Still can't use Jmol

acmemetalfab · #1 25th December 2006, 01:50 AM

I tried using the info provided to me in a previous post in Oct. for running Jmol. I downloaded a RPM and used the command I was instructed to, that being "rpm -Uvh jmol-5-1.src.rpm"; I did this while I was root and while in the directory that contained the RPM. Here's the error message I got:

" 1:jmol warning: user basmith does not exist - using root
warning: group basmith does not exist - using root
warning: user basmith does not exist - using root)
warning: group basmith does not exist - using root
########################################### [100%]
warning: user basmith does not exist - using root
warning: group basmith does not exist - using root"

What am I doing wrong?

acmemetalfab · #2 25th December 2006, 01:55 AM

Oh yeah, I did try the easy way out through Gnome, but it said the following:

"Cannot install source packages"

followed by:

"No packages were given for installation"

This is what happened when I doubled clicked the package on the Gnome desktop.

Jman · #3 25th December 2006, 03:15 AM

Jmol does work, I've done it.

You got the source rpm. Get the noarch one instead.

You also can get the jmol binary package from their download page. Since it's Java you really just need to extract it somewhere (your home's fine) and launch the .sh launcher script.

acmemetalfab · #4 25th December 2006, 05:06 PM

That did work! Just to confirm, what I did was download a binary which is basically just a source code that somebody already compiled for me and then I ran the executable for that precompiled binary by typing in "./jmol.sh". Do I have that right? If so, why do people use RPM instead of just using binarys?
Also, for what it's worth, the program is having a really strained time running on this computer, which is a 4 gig RAM 3 Ghtz P4 hyperthreading. Why does the PC run this program better in Wndows?

Jman · #5 26th December 2006, 10:03 PM

Quote:

Originally Posted by acmemetalfab

That did work! Just to confirm, what I did was download a binary which is basically just a source code that somebody already compiled for me and then I ran the executable for that precompiled binary by typing in "./jmol.sh". Do I have that right? If so, why do people use RPM instead of just using binarys?

Correct.

In this case rpms are not very useful as you can just get a "binary" package, drop it somewhere, run the script, and it works. However you might want to keep track of it being installed along with everything else via rpm.

Quote:

Originally Posted by acmemetalfab

Also, for what it's worth, the program is having a really strained time running on this computer, which is a 4 gig RAM 3 Ghtz P4 hyperthreading. Why does the PC run this program better in Wndows?

What kind of molecule you viewing? The biggest stress test I've done is the protein bits from Folding@Home.

I believe it uses 3D acceleration, so check that you do have direct rendering in Linux. Run glxinfo and see if direct is yes. To get glxinfo

Code:

yum install /usr/bin/glxinfo

acmemetalfab · #6 27th December 2006, 04:05 AM

Thanks again for your useful help Jman. The system I'm looking at is a buckyball electron accepter covalently bound to a heme (heme acts here as nothing more than a wire, really any properly conjugated system would have done) and the heme has a ferrocene electron donor attached to it's other end. Jmol was choking just on the c60, so you see my concern; the triad would have frozen it for sure.
Anyhow, I tried to use YUM as you instructed and I think I got an error. The message is as follows:

[jchili73@localhost ~]$ yum install /usr/bin/glxinfo
Loading "installonlyn" plugin
You need to be root to perform this command.
[jchili73@localhost ~]$ su -
Password:
[root@localhost ~]# yum install /usr/bin/glxinfo
Loading "installonlyn" plugin
Setting up Install Process
Setting up repositories
livna 100% |=========================| 1.1 kB 00:00
updates 100% |=========================| 1.2 kB 00:00
core 100% |=========================| 1.1 kB 00:00
freshrpms 100% |=========================| 1.1 kB 00:00
extras 100% |=========================| 1.1 kB 00:00
Reading repository metadata in from local files
primary.xml.gz 100% |=========================| 1.6 MB 00:04
################################################## 5232/5232
Parsing package install arguments
Nothing to do
[root@localhost ~]#

What does "nothing to do" mean here? Did it not work?

Jman · #7 28th December 2006, 02:37 AM

Quote:

Originally Posted by acmemetalfab

What does "nothing to do" mean here? Did it not work?

Actually, it probably means it is already installed.

Just run

Code:

glxinfo

and look for direct rendering.

What kind of video card do you have?

acmemetalfab · #8 28th December 2006, 09:47 PM

I've got Linux FC 5 on one box that has a 256MB card (nvidia) and I've got FC 6 on two different laptops. I don't know the video card models on the laptops, but they are both 128MB cards and none of the three machines is set to "direct rendering: yes".
I'm guessing that by typing in "yum install /usr/bin/glxinfo" I'm installing something called glxinfo into my usr/bin that allows me to see the status of my video card's settings. If that's true, what must one do to turn the direct rendering to yes? Will it be a "yum install /usr/bin/some-driver-or-other" command?
Thanks!

Jman · #9 29th December 2006, 05:55 AM

Correct, you are installing a tool to examine the acceleration of your X server. Why don't you post the complete output of it from the machine you want accelerated the most.

For nvidia merely enable this repository and

Code:

yum install kmod-nvidia

It and ATI are pretty common cards, but unfortunately can't be had direct from the Fedora project.

acmemetalfab · #10 29th December 2006, 11:45 AM

The thing that really makes this conversation worthwhile for me isn't just that I'm getting this or that driver installed or getting to use a specific program (very worthwhile), but even more usefull is you answering the operational questions so that I may better understand how Linux works. Thanks for taking the time.

Anyhow, I already had Livna installed on the nVidia card computer (the card is a NV38 GeForce FX 59 according to the display settings manager in Fedora) which is a desktop; I'll stick to getting that working first. I ran the code that you recommended and than ran the glxinfo command and I got this:

-bash-3.1# yum install kmod-nvidia
Loading "installonlyn" plugin
Setting up Install Process
Setting up repositories
livna [1/4]
livna 100% |=========================| 951 B 00:00
core [2/4]
core 100% |=========================| 1.1 kB 00:00
updates [3/4]
updates 100% |=========================| 1.2 kB 00:00
extras [4/4]
extras 100% |=========================| 1.1 kB 00:03
Reading repository metadata in from local files
primary.xml.gz 100% |=========================| 355 kB 00:01
updates : ################################################## 1004/1004
Added 1 new packages, deleted 17 old in 1.15 seconds
primary.xml.gz 100% |=========================| 1.8 MB 02:33
extras : ################################################## 5979/5979
Added 13 new packages, deleted 0 old in 4.94 seconds
Parsing package install arguments
Resolving Dependencies
--> Populating transaction set with selected packages. Please wait.
---> Downloading header for kmod-nvidia to pack into transaction set.
kmod-nvidia-1.0.8776-1.2. 100% |=========================| 17 kB 00:00
---> Package kmod-nvidia.i686 0:1.0.8776-1.2.6.18_1.2257.fc5 set to be installed--> Running transaction check
--> Processing Dependency: nvidia-kmod-common >= 1.0.8776 for package: kmod-nvidia
--> Processing Dependency: kernel-i686 = 2.6.18-1.2257.fc5 for package: kmod-nvidia
--> Restarting Dependency Resolution with new changes.
--> Populating transaction set with selected packages. Please wait.
---> Downloading header for kernel to pack into transaction set.
kernel-2.6.18-1.2257.fc5. 100% |=========================| 195 kB 00:00
---> Package kernel.i686 0:2.6.18-1.2257.fc5 set to be installed
---> Downloading header for xorg-x11-drv-nvidia to pack into transaction set.
xorg-x11-drv-nvidia-1.0.8 100% |=========================| 31 kB 00:00
---> Package xorg-x11-drv-nvidia.i386 0:1.0.8776-1.lvn5 set to be updated
--> Running transaction check
--> Populating transaction set with selected packages. Please wait.
---> Package kernel.i686 0:2.6.17-1.2145_FC5 set to be erased
--> Running transaction check
--> Processing Dependency: kernel-i686 = 2.6.17-1.2145_FC5 for package: kmod-ntfs
--> Restarting Dependency Resolution with new changes.
--> Populating transaction set with selected packages. Please wait.
---> Package kmod-ntfs.i686 0:2.1.27-1.2.6.17_1.2145_FC5 set to be erased
--> Running transaction check

Dependencies Resolved

================================================== ===========================
Package Arch Version Repository Size
================================================== ===========================
Installing:
kmod-nvidia i686 1.0.8776-1.2.6.18_1.2257.fc5 livna 1.6 M
Removing:
kernel i686 2.6.17-1.2145_FC5 installed 37 M
Installing for dependencies:
kernel i686 2.6.18-1.2257.fc5 updates 15 M
xorg-x11-drv-nvidia i386 1.0.8776-1.lvn5 livna 4.0 M
Removing for dependencies:
kmod-ntfs i686 2.1.27-1.2.6.17_1.2145_FC5 installed 242 k

Transaction Summary
================================================== ===========================
Install 3 Package(s)
Update 0 Package(s)
Remove 2 Package(s)
Total download size: 21 M
Is this ok [y/N]: y
Downloading Packages:
(1/3): kernel-2.6.18-1.22 100% |=========================| 15 MB 00:49
(2/3): xorg-x11-drv-nvidi 100% |=========================| 4.0 MB 00:13
(3/3): kmod-nvidia-1.0.87 100% |=========================| 1.6 MB 00:06
Running Transaction Test
Finished Transaction Test
Transaction Test Succeeded
Running Transaction
Installing: kernel ######################### [1/5]
Removing : kmod-ntfs ######################### [2/5]
Installing: kmod-nvidia ######################### [3/5]
Installing: xorg-x11-drv-nvidia ######################### [4/5]
FATAL: Module nvidia not found.
Cleanup : kernel ######################### [5/5]

Removed: kernel.i686 0:2.6.17-1.2145_FC5
Dependency Removed: kmod-ntfs.i686 0:2.1.27-1.2.6.17_1.2145_FC5
Installed: kmod-nvidia.i686 0:1.0.8776-1.2.6.18_1.2257.fc5
Dependency Installed: kernel.i686 0:2.6.18-1.2257.fc5 xorg-x11-drv-nvidia.i386 0:1.0.8776-1.lvn5
Complete!
You have new mail in /var/spool/mail/root
-bash-3.1# glxinfo
name of display: :0.0
display: :0 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_OML_swap_method, GLX_SGI_make_current_read,
GLX_SGIS_multisample, GLX_SGIX_hyperpipe, GLX_SGIX_swap_barrier,
GLX_SGIX_fbconfig
client glx vendor string: NVIDIA Corporation
client glx version string: 1.4
client glx extensions:
GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_visual_info,
GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_SGI_video_sync,
GLX_NV_swap_group, GLX_NV_video_out, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer,
GLX_SGI_swap_control, GLX_NV_float_buffer, GLX_ARB_fbconfig_float
GLX version: 1.2
GLX extensions:
GLX_ARB_multisample, GLX_EXT_visual_info, GLX_EXT_visual_rating,
GLX_EXT_import_context, GLX_SGIX_fbconfig, GLX_ARB_get_proc_address
OpenGL vendor string: Mesa project: www.mesa3d.org
OpenGL renderer string: Mesa GLX Indirect
OpenGL version string: 1.2 (1.5 Mesa 6.4.2)
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_texture_border_clamp, GL_ARB_texture_cube_map,
GL_ARB_texture_env_add, GL_ARB_texture_env_combine,
GL_ARB_texture_env_dot3, GL_ARB_texture_mirrored_repeat,
GL_ARB_window_pos, GL_ATI_texture_mirror_once, GL_EXT_texture_env_add,
GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color, GL_EXT_blend_func_separate,
GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_clip_volume_hint,
GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_multi_draw_arrays,
GL_EXT_packed_pixels, GL_EXT_rescale_normal, GL_EXT_secondary_color,
GL_EXT_separate_specular_color, GL_EXT_shadow_funcs, GL_EXT_stencil_wrap,
GL_EXT_texture3D, GL_EXT_texture_edge_clamp, GL_EXT_texture_env_combine,
GL_EXT_texture_env_dot3, GL_EXT_texture_lod_bias, GL_EXT_texture_object,
GL_EXT_vertex_array, GL_HP_occlusion_test, GL_IBM_texture_mirrored_repeat,
GL_NV_blend_square, GL_NV_texgen_reflection, GL_NV_texture_rectangle,
GL_SGIS_generate_mipmap, GL_SGIS_texture_lod, GL_SGIX_depth_texture,
GL_SGIX_shadow
glu version: 1.3
glu extensions:
GLU_EXT_nurbs_tessellator, GLU_EXT_object_space_tess

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
----------------------------------------------------------------------
0x23 24 tc 0 24 0 r y . 8 8 8 0 0 16 0 0 0 0 0 0 0 None
0x24 24 tc 0 24 0 r y . 8 8 8 0 0 16 8 16 16 16 0 0 0 None
0x25 24 tc 0 32 0 r y . 8 8 8 8 0 16 8 16 16 16 16 0 0 None
0x26 24 tc 0 32 0 r . . 8 8 8 8 0 16 8 16 16 16 16 0 0 None
0x27 24 dc 0 24 0 r y . 8 8 8 0 0 16 0 0 0 0 0 0 0 None
0x28 24 dc 0 24 0 r y . 8 8 8 0 0 16 8 16 16 16 0 0 0 None
0x29 24 dc 0 32 0 r y . 8 8 8 8 0 16 8 16 16 16 16 0 0 None
0x2a 24 dc 0 32 0 r . . 8 8 8 8 0 16 8 16 16 16 16 0 0 None
-bash-3.1#

It still says that it isn't direct rendering.
At the risk of asking too much, if Livna wasn't there already, how would one make it available? How does one install or remove repository availability? Can you do that with YUM?

Jman · #11 1st January 2007, 09:13 PM

Quote:

Originally Posted by acmemetalfab

At the risk of asking too much, if Livna wasn't there already, how would one make it available? How does one install or remove repository availability? Can you do that with YUM?

You add it via the procedure I linked to. Remove by removing livna-release package.

You do need to restart to make it take effect. As you seem to have upgraded your kernel, you need a complete system reboot.

acmemetalfab · #12 2nd January 2007, 05:58 PM

I tried to reboot, it told me there was a problem with the Nvidia driver. I tried again to reboot, this time choosing the most recent kernel. It turns out that the most recent kernel wasn't the default, God only knows why. Anyhow, the glxinfo command now says that all is well, and it would appear that I'm good to go. I'll try the Jmol program again.
Thanks for the help!

acmemetalfab · #13 2nd January 2007, 06:03 PM

WOW!!!!!!!!!!!!!!!!!
That made all the difference in the world. The program works better now than I could have expected, thanks!

Jman · #14 4th January 2007, 07:11 AM

You're welcome.

Actually using the dedicated graphics hardware does speed things up.

Good luck with your chemistry.