VMD-L Mailing List

From: He, Xibing (xibing.he_at_pitt.edu)
Date: Wed Feb 07 2024 - 11:17:51 CST

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
 * epel: ftp-nyc.osuosl.org
 * extras: coresite.mm.fcix.net
 * updates: mirror.ash.fastserv.com
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
 * epel: ftp-nyc.osuosl.org
 * extras: coresite.mm.fcix.net
 * updates: mirror.ash.fastserv.com
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>
Sent: Wednesday, February 7, 2024 3:13 AM
To: He, Xibing <xibing.he_at_pitt.edu>
Cc: vmd-l <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.


Screenshot 2024-02-07 at 1.20.30 AM.png