| 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.
|