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Messages - gellen

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1
Installation and License Questions / Re: VNL also closes down directly in the lastest version atk-10.8.2-linux64
« on: October 12, 2010, 17:16 »
Today I found out the vendor-specific drivers for my graphics card in the vendor-specific  CD. It is :  /media/Setup/Matrox/G200e/Linux/xorg-x11-drv-mga-1.4.2-8.el5.x86_64.rpm, then I installed it:
. After that， I wanted to update the driver, but it said that I had installed  the newer version of it in my server before:
 rpm -Uvh xorg-x11-drv-mga-1.4.2-8.el5.x86_64.rpm
Preparing...                ########################################### [100%]
        package xorg-x11-drv-mga-1.4.2-10.el5.x86_64 (which is newer than xorg-x11-drv-mga-1.4.2-8.el5.x86_64) is already installed
        package xorg-x11-drv-mga-1.4.2-8.el5.x86_64 is already installed

Oh. That is say, I had installed the vendor-specific drivers (xorg-x11-drv-mga-1.4.2-10.el5.x86_64 ) for my graphics card before I came to the problem of installing atk10.8.2.  
Is the xorg-x11-drv-mga-1.4.2-10.el5.x86_64 driver still too old and I have to update it again (where can I download the newer one?) ? Do I still need to update the the latest MESA drivers? What should I do then?Thanks.
---------------------------------------------------------------------------------------------------------------
some information:
[zgh@m200 license]$ rpm -qf /usr/lib64/xorg/modules/drivers/mga_drv.so
xorg-x11-drv-mga-1.4.2-10.el5
xorg-x11-drv-mga-1.4.2-8.el5
[zgh@m200 license]$ rpm -qi xorg-x11-drv-mga-1.4.2-10.el5
Name        : xorg-x11-drv-mga             Relocations: (not relocatable)
Version     : 1.4.2                             Vendor: Red Hat, Inc.
Release     : 10.el5                        Build Date: Tue 06 Jan 2009 12:26:06 AM HKT
Install Date: Thu 06 May 2010 12:43:47 AM HKT      Build Host: ls20-bc2-13.build.redhat.com
Group       : User Interface/X Hardware Support   Source RPM: xorg-x11-drv-mga-1.4.2-10.el5.src.rpm
Size        : 176852                           License: MIT/X11
Signature   : DSA/SHA1, Wed 07 Jan 2009 02:07:41 AM HKT, Key ID 5326810137017186
Packager    : Red Hat, Inc. <http://bugzilla.redhat.com/bugzilla>
URL         : http://www.x.org
Summary     : Xorg X11 mga video driver
Description :
X.Org X11 mga video driver.

[zgh@m200 license]$ rpm -qi xorg-x11-drv-mga-1.4.2-8.el5
Name        : xorg-x11-drv-mga             Relocations: (not relocatable)
Version     : 1.4.2                             Vendor: (none)
Release     : 8.el5                         Build Date: Fri 04 Jul 2008 02:36:41 AM HKT
Install Date: Tue 12 Oct 2010 10:23:30 PM HKT      Build Host: dyn-152-165.matrox.com
Group       : User Interface/X              Source RPM: xorg-x11-drv-mga-1.4.2-8.el5.src.rpm
Size        : 187594                           License: MIT/X11
Signature   : (none)
URL         : http://www.x.org
Summary     : Xorg X11 mga video driver
Description :
X.Org X11 mga video driver.

[zgh@m200 license]$ cat /etc/X11/xorg.conf
# Xorg configuration created by system-config-display

Section "ServerLayout"
        Identifier     "Default Layout"
        Screen      0  "Screen0" 0 0
        InputDevice    "Keyboard0" "CoreKeyboard"
EndSection

Section "ServerFlags"
        Option      "AllowMouseOpenFail" "yes"
EndSection

Section "InputDevice"
        Identifier  "Keyboard0"
        Driver      "kbd"
        Option      "XkbModel" "pc105"
        Option      "XkbLayout" "us"
EndSection

Section "Device"
        Identifier  "Videocard0"
        Driver      "mga"
EndSection

Section "Screen"
        Identifier "Screen0"
        Device     "Videocard0"
        DefaultDepth     24
        SubSection "Display"
                Viewport   0 0
                Depth     24
        EndSubSection
EndSection

[zgh@m200 license]$ ls /usr/lib64/xorg/modules/drivers/
ast_drv.so        cirrus_drv.so     nv_drv.so         sil164.so             vga_drv.so
ati_drv.so        cirrus_laguna.so  r128_drv.so       siliconmotion_drv.so  via_drv.so
atimisc_drv.so    dummy_drv.so      r500_drv.so       sis_drv.so            vmware_drv.so
ati_r500_drv.so   fbdev_drv.so      radeon_drv.so     sisusb_drv.so         voodoo_drv.so
ati_tp_drv.so     i810_drv.so       radeon_tp_drv.so  tdfx_drv.so
ch7017.so         intel_drv.so      s3_drv.so         tfp410.so
ch7xxx.so         ivch.so           s3virge_drv.so    trident_drv.so
cirrus_alpine.so  mga_drv.so        savage_drv.so     vesa_drv.so

2
Installation and License Questions / Re: VNL also closes down directly in the lastest version atk-10.8.2-linux64
« on: October 12, 2010, 15:05 »
It is hard  to upgrade to RHEL 5.5 since the computer is a server but not a personal computer. But it maybe a good idea to update the driver. I will try it later. Thank you.

3
Installation and License Questions / Re: VNL also closes down directly in the lastest version atk-10.8.2-linux64
« on: October 10, 2010, 12:29 »
Yes, I can run "glxgears".Here is some of the results after I run the  glxgears:
[root@m200 ~]# glxgears
8808 frames in 5.0 seconds = 1757.764 FPS
8640 frames in 5.0 seconds = 1716.051 FPS


Then I run "glxinfo" and the results is :
[root@m200 ~]# glxinfo
name of display: :401.0
display: :401  screen: 0
direct rendering: No
server glx vendor string: SGI
server glx version string: 1.2
server glx extensions:
    GLX_ARB_multisample, GLX_EXT_visual_info, GLX_EXT_visual_rating,
    GLX_EXT_import_context, GLX_EXT_texture_from_pixmap, GLX_OML_swap_method,
    GLX_SGI_make_current_read, GLX_SGIS_multisample, GLX_SGIX_hyperpipe,
    GLX_SGIX_swap_barrier, GLX_SGIX_fbconfig, GLX_MESA_copy_sub_buffer
client glx vendor string: SGI
client glx version string: 1.4
client glx extensions:
    GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context,
    GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_MESA_allocate_memory,
    GLX_MESA_copy_sub_buffer, GLX_MESA_swap_control,
    GLX_MESA_swap_frame_usage, GLX_OML_swap_method, GLX_OML_sync_control,
    GLX_SGI_make_current_read, GLX_SGI_swap_control, GLX_SGI_video_sync,
    GLX_SGIS_multisample, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer,
    GLX_SGIX_visual_select_group, GLX_EXT_texture_from_pixmap
GLX version: 1.2
GLX extensions:
    GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_import_context,
    GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_MESA_copy_sub_buffer,
    GLX_OML_swap_method, GLX_SGI_make_current_read, GLX_SGIS_multisample,
    GLX_SGIX_fbconfig, GLX_EXT_texture_from_pixmap
OpenGL vendor string: Mesa project: www.mesa3d.org
OpenGL renderer string: Mesa GLX Indirect
OpenGL version string: 1.2 (1.5 Mesa 6.5.1)
OpenGL extensions:
    GL_ARB_depth_texture, GL_ARB_imaging, GL_ARB_multitexture,
    GL_ARB_point_parameters, GL_ARB_point_sprite, GL_ARB_shadow,
    GL_ARB_shadow_ambient, GL_ARB_texture_border_clamp,
    GL_ARB_texture_cube_map, GL_ARB_texture_env_add,
    GL_ARB_texture_env_combine, GL_ARB_texture_env_crossbar,
    GL_ARB_texture_env_dot3, GL_ARB_texture_mirrored_repeat,
    GL_ARB_texture_non_power_of_two, GL_ARB_texture_rectangle,
    GL_ARB_transpose_matrix, GL_ARB_window_pos, GL_EXT_abgr, GL_EXT_bgra,
    GL_EXT_blend_color, GL_EXT_blend_func_separate, GL_EXT_blend_logic_op,
    GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint,
    GL_EXT_copy_texture, GL_EXT_draw_range_elements, GL_EXT_fog_coord,
    GL_EXT_framebuffer_object, GL_EXT_multi_draw_arrays, GL_EXT_packed_pixels,
    GL_EXT_point_parameters, GL_EXT_polygon_offset, GL_EXT_rescale_normal,
    GL_EXT_secondary_color, GL_EXT_separate_specular_color,
    GL_EXT_shadow_funcs, GL_EXT_stencil_wrap, GL_EXT_subtexture,
    GL_EXT_texture, GL_EXT_texture3D, GL_EXT_texture_edge_clamp,
    GL_EXT_texture_env_add, GL_EXT_texture_env_combine,
    GL_EXT_texture_env_dot3, GL_EXT_texture_lod_bias, GL_EXT_texture_object,
    GL_EXT_texture_rectangle, GL_EXT_vertex_array, GL_APPLE_packed_pixels,
    GL_ATI_texture_env_combine3, GL_ATI_texture_mirror_once,
    GL_ATIX_texture_env_combine3, GL_IBM_texture_mirrored_repeat,
    GL_INGR_blend_func_separate, GL_MESA_pack_invert, GL_MESA_ycbcr_texture,
    GL_NV_blend_square, GL_NV_point_sprite, GL_NV_texgen_reflection,
    GL_NV_texture_rectangle, GL_SGIS_generate_mipmap,
    GL_SGIS_texture_border_clamp, GL_SGIS_texture_edge_clamp,
    GL_SGIS_texture_lod, GL_SGIX_depth_texture, GL_SGIX_shadow,
    GL_SGIX_shadow_ambient, GL_SUN_multi_draw_arrays

   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
----------------------------------------------------------------------
0x22 16 tc  0 16  0 r  y  .  5  6  5  0  0 16  0  0  0  0  0  0 0 None
0x23 16 tc  0 16  0 r  y  .  5  6  5  0  0 16  8 16 16 16  0  0 0 None
0x24 16 tc  0 24  0 r  y  .  5  6  5  8  0 16  8 16 16 16 16  0 0 None
0x25 16 tc  0 24  0 r  .  .  5  6  5  8  0 16  8 16 16 16 16  0 0 None



The informations of graphics hardware and driver are :
[root@m200 ~]# /sbin/lspci |grep VGA
08:01.0 VGA compatible controller: Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a)

[root@m200 ~]# /sbin/lspci
00:00.0 Host bridge: Intel Corporation X58 I/O Hub to ESI Port (rev 22)
00:01.0 PCI bridge: Intel Corporation X58 I/O Hub PCI Express Root Port 1 (rev 22)
00:03.0 PCI bridge: Intel Corporation X58 I/O Hub PCI Express Root Port 3 (rev 22)
00:07.0 PCI bridge: Intel Corporation X58 I/O Hub PCI Express Root Port 7 (rev 22)
00:09.0 PCI bridge: Intel Corporation X58 I/O Hub PCI Express Root Port 9 (rev 22)
00:13.0 PIC: Intel Corporation X58 I/O Hub I/OxAPIC Interrupt Controller (rev 22)
00:14.0 PIC: Intel Corporation X58 I/O Hub System Management Registers (rev 22)
00:16.0 System peripheral: Intel Corporation X58 Chipset QuickData Technology Device (rev 22)
00:16.1 System peripheral: Intel Corporation X58 Chipset QuickData Technology Device (rev 22)
00:16.2 System peripheral: Intel Corporation X58 Chipset QuickData Technology Device (rev 22)
00:16.3 System peripheral: Intel Corporation X58 Chipset QuickData Technology Device (rev 22)
00:16.4 System peripheral: Intel Corporation X58 Chipset QuickData Technology Device (rev 22)
00:16.5 System peripheral: Intel Corporation X58 Chipset QuickData Technology Device (rev 22)
00:16.6 System peripheral: Intel Corporation X58 Chipset QuickData Technology Device (rev 22)
00:16.7 System peripheral: Intel Corporation DMA Engine (rev 22)
00:1a.0 USB Controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #4
00:1a.1 USB Controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #5
00:1a.2 USB Controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #6
00:1a.7 USB Controller: Intel Corporation 82801JI (ICH10 Family) USB2 EHCI Controller #2
00:1b.0 Audio device: Intel Corporation 82801JI (ICH10 Family) HD Audio Controller
00:1c.0 PCI bridge: Intel Corporation 82801JI (ICH10 Family) PCI Express Port 1
00:1c.4 PCI bridge: Intel Corporation 82801JI (ICH10 Family) PCI Express Port 5
00:1c.5 PCI bridge: Intel Corporation 82801JI (ICH10 Family) PCI Express Port 6
00:1d.0 USB Controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #1
00:1d.1 USB Controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #2
00:1d.2 USB Controller: Intel Corporation 82801JI (ICH10 Family) USB UHCI Controller #3
00:1d.7 USB Controller: Intel Corporation 82801JI (ICH10 Family) USB2 EHCI Controller #1
00:1e.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev 90)
00:1f.0 ISA bridge: Intel Corporation 82801JIR (ICH10R) LPC Interface Controller
00:1f.2 IDE interface: Intel Corporation 82801JI (ICH10 Family) 4 port SATA IDE Controller
00:1f.3 SMBus: Intel Corporation 82801JI (ICH10 Family) SMBus Controller
00:1f.5 IDE interface: Intel Corporation 82801JI (ICH10 Family) 2 port SATA IDE Controller
06:00.0 Ethernet controller: Intel Corporation 82574L Gigabit Network Connection
07:00.0 Ethernet controller: Intel Corporation 82574L Gigabit Network Connection
08:01.0 VGA compatible controller: Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a)



Is there anything wrong?
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Here I have another question.
Today I uninstalled the 64bit version and try to install atk-10.8.2_32bit version. In my surprise, this time the vnl works well.
But my computer and system is 64bit(see the following informations), then why can't I install the 64bit version? Is atk-10.8.2_64bit version  only for the IA-64 platforms but not X86_64 ? Thank you!
By the way, I can run the aktpython in my computer both of the atk-10.8.2_32bit version and 64bit version.


My system:
[root@m200 ~]# uname -a
Linux m200 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
[root@m200 ~]# more /proc/version
Linux version 2.6.18-128.el5 (mockbuild@hs20-bc1-7.build.redhat.com) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)) #1 SMP Wed
Dec 17 11:41:38 EST 2008
[root@m200 ~]# lsb_release -a
LSB Version:    :core-3.1-amd64:core-3.1-ia32:core-3.1-noarch:graphics-3.1-amd64:graphics-3.1-ia32:graphics-3.1-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 5.3 (Tikanga)
Release:        5.3
Codename:       Tikanga
[zgh@m200 ~]$ less /proc/cpuinfo
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 26
model name      : Intel(R) Xeon(R) CPU           E5520  @ 2.27GHz
stepping        : 5
cpu MHz         : 1600.000
cache size      : 8192 KB
physical id     : 0
siblings        : 8
core id         : 0
cpu cores       : 4
apicid          : 0
fpu             : yes
fpu_exception   : yes
cpuid level     : 11
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss
ht tm syscall nx rdtscp lm constant_tsc ida pni monitor ds_cpl vmx est tm2 cx16 xtpr popcnt lahf_lm
bogomips        : 4536.89
clflush size    : 64
cache_alignment : 64
address sizes   : 40 bits physical, 48 bits virtual
power management:


4
Installation and License Questions / VNL also closes down directly in the lastest version atk-10.8.2-linux64
« on: October 9, 2010, 11:42 »
Hi, is somebody help?
The following problem still exist in the latest updated atk -10.8.2-linux64.

the VNL can start, but once you open the icon such as viewer, database,custom,builder. the program will shut down directly.
the error message is :

./vnl: line 3:  1815 Segmentation fault      VNL_PATH=$EXEC_DIR/../.. PSEUDOPOTENTIALS_PATH=$EXEC_DIR/../../atkpython/share/pseudopotentials PYTHONHOME=$EXEC_DIR/.. PYTHONPATH= LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/vnl_exec $*

Tip:
here, the version of atk is atk-10.8.2,linux64. (the same problem also appear in the atk-10.8.1)  The linux version is Redhat 5.3 Enterprise x86_64. and my ulimit is :
$ ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 106496
max locked memory       (kbytes, -l) 32
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) unlimited
cpu time               (seconds, -t) unlimited
max user processes              (-u) 106496
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

5
Installation and License Questions / Re: VNL closes down directly when opening Viewer
« on: September 29, 2010, 04:29 »
I have never installed the ATK 2010.02 or 2010.08 in my cluster since I can't download these two versions now. But I had installed ATK-10.8.0 in my cluster and it works well. Now I want to update to the 10.8.1, then  I come to the problem reported above.

6
Installation and License Questions / VNL closes down directly when opening Viewer
« on: September 28, 2010, 10:36 »
hi, everyone.
I also have the problem which had been reported by ipsecog on February 8, 2010, 22:28 in this forum:

I can run VNL fine (it starts) and can open the Editor, Job, and the Analyzer icons, but none of the other tools, such as viewer, database,custom,builder.As soon as I click on these icons, the program just shuts down directly.
Then it reports:
./vnl: line 3:  1815 Segmentation fault      VNL_PATH=$EXEC_DIR/../.. PSEUDOPOTENTIALS_PATH=$EXEC_DIR/../../atkpython/share/pseudopotentials PYTHONHOME=$EXEC_DIR/.. PYTHONPATH= LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/vnl_exec $*

Tip:
here, the version of atk is atk-10.8.1,linux64.  The linux version is Redhat 5.3 Enterprise x86_64. and my ulimit is :
$ ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 106496
max locked memory       (kbytes, -l) 32
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) unlimited
cpu time               (seconds, -t) unlimited
max user processes              (-u) 106496
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

Is there something wrong? and how can I deal with this error?
thankyou！

7
Scripts, Tutorials and Applications / Re: Export geometries to VASP
« on: June 7, 2010, 16:43 »
Thank you for your script. It will be perfect if you also give out an option to write poscar in Cartesian coordinates ^_^

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