VMD-L Mailing List

From: He, Xibing (xibing.he_at_pitt.edu)
Date: Fri Feb 09 2024 - 14:52:08 CST

Dear all,

Thank you very much for help and suggestions!
Happy New Year of Dragon!

Xibing He, Ph.D.
Research Scientist
Department of Pharmaceutical Sciences
School of Pharmacy
University of Pittsburgh
________________________________
From: Gumbart, JC <gumbart_at_physics.gatech.edu>
Sent: Thursday, February 8, 2024 11:30 AM
To: He, Xibing <xibing.he_at_pitt.edu>
Cc: Diego Gomes <diego.enry_at_gmail.com>; vmd-l <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: unable to open VMD as normal

Back in my day, a motherboard replacement was a guaranteed “wipe and reinstall”. While I was surprised to learn recently that modern OSes appear to be more tolerant, it’s probably the safest bet here. Even if you eventually get VMD working, who knows what other issues may be lingering?

Just my two cents!

Best,
JC

On Feb 7, 2024, at 12:17 PM, He, Xibing <xibing.he_at_pitt.edu> wrote:

Hi Diego,

(1) The vmd file is similar to what you showed:

[xibing_at_qin lib]$ cd /home2/xibing/vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185-RTXRTRT.opengl/bin
[xibing_at_qin bin]$ ls
vmd
[xibing_at_qin bin]$ head vmd
#!/bin/csh
set defaultvmddir="/home2/xibing/vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185-RTXRTRT.opengl/lib"
set vmdbasename=vmd
#!/bin/csh -f
## In case the installation didn't add these (which means you didn't
# do the 'configure', here's the default settings:
#set defaultvmddir=/usr/local/lib/vmd
#set vmdbasename=vmd
############################################################################

(2) The claimed missing library files are actually in the sub-directory lib:
[xibing_at_qin lib]$ pwd
/home2/xibing/vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185-RTXRTRT.opengl/lib
[xibing_at_qin lib]$ ls -l libospray.so.0
lrwxrwxrwx. 1 xibing wanglab 18 Dec 12 2019 libospray.so.0 -> libospray.so.1.8.5
[xibing_at_qin lib]$ ls -l libospray_common.so.0
lrwxrwxrwx. 1 xibing wanglab 25 Dec 12 2019 libospray_common.so.0 -> libospray_common.so.1.8.5
[xibing_at_qin lib]$ ls -l libembree3.so.3
-rwxr-xr-x. 1 xibing wanglab 38823910 Apr 17 2018 libembree3.so.3
[xibing_at_qin lib]$ ls -l libpng16.so.16
lrwxrwxrwx. 1 xibing wanglab 19 Mar 22 2018 libpng16.so.16 -> libpng16.so.16.34.0

I don't understand why vmd_LINUXAMD64 complains "cannot find files" under the same directory.

(3) The csh and tcsh has already been in stalled:
[root_at_qin xibing]# yum install csh
Loaded plugins: fastestmirror, langpacks
Loading mirror speeds from cached hostfile
 * base: mirror.umd.edu<https://urldefense.com/v3/__http://mirror.umd.edu/__;!!DZ3fjg!7nUdoja-ROSJS7EgzB8PlNiPyjBamMTCpVA4caRuOFrq4myU48iGbOhpKvQQlohJmCCtROIox2fTGG6openllA$ >
 * epel: ftp-nyc.osuosl.org<https://urldefense.com/v3/__http://ftp-nyc.osuosl.org/__;!!DZ3fjg!7nUdoja-ROSJS7EgzB8PlNiPyjBamMTCpVA4caRuOFrq4myU48iGbOhpKvQQlohJmCCtROIox2fTGG7QOJLs1g$ >
 * extras: coresite.mm.fcix.net<https://urldefense.com/v3/__http://coresite.mm.fcix.net/__;!!DZ3fjg!7nUdoja-ROSJS7EgzB8PlNiPyjBamMTCpVA4caRuOFrq4myU48iGbOhpKvQQlohJmCCtROIox2fTGG4wHIMOhw$ >
 * updates: mirror.ash.fastserv.com<https://urldefense.com/v3/__http://mirror.ash.fastserv.com/__;!!DZ3fjg!7nUdoja-ROSJS7EgzB8PlNiPyjBamMTCpVA4caRuOFrq4myU48iGbOhpKvQQlohJmCCtROIox2fTGG6xSwLc2w$ >
Package tcsh-6.18.01-17.el7_9.1.x86_64 already installed and latest version
Nothing to do
[root_at_qin xibing]# yum install tcsh
Loaded plugins: fastestmirror, langpacks
Loading mirror speeds from cached hostfile
 * base: mirror.umd.edu<https://urldefense.com/v3/__http://mirror.umd.edu/__;!!DZ3fjg!7nUdoja-ROSJS7EgzB8PlNiPyjBamMTCpVA4caRuOFrq4myU48iGbOhpKvQQlohJmCCtROIox2fTGG6openllA$ >
 * epel: ftp-nyc.osuosl.org<https://urldefense.com/v3/__http://ftp-nyc.osuosl.org/__;!!DZ3fjg!7nUdoja-ROSJS7EgzB8PlNiPyjBamMTCpVA4caRuOFrq4myU48iGbOhpKvQQlohJmCCtROIox2fTGG7QOJLs1g$ >
 * extras: coresite.mm.fcix.net<https://urldefense.com/v3/__http://coresite.mm.fcix.net/__;!!DZ3fjg!7nUdoja-ROSJS7EgzB8PlNiPyjBamMTCpVA4caRuOFrq4myU48iGbOhpKvQQlohJmCCtROIox2fTGG4wHIMOhw$ >
 * updates: mirror.ash.fastserv.com<https://urldefense.com/v3/__http://mirror.ash.fastserv.com/__;!!DZ3fjg!7nUdoja-ROSJS7EgzB8PlNiPyjBamMTCpVA4caRuOFrq4myU48iGbOhpKvQQlohJmCCtROIox2fTGG6xSwLc2w$ >
Package tcsh-6.18.01-17.el7_9.1.x86_64 already installed and latest version
Nothing to do

(4) I apologize for bothering you and other experts in VMD list, but I have to. The IT team for the Health Sciences in our university (including our School of Pharmacy) know little about Linux. I have been bothering them for two months, but they only managed to get my computer connected to internet. I even went to the School of Computing and Information in our university for help. Their dean told me that his IT guys have the same issue: knowing a lot about windows but a little about Linux. "It's a shame!" he said. Hence, experts from VMD list, like you and Axel, are my only hope now!

Regards,

Xibing He, Ph.D.
Research Scientist
Department of Pharmaceutical Sciences
School of Pharmacy
University of Pittsburgh
________________________________
From: Diego Gomes <diego.enry_at_gmail.com<mailto:diego.enry_at_gmail.com>>
Sent: Wednesday, February 7, 2024 3:13 AM
To: He, Xibing <xibing.he_at_pitt.edu<mailto:xibing.he_at_pitt.edu>>
Cc: vmd-l <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: Re: vmd-l: unable to open VMD as normal

Those libraries are shipped with the VMD you downloaded.
      liboptixu.so.6.5.0 => not found
      liboptix.so.6.5.0 => not found
      libospray.so.0 => not found
      libospray_common.so.0 => not found
      libembree3.so.3 => not found

Based on the outputs you showed, your installation sets the paths to locate them, similarly to the image.
<Screenshot 2024-02-07 at 1.20.30 AM.png>

I vaguely remember having to install "csh" because the "bash" launcher failed... please check if yours has "#!/bin/bash" instead.
If that's the case, make sure to install "csh" or "tcsh" & repeat the VMD install procedure ( configure; cd src ; make install )
Please let me know if that's the case.

Anyway you initially mentioned a few issues after replacing the motherboard and power supply. This issue might be unrelated to VMD.
I reinforce Axel's advice to seek local support to complete the computer repair. (reinstall the OS?)

Friendly,
Diego.