From masoudnahali at live.com Thu Mar 4 08:45:07 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Thu, 4 Mar 2010 07:45:07 +0000
Subject: [xcrysden] running XCrysden on SUSE 11.2 (64 bit) error
Message-ID: <COL114-W38E0F45C693CBD37061516A1390@phx.gbl>
Dear Xcrysden users
I had many problems to compile XCrysden in SUSE 11.2 (64 bit) and Tobias suggested using the pre-compiled i586 in this link :
http://software.opensuse.org/search?baseproject=openSUSE:11.2&p=1&q=XCrySDen
this is a good idea and works well with Intel CPU but do not work with my AMD CPU !! I am not sure it may be related to Graphic or ...
when I write ./xcrysden I see the graphic page of Xcrysden only for 1 second and then unfortunately dissappeares.
koa at linux-vs0r:~/XCrysden/usr/bin> ./xcrysden
ls: cannot access /usr/share/tcl/bwidget*: No such file or directory
+----------------------------------------------------------------+
|****************************************************************|
|* *|
|* XCrySDen - (X-Window) CRYstalline Structures and DENsities *|
|* = === = === *|
|*--------------------------------------------------------------*|
|* *|
|* Anton Kokalj (Tone.Kokalj at ijs.si) *|
|* Jozef Stefan Institute, Ljubljana, Slovenia *|
|* *|
|* Copyright (c) 1996--2009 by Anton Kokalj *|
|* *|
|****************************************************************|
+----------------------------------------------------------------+
Version: 1.5.21
Please report bugs to: Tone.Kokalj at ijs.si
?
TERMS OF USE:
-------------
XCRYSDEN is released under the GNU General Public License.
Whenever graphics generated by XCRYSDEN are used in scientific
publications, it shall be greatly appreciated to include an explicit
reference. The preferred form is the following:
[ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
Code available from http://www.xcrysden.org/.
XCRYSDEN_TOPDIR=/home/koa/XCrysden/usr/lib/xcrysden
XCRYSDEN_SCRATCH=/tmp
Running on platform : unix
Operating system : Linux
Package ImageMagick's convert: /usr/bin/convert
Package ImageMagick's import: /usr/bin/import
Package Gifsicle: /usr/bin/gifsicle
Package Xwd: /usr/bin/xwd
Executing: /home/koa/XCrysden/usr/lib/xcrysden/bin/ftnunit
drmRadeonCmdBuffer: -22. Kernel failed to parse or rejected command stream. See dmesg for more info.
XCrysden is too important to see the resuls of Quantum ESpresso and there is not another way. Your help is a good gift to me.
Many Thanks
Masoud Nahali
Sharif University of Technology
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From burnus at net-b.de Thu Mar 4 10:11:38 2010
From: burnus at net-b.de (Tobias Burnus)
Date: Thu, 04 Mar 2010 10:11:38 +0100
Subject: [xcrysden] running XCrysden on SUSE 11.2 (64 bit) error
In-Reply-To: <COL114-W38E0F45C693CBD37061516A1390@phx.gbl>
References: <COL114-W38E0F45C693CBD37061516A1390@phx.gbl>
Message-ID: <4B8F794A.5090203@net-b.de>
Hi,
On 03/04/2010 08:45 AM, Masoud Nahali wrote:
> I had many problems to compile XCrysden in SUSE 11.2 (64 bit) and
> Tobias suggested using the pre-compiled i586 in this link :
> http://software.opensuse.org/search?baseproject=openSUSE:11.2&p=1&q=XCrySDen
> <http://software.opensuse.org/search?baseproject=openSUSE:11.2&p=1&q=XCrySDen>
I think in this case it could be rather a packaging or dependency
problem than a real xcrysden issue.
> when I write ./xcrysden I see the graphic page of Xcrysden only for 1
> second [...]
>
> ls: cannot access /usr/share/tcl/bwidget*: No such file or directory
Can you check whether "bwidget" is installed by running "rpm -q
bwidget". It should due to the dependency of the .rpm. If it doesn't,
can you install "bwidget" and try again?
As the RPM contains:
Requires: bwidget gawk ImageMagick netpbm
this should not fail.
If it worked, can you run:
rpm -ql bwidget|grep widget.tcl
Here, with openSUSE Factory, it prints:
/usr/share/tcl/bwidget1.9.0/widget.tcl
However, this should also not be the issue as also openSUSE 11.2 has
bwidget in the smae directory.
Can you run "cat /etc/SuSE-release" to confirm that you use openSUSE 11.2?
Tobias
From masoudnahali at live.com Thu Mar 4 20:24:06 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Thu, 4 Mar 2010 19:24:06 +0000
Subject: [xcrysden] running XCrysden on SUSE 11.2 (64 bit) error [2]
Message-ID: <COL114-W53E182829AE36D0BDF1CDEA1390@phx.gbl>
?Dear XCrysden users
At first, I thanks Tobias because of his kind attention and helps. I cannot run XCrysden as mentioned in my previous post. when I write ./xcrysden I see the XCrysden graphical page only for one second and then disappears. I have installed Parallel Quantum Espresso successfully on my system and without XCrysden I cannot see the results.
Reply to Tobias's suggestions:
linux-vs0r:/home/koa # rpm -q bwidget
bwidget-1.9.0-2.2.noarch
linux-vs0r:/home/koa # rpm -ql bwidget|grep widget.tcl
/usr/share/tcl/bwidget1.9.0/widget.tcl
linux-vs0r:/home/koa # cat /etc/SuSE-release
openSUSE 11.2 (x86_64)
VERSION = 11.2
I am sure about the specification of my system: the OS is SUSE 11.2 (64 bit). I have installed Openmpi for parallel installation of QE. SUSE 11.2 (64 bit) has not "libstdc++33-3.3.3-7.4.x86_64" and I have installed it previously on my system. I have a single PC with these specifications:
CPU: AMD(3 Cores, 790 GX), M.B: ASUS(M4A78T-E), Graphics: ATi RAEON HD 3300, and 8 Gigs DDR3 memory.
the error :
XCRYSDEN_TOPDIR=/home/koa/XCrysden/usr/lib/xcrysden
XCRYSDEN_SCRATCH=/tmp
Running on platform : unix
Operating system : Linux
Package ImageMagick's convert: /usr/bin/convert
Package ImageMagick's import: /usr/bin/import
Package Gifsicle: /usr/bin/gifsicle
Package Xwd: /usr/bin/xwd
Executing: /home/koa/XCrysden/usr/lib/xcrysden/bin/ftnunit
drmRadeonCmdBuffer: -22. Kernel failed to parse or rejected command stream. See dmesg for more info.
koa at linux-vs0r:~/XCrysden/usr/bin> ./xcrysden
ls: cannot access /usr/share/tcl/bwidget*: No such file or directory
+----------------------------------------------------------------+
|****************************************************************|
|* *|
|* XCrySDen - (X-Window) CRYstalline Structures and DENsities *|
|* = === = === *|
|*--------------------------------------------------------------*|
|* *|
|* Anton Kokalj (Tone.Kokalj at ijs.si) *|
|* Jozef Stefan Institute, Ljubljana, Slovenia *|
|* *|
|* Copyright (c) 1996--2009 by Anton Kokalj *|
|* *|
|****************************************************************|
+----------------------------------------------------------------+
Version: 1.5.21
Please report bugs to: Tone.Kokalj at ijs.si
TERMS OF USE:
-------------
XCRYSDEN is released under the GNU General Public License.
Whenever graphics generated by XCRYSDEN are used in scientific
publications, it shall be greatly appreciated to include an explicit
reference. The preferred form is the following:
[ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
Code available from http://www.xcrysden.org/.
XCRYSDEN_TOPDIR=/home/koa/XCrysden/usr/lib/xcrysden
XCRYSDEN_SCRATCH=/tmp
Running on platform : unix
Operating system : Linux
Package ImageMagick's convert: /usr/bin/convert
Package ImageMagick's import: /usr/bin/import
Package Gifsicle: /usr/bin/gifsicle
Package Xwd: /usr/bin/xwd
Executing: /home/koa/XCrysden/usr/lib/xcrysden/bin/ftnunit
drmRadeonCmdBuffer: -22. Kernel failed to parse or rejected command stream. See dmesg for more info.
Another stupendous problem: commonly I write ./xcrysden in the konsole from my home (not root, without sudo su and going to root) but when I do the same in root konsole I will take another lines and do not see
the graphical page for that 1 second !!
Directory: /home/koa/XCrysden/usr/bin
Thu Mar 4 21:35:26 IRST 2010
koa at linux-vs0r:~/XCrysden/usr/bin> sudo su
root's password:
linux-vs0r:/home/koa/XCrysden/usr/bin # ./xcrysden
ls: cannot access /usr/share/tcl/bwidget*: No such file or directory
+----------------------------------------------------------------+
|****************************************************************|
|* *|
|* XCrySDen - (X-Window) CRYstalline Structures and DENsities *|
|* = === = === *|
|*--------------------------------------------------------------*|
|* *|
|* Anton Kokalj (Tone.Kokalj at ijs.si) *|
|* Jozef Stefan Institute, Ljubljana, Slovenia *|
|* *|
|* Copyright (c) 1996--2009 by Anton Kokalj *|
|* *|
|****************************************************************|
+----------------------------------------------------------------+
Version: 1.5.21
Please report bugs to: Tone.Kokalj at ijs.si
TERMS OF USE:
-------------
XCRYSDEN is released under the GNU General Public License.
Whenever graphics generated by XCRYSDEN are used in scientific
publications, it shall be greatly appreciated to include an explicit
reference. The preferred form is the following:
[ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
Code available from http://www.xcrysden.org/.
XCRYSDEN_TOPDIR=/home/koa/XCrysden/usr/lib/xcrysden
XCRYSDEN_SCRATCH=/tmp
Application initialization failed: no display name and no $DISPLAY environment variable
Error in startup script: can't read "xcrys(platform)": no such variable
while executing
"if { $xcrys(platform) == "windows" } {
# testing ...
rename exec _tcl_exec
proc exec {args} {
global env
# first try a normal exec..."
(file "/home/koa/XCrysden/usr/lib/xcrysden/Tcl/cygwin.tcl" line 19)
invoked from within
"source $system(TOPDIR)/Tcl/cygwin.tcl"
(file "/home/koa/XCrysden/usr/lib/xcrysden/Tcl/xcInit.tcl" line 433)
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From burnus at net-b.de Thu Mar 4 21:20:34 2010
From: burnus at net-b.de (Tobias Burnus)
Date: Thu, 04 Mar 2010 21:20:34 +0100
Subject: [xcrysden] running XCrysden on SUSE 11.2 (64 bit) error [2]
In-Reply-To: <COL114-W53E182829AE36D0BDF1CDEA1390@phx.gbl>
References: <COL114-W53E182829AE36D0BDF1CDEA1390@phx.gbl>
Message-ID: <4B901612.4050907@net-b.de>
Hi,
Masoud Nahali wrote:
>
> ls: cannot access /usr/share/tcl/bwidget*: No such file or directory
>
This is a mistake of mine when modifying xcrysden to use the system's
bwidget - one needs a "set +f" before:
BWIDGET_DIR=`ls -d /usr/share/tcl/bwidget*`
however, this does not seem to cause any problems. (It will be corrected
in the next build which should be ready in a moment.)
Note: This only affects the openSUSE builds at
http://software.opensuse.org/search
> Executing: /home/koa/XCrysden/usr/lib/xcrysden/bin/ftnunit
>
> drmRadeonCmdBuffer: -22. Kernel failed to parse or rejected command
> stream. See dmesg for more info
>
That seems to be the problem on your system. Do as the command asks for:
Run "dmesg". It seems to be a problem with Mesa on your Radeon graphics
card.
> * Another stupendous problem **:* commonly I write ./xcrysden in the
> konsole from my home (not root, without sudo su and going to root) but
> when I do the same in root konsole I will take another lines and do
> not see the graphical page for that 1 second !!
>
> koa at linux-vs0r:~/XCrysden/usr/bin> sudo su
> [...]
> Application initialization failed: no display name and no $DISPLAY
> environment variable
Well, that's the reason: In order to access the screen, one needs to
have a $DISPLAY variable. Try:
sudo -E su
(untested). The -E option preserves the environment variable (if allowed
by "/etc/sudoers").
Tobias
PS: Question: Why do not simply install the program like normal in /usr
instead of unpacking it in a local directory under $HOME? That has
nothing to do with this problem, however. Additionally, running such
programs as xcrysden as root counts as bad practice. (It is regarded as
insecure to run bigger programs as root; on the other hand: programs can
also do bad things if run as a normal user. Thus one can argue whether
it is really more insecure - at least on single-user systems.)
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From masoudnahali at live.com Sat Mar 6 21:30:32 2010
From: masoudnahali at live.com (Masoud Nahali)
Date: Sat, 6 Mar 2010 20:30:32 +0000
Subject: [xcrysden] running XCrysden on SUSE 11.2 (64 bit) error [3]
Message-ID: <COL114-W3842F40FF5F26AD5327B7BA1370@phx.gbl>
Dear XCrysden Users
I executed "dmesg" in the /bin for finding the probelm and in the results there is a line included an error :
?
[ 8.255075] amd64_edac: probe of 0000:00:18.2 failed with error -22
I think that the line is related to the error of XCrysden when I execute it :
> drmRadeonCmdBuffer: -22. Kernel failed to parse or rejected command
> stream. See dmesg for more info
I am trying to solve the problem but there is not any success, your help is appreciated.
Many Thanks
Masoud Nahali
Sharif University of Technology
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