA_GLX-1.0/README
It is especially important to adapt the file /etc/X11/XF86Config or
/etc/X11/xorg.conf:
- In the 'Device' section, replace the line
Driver "nv"
with Driver "nvidia"
- In the 'Module' section, delete the lines
Load "dri"
and (if present) Load "GLcore"
and make sure you have Load "glx"
Now type
init 5
to restart X. If completed successfully, 'glxinfo' should show
'NVIDIA Corporation' as OpenGL vendor. You can now restart YASARA. Additional hints:
- SuSE Linux requires to run sax2 after installing the nVIDIA drivers:
sax2 -r -m 0=nvidia (0 is a digit, not a letter!)
- The Linux Compiz window manager for advanced desktop 3D effects was
once reported to make the sticks between atoms disappear as soon as a non-standard
atom colors are chosen.
- On a Fedore Core 1 installation, you may get a complaint about a "Failed cc sanity check",
which should be taken seriously. Do not follow the possibility to set the 'IGNORE_CC_MISMATCH'
flag, this causes serious graphics problems and can freeze your system. Instead download
the latest nVIDIA driver to solve this issue.
When running OpenGL applications in Linux, you should buy a graphics card from nVIDIA,
since they provide the best graphics drivers that cause the least number of problems. ATI Linux drivers tend to expose graphics bugs,
are often impossible to install or do not support the latest chips. This has gotten better lately with the takeover by AMD.
If your computer already contains an ATI Radeon card, there is a resonable chance that everything works correctly if you follow these hints:
NOTE: If you successfully installed the Radeon drivers and
YASARA's user interface still lags behind, scroll to the end of this section.
Most default Linux installations (e.g. RedHat, Fedora) do not activate hardware accelerated OpenGL graphics for newer Radeon cards. Instead,
only the unusably slow Mesa software emulation is available. Open a terminal and type If the output indicates that your OpenGL vendor is 'Tungsten Graphics',
then there is a good chance that YASARA works correctly, especially on older Radeon chips
(on Radeon 9600, you may get a 'Mesa implementation error' however, which can be worked around by disabling shadow and lighting at View
> Lighting):
OpenGL vendor string: Tungsten Graphics, Inc.
OpenGL renderer string: Mesa DRI Radeon 20020611 AGP 1x x86/MMX/SSE NO-TCL
OpenGL version string: 1.2 Mesa 4.0.4
On the other hand, if you find the following in the output,
you do not have hardware accelerated 3D graphics activated, and using YASARA with this configuration is hopeless:
OpenGL vendor string: Mesa project: www.mesa3d.org
OpenGL renderer string: Mesa GLX Indirect
OpenGL version string: 1.3 Mesa 4.0.4
In latter case, you need to install the proper driver from ATI: click on
www.ati.com and download the latest Linux Radeon driver. Installation instructions for Fedora Core At least in Fedora Core 5 and 6, the drivers available from the ATI web site cannot be installed. The Fedora project however provides customized drivers as RPM packages in the livna repository:
- Become root
- Add the Livna repository to yum:
rpm -Uhv http://rpm.livna.org/livna-release-6.rpm
- Install the ATI kernel module and OpenGL driver (you can leave out *-32bit on 32bit systems)
yum install kmod-fglrx xorg-x11-drv-fglrx xorg-x11-drv-fglrx-libs-32bit
yum update kmod-fglrx xorg-x11-drv-fglrx xorg-x11-drv-fglrx-libs-32bit
- Configure the driver:
service ati-fglrx restart
ati-fglrx-config-display enable
- If you did not disable SELinux during installation:
setsebool -P allow_execstack=1
setsebool -P allow_execmod=1
- Make sure that the file /etc/X11/xorg.conf contains the following sections:
Section "Module"
Load "dbe"
Load "extmod"
Load "fbdevhw"
Load "glx"
Load "record"
Load "freetype"
Load "type1"
Load "dri"
EndSection
Section "Device"
Identifier "aticonfig-Device[0]"
Driver "fglrx"
Option "VideoOverlay" "on"
# This enables VSYNC
Option "Capabilities" "0x00000800"
EndSection
Section "ServerFlags"
Option "AIGLX" "False"
EndSection
Section "DRI"
Group 0
Mode 0666
EndSection
Section "Extensions"
Option "Composite" "False"
EndSection
Installation instructions for other Linux distributions and the new
*.run drivers (2005 and later) In 2005, ATI introduced a new installer
(usually a big file >50 MB) with the extension '.run'.
- Check that you have the GCC compiler as well as the Linux kernel sources installed, type
ls /usr/src
If no directory named 'linux-[YourKernelVersion]' appears, you must install the kernel sources,
e.g. in RedHat/Fedora, click on System Settings > Add/Remove Applications,
scroll to the 'Development' section and check the 'Kernel Development' box.
Then click 'Update' to install the RPMs. In SuSE, click System > YaST.
Now check that /usr/src/linux-[YourKernelVersion] is present.
- Download the installer from the ATI website, e.g. ati-driver-installer-8.19.10-i386.run.
Example output:
ATI/XFree86-4_1_X
ATI/XFree86-4_2_X
Debian/woody
Debian/oldstable
Debian/3.0
Debian/sarge
Debian/stable
Debian/3.1
Debian/etch
Debian/testing
Debian/sid
Debian/unstable
RedHat/RHEL3
RedHat/RHEL4
SuSE/SLES9-IA32
SuSE/SUSE91-IA32
SuSE/SUSE100-IA32
SuSE/SUSE92-IA32
SuSE/SUSE93-IA32
SuSE/SUSE101-IA32
Ubuntu/warty
Ubuntu/4.10
Ubuntu/hoary
Ubuntu/5.04
Ubuntu/breezy
Ubuntu/5.10
- Make sure that the X-server is not running when installing the RPM:
Press <Ctrl>+<F2> to switch to a text terminal, log in as root and type
/sbin/init 3
- Check that the GCC compiler output does not say 'ERROR' (warnings are allowed).
- Configure the ATI driver and X-server:
fglrxconfig
You will get lots of questions to answer, usually it is safe to pick the suggested default.
Only when the question is "Do you want to synchronize buffer swaps with the vertical sync
signal", choose "yes".
- Log in, open a console and type
fglrxinfo
The output should now look similar to this one, with
ATI Technologies as the OpenGL vendor:
display: :0.0 screen: 0
OpenGL vendor string: ATI Technologies Inc.
OpenGL renderer string: RADEON 9200SE DDR Generic
OpenGL version string: 1.3.1017 (X4.3.0-8.19.10)
If this worked, you are done and ready to run YASARA. Congratulations.
If you finally run YASARA, and everything looks OK, but the user interface is slow and lags behind the mouse pointer,
exit the X-server and start
fglrxconfig
a second time, but now do not synchronize buffer swaps with the vertical sync signal
. Installation instructions for the old *.rpm drivers
(until 2005) You receive an RPM whose name usually looks like
fglrx-[XServerVersion]-[DriverVersion].i386.rpm, e.g. fglrx-4.3.0-3.7.6.i386.rpm
ATI provides detailed installation instructions, however installation tends to fail easily.
Here are some hints:
- Make sure that the X-server is not running when installing the RPM:
Press <Ctrl>+<F2> to switch to a text terminal, log in as root and type
/sbin/init 3
If you accidentally tried to install the RPM without the kernel source present,
you may have gotten this error message:
*** Error: no kernel module build environment - please consult readme.
- Configure the ATI driver and X-server:
fglrxconfig
You will get lots of questions to answer, usually it is safe to pick the suggested default.
Only when the question is "Do you want to synchronize buffer swaps with the vertical sync
signal", choose "yes".
There is also a question about quad-buffered stereo, but we have not had much luck with this one.
- Restart the X-server:
startx
- Check the configuration:
fglrxinfo
If the output looks about like that, you are done and can run YASARA:
display: :0.0 screen: 0
OpenGL vendor string: ATI Technologies Inc.
OpenGL renderer string: RADEON 9200SE DDR Generic
OpenGL version string: 1.3 (X4.3.0-3.7.6)
If you still see "Mesa" in the OpenGL vendor string, open the file
/var/log/XFree86.0.log in a text editor and search for this message:
(EE) fglrx(0): [agp] unable to acquire AGP, error "xf86_ENOMEM"
(EE) fglrx(0): cannot init AGP
....
(WW) fglrx(0): ***********************************************
(WW) fglrx(0): * DRI initialization failed! *
(WW) fglrx(0): * (maybe driver kernel module missing or bad) *
(WW) fglrx(0): * 2D acceleraton available (MMIO) *
(WW) fglrx(0): * no 3D acceleration available *
(WW) fglrx(0): ********************************************* *
This error message indicates problems with your AGP support. Exit X and type as root
/sbin/insmod agpgart
. Restart X and try again
fglrxinfo
. If it works now, you are ready for YASARA. Note that this fix is temporary. If you still have problems, make sure that you really install the latest ATI driver. The first releases were very buggy,
and only with version 3.7.6 did ATI reach good quality. Version 3.7.6 works well with most Radeon cards,
e.g. the 9200, 9600 series. If YASARA finally runs, and everything looks OK,
but the user interface is slow and lags behind the mouse pointer, exit the X-server and start
fglrxconfig
a second time, but now do not synchronize buffer swaps with the vertical sync signal
. Xi graphics www.xig.com
distributes a commercial X-server with hardware accelerated OpenGL graphics that supports mainly ATI graphics chips up to the Radeon
9200. Prices for these drivers with OpenGL functionality start at
69$, which is the same amount of money you would have to pay for a new GeforceFX card including drivers from nVIDIA that deliver significantly higher performance. ATI also provides faster Linux drivers.
There is mainly one situation where the Xig drivers can be very helpful: if you already own a fast ATI
9200 card and absolutely need quad-buffered stereo. Then you can buy the Xig Summit DX Platinum driver for
89$, which is much cheaper than a stereo-capable Quadro card from nVIDIA.
YASARA was tested with an ATI Radeon 9200 and the Summit_DX-Platinum driver version
2.2-16. Once some installation issued are solved, the Xig OpenGL driver runs out of the box without any visual glitches,
albeit at lower speed and less smoothly than the flgrx driver from ATI.
Xig provides detailed installation instructions, nevertheless here are some hints to avoid common pitfalls:
- Download the file Summit_DX-Platinum-[Version].tar from www.xig.com.
- If your directory /usr/src does not contain a linux* subdirectory, install
the kernel source RPMs for your Linux distribution.
- Try to remove existing Mesa drivers:
rpm -e --nodeps Mesa
This may fail.
- Make sure the kernel driver is loaded:
/sbin/modprobe xsvc
- Configure your desktop: run
Xsetup
- Start the Xserver:
startx
- Open a terminal and type
glxinfo
If you see the following output, you are done and
can start YASARA:
server glx vendor string: Xi Graphics, Inc.
server glx version string: 1.4
server glx extensions:
GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_visual_info,
GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_SGI_make_current_read,
GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer
client glx vendor string: Xi Graphics, Inc.
client glx version string: 1.4
client glx extensions:
If it did not work, look at the various FAQ files provided by Xig in the Summit_DX-Platinum directory you untared and in
/usr/src/xig. Apart from the trivial fact that notebooks often do not have sufficient OpenGL capabilities,
another speed issue was reported on some notebooks with Pentium 4 processor, which react very slowly when using animated windows
(blend, rotate). The reason is that many companies sell expensive 2GHz notebooks,
but the processor runs permanently at 1.2GHz, even with heavy system load and a connected power supply. Nevertheless,
Windows reports a CPU clock frequency of 2GHz, which leads to timing issues. To solve this problem,
go to Control Panel > Power options > Power schemes and make sure that you choose a
'Desktop' setting.
While YASARA normally runs nicely with this chipset, performance drops heavily as soon as you assign atom colors other than red,
green, blue, cyan, magenta, yellow and gray. The driver seems to switch back to software rendering in this case. Edit the file yasara.ini and set VisualQual to
1.
YASARA runs nicely on this chip unless you have an old broken driver installed. Go to Start
> Control Panel > Display > Settings > Advanced > Adapter > Properties.
(In WinXP, location may differ slightly in WinNT). You will see the driver date and driver version.
YASARA has been tested with driver version number 6.13.10.3510 and date
15-4-2003. If your driver is from an earlier date with a smaller version number,
it contains too many bugs and you have to update it (go to www.intel.com
). At the time of writing, version 13.5.0.3691 is the latest one.
YASARA runs nicely on this chip unless you have an old broken driver installed. Go to Start
> Control Panel > Display > Settings > Advanced > Adapter > Properties. You will see the driver date and driver version.
YASARA has been tested with driver version number 6.14.10.3943 and date
02-11-2004. If your driver is from an earlier date with a smaller version number,
it contains serious bugs like the menus turning black when you move the pointer out of the YASARA window. Please install the latest drivers from
www.intel.com.
- Drivers 6.14.10.3889 and older have a problem with the task manager. If you bring it
up with <Ctrl>+<Alt>+<Del>, the OpenGL graphics may be corrupted after returning.
Also if you request too much memory in yasara.ini, the driver may switch to software
rendering, thus making everything unusably slow.
- Driver 6.14.10.3943 still has a little bug that occasionally
makes the mouse pointer freeze for half a second.
Many of the S3 chips (e.g. ProSavage DDR) are advertised with OpenGL compatibility but use terribly slow software rendering instead. You can try to download their latest drivers from
www.s3graphics.com, maybe they fixed the problems in the mean time. Do not be disappointed if you cannot run YASARA at a usable speed with these chips.
When using a SiS M650 graphics chip (sometimes found in cheap notebooks),
it may happen that molecules are too dark and change their brightness abruptly. Debugging indicated that the SiS OpenGL driver does not display the fog properly. Click on View
> Lightning > Fog and set it to 0 to disable the fog completely.
Problems running YASARA were reported for a Wildcat III 6110. The problem has been reported to
3DLabs. |
Windows XP up to Service Pack III has several bugs that can cause high CPU usage or even crashes when running programs like YASARA. Microsoft provides more details and a hotfix at
http://support.microsoft.com/?id=
896256
Molecules may be small, but they are not simple. Consequently,
a lot of things can go wrong with atom names, bond orders, chemical elements etc.
| To support the millions of fileformats out there, YASARA uses OpenBabel,
a library available from http://openbabel.sourceforge.net
. OpenBabel has mainly one weak spot, and that's residue names and numbers. Many of the supported file formats do not even know the concept of
'residues' because they come from quantum chemistry, where one usually works with just one molecule. So after loading a structure with OpenBabel,
click on various residues and check that the names and numbers are correct. Otherwise try to export the structure in PDB format before loading it in YASARA.
|
If you connect two or more monitors or beamers to your graphics card,
there are normally two ways of making use of the extra space:
- A single desktop covers both monitors: this approach is called 'TwinView' by nVIDIA and
'DualHead' by ATI.
You can in principle resize the YASARA window to cover both monitors, as long as the window
size does not exceed YASARA's maximal resolution. (In the latter case, YASARA
will reduce the size again). Mac OS X may not allow you to move the YASARA window to a certain
monitor and keep it there, in this case simply click Window > Fix on screen. Windows
may interfere with your attempts to place the YASARA window correctly, in this case it may
help to set 'CorrectWin' in yasara.ini to 0 to avoid window size corrections.
If you go fullscreen, it depends on your operating system and graphics card what will happen.
The YASARA window may fully cover both monitors (this can fail with nVIDIA
cards in Linux, which may show you (part of) the same image on both monitors), or it may
cover only one of the monitors. YASARA cannot influence on which monitor it goes fullscreen.
You have to adjust this behavior yourself in the DualHead/TwinView section of your video driver.
- Each monitor shows its own desktop: this approach is available in Linux. There is an
application menu on each monitor, and programs stay on the monitor where you launched them.
If you maximize the YASARA window, it will cover the monitor where it was launched.
If you go fullscreen, YASARA will go fullscreen where you launched it. Since this
also captures the mouse, you will not be able to move the pointer back to the other
monitor unless you leave fullscreen mode.
Here are instructions on how to modify the file /etc/X11/xorg.conf to activate the mode described above on nVIDIA cards:
First, create two separate Device sections, each listing the BusID of the graphics card to be shared and listing the driver as
"nvidia", and assign each a separate screen:
Section "Device"
Identifier "nvidia0"
Driver "nvidia"
# Edit the BusID with the location of your graphics card
BusID "PCI:2:0:0"
Screen 0
EndSection
Section "Device"
Identifier "nvidia1"
Driver "nvidia"
# Edit the BusID with the location of your graphics card
BusId "PCI:2:0:0"
Screen 1
EndSection
Then, create two Screen sections, each using one of the Device sections:
Section "Screen"
Identifier "Screen0"
Device "nvidia0"
Monitor "Monitor0"
DefaultDepth 24
Subsection "Display"
Depth 24
Modes "1600x1200" "1024x768" "800x600" "640x480"
EndSubsection
EndSection
Section "Screen"
Identifier "Screen1"
Device "nvidia1"
Monitor "Monitor1"
DefaultDepth 24
Subsection "Display"
Depth 24
Modes "1600x1200" "1024x768" "800x600" "640x480"
EndSubsection
EndSection
(Note: You'll also need to create a second Monitor section) Finally, update the ServerLayout section to use and position both Screen sections:
Section "ServerLayout"
...
Screen 0 "Screen0"
Screen 1 "Screen1" leftOf "Screen0"
...
EndSection
For further details, please refer to the XF86Config(5x) or xorg.conf(5x) manpages.
Apart from the trivial fact that YASARA Model+ is required for true stereo support,
and flat LCD/TFT screens are too slow for stereo, a few additional things can go wrong:
If you click on Window > Stereo > Quad buffered and get an error message that this video mode is not supported,
then your OpenGL driver does not allow to display stereo graphics this way.
Companies like nVIDIA and ATI usually provide the real stereo option only in their expensive workstation products
(nVIDIA Quadro or ATI FireGL). YASARA does currently not support workarounds with reduced resolution like interlaced or sync-doubling stereo modes. The reason is that most of the time,
you can enable quad-buffered stereo by fudging your video driver, e.g. to make a Geforce believe it is a Quadro,
google for: nvidia enable geforce OpenGL stereo.
- If you use Linux, stereo can be activated on Geforce cards with drivers 3XXX to 4496
or true Quadro cards with any driver version. No matter if you own a fudged Geforce or a
real Quadro, it is still required to enable stereo by adding the Option "Stereo" to the file
/etc/X11/xorg.conf, like in the example below:
Section "Device"
Identifier "Videocard0"
Driver "nvidia"
VendorName "Videocard vendor"
BoardName "nVidia GeForce 2 Go"
VideoRam 32768
Option "Stereo" "1"
EndSection
- If you use Windows and have a Quadro-like card, follow these steps:
1. Right-click on the Windows-background -> Click the properties item
2. Display Properties opens -> Click on the Settings tab
-> Click on the Advanced button 3. Click on the Quadro tab
-> Click on the Additional Properties... button 4. Click on the OpenGL Settings tab
5. Scroll down the Performance and Compatibility Options list
6. Enable the Enable quadbuffered stereo API list item
7. Optional: Click on the Additional OpenGL Properties... if you want to change more stereo options
8. Close all setting dialogs After that,
stereo should work. When switching the monitor off and on again,
it might be that the shutter-glasses will be out of sync. To fix this, just click on Window
> Stereo > Swap If stereo works but the image flickers
, this indicates that the screen update frequency is not set high enough. As an application,
YASARA can unfortunately not influence the screen update frequency all by itself,
you have to do that manually:
- If you use Linux, edit the file /etc/X11/xorg.conf. Make sure that the VertRefresh setting
in the "Monitor" Section is high enough, which is however only accepted by the X-server if the
HorizSync setting is also high enough. Setting HorizSync higher than your screen
supports can destroy the screen, check the maximally supported KHz in the screen manual.
- If you use Windows, follow this protocol:
1. Click Start, click Control Panel, click Appearance and Themes,
and then click Display. 2. Click the Settings tab, and then click Advanced.
3. Click the Monitor tab, and then click the screen refresh rate that you want to use,
at least 100 Hz for stereo. Apart from the trivial reason that the program may not be installed
(PovRay, MSMS), the likely explanation is that your hard disk has run full. If this is not the case,
your computer may not have enough swap space left. Especially in Linux, running other programs fails silently when the swap space is exhausted.
Look here for more details.
|
| What looks like a freeze, may actually only be a long delay caused by a lengthy calculation. YASARA normally uses progress bars to provide visual feedback,
but if you are working with extremely large structures containing 100000s of atoms,
even simple things can take a long time. Look here
for some hints how to improve performance.
- If you are using the Twinset, just switching to a WHAT IF menu can already take
a long time (30+ seconds), especially if there are 10000s of water molecules present.
Try to remove the objects containing water molecules before using WHAT IF functions.
- If your molecule is not extremely large and you are not using WHAT IF functions,
then please contact support@yasara.org, providing the scene that caused the hang.
This problem was reported for notebooks with ATI Radeon
9600 Mobility running Windows with a Radeon driver around 6.14.10.6422. Please update your graphics driver.
This 'issue' was observed on a Dual-Athlon PC with a Geforce card and Linux. Due to a bug in NVIDIA's driver
(verified for V31.23), opening two YASARA windows at the same time can freeze the PC,
please download the latest driver from www.nvidia.com
. |
The following reasons for a red error box are known inconveniences:
- Error 2 - Essential videomode not supported: if you try to go fullscreen on an
extremely high resolution screen (or two screens combined with TwinView), YASARA's resolution
limits may be exceeded. More details can be found here and here.
In some very rare cases, YASARA may encounter a serious problem that makes it impossible to continue running the program. You will then see a red error box with a problem description and the option to rescue your work by saving it as a complete YASARA scene
'errorexit.sce', which you can load after restarting YASARA. In some even rarer cases, YASARA might even crash completely without furthur notice. In either case,
you will get a 10 EUR reward for reporting this problem in a reproducible way.
If you have Python installed, simply restart YASARA and click on Help
> Report error. If you do not have Python installed,
do it manually by going to www.yasara.org/bugreport
. For problems that are not obvious, it is usually essential to send us the last execution log. You can find these logs in the directory yasara\log with names like exec_XXXX.log,
and usually the newest file is the one which contains the list of commands that lead to the crash. Other potential causes for Windows crashes:
- Occasional crashes were reported for a dual core machine equipped with an ATI Radeon
X600 PRO card and ATI driver version 6.14.10.6542 from 2005. The Windows crash report
indicated that the ATI driver module atioglxx.dll was to be blamed. Updating the Radeon
driver to Catalyst 6.6 solved the problem.
- ATI Catalyst 6.11 from 2006 with OpenGL driver 6.14.10.5819 was reported to crash
on an ATI Radeon 7000 card with only 32MB video ram and two connected monitors.
Closer inspection showed that the driver couldn't cope
with the exhausted video ram. The problem could be solved by not expanding the
desktop over both monitors.
Other potential causes for Linux crashes:
- You run a 64bit Linux with an nVIDIA card: driver version 76.76 (see output of glxinfo)
was reported to occasionally crash Linux, causing the following message in /var/log/messages:
Kernel BUG at "arch/x86_64/mm/pageattr.c":154. Update to the latest driver version.
As the Twinset consists of two programs, each with its own support infrastructure,
it may not always be clear where to report problems.
- The Twinset YASARA for Linux and Windows: Report all problems at http://www.yasara.org/bugreport,
except if you typed 'WIF' to enter the WHAT IF subsystem. Then please check if
your problem persists in the normal WHAT IF program, and if yes, then report it
directly at http://www.cmbi.ru.nl/whatif. Some WHAT IF options require
additional programs to be installed, that you probably have to download
yourself and that may not be available at all for Windows.
There is no bonus reward for problems traced to the WHAT IF source code.
- The Twinset WHAT IF for Linux: Report all problems at http://www.cmbi.ru.nl/whatif
except if they involve the YASARA menu or you have other reasons to believe
that they are related to the Twinset and not present in the standard WHAT IF.
In this case please report the problem at http://www.yasara.org/bugreport.
Some WHAT IF options require additional programs to be installed, that you probably
have to download yourself. We cannot provide support for those.
- The Twinset WHAT IF for Windows: This is an experimental version without
graphics, that is waiting for the completion of the WHAT IF for Windows OpenGL interface.
There is currently no support for this version available.
This problem was reported for some combinations of RedHat and Fedora Linux. The solution: use the ssh command line parameter
-Y. |
