VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Tue Feb 06 2024 - 15:07:22 CST

This time you downloaded the source code (vmd-1.9.4a57.src.tar.gz), that's
why "plugins" and "vmd" are separate folders.
( Don't worry about 1.9.58, it is a development version )

Please download one of the binary distributions for Linux and repeat the
"configure" steps.

LINUX_64 (RHEL 7+) OpenGL, CUDA, OptiX RTX, OSPRay
LINUX_64 (RHEL 7+) OpenGL, CUDA, OptiX RTX, OSPRay, RTX RTRT

Friendly,
Diego.

On Tue, Feb 6, 2024 at 2:43 PM He, Xibing <xibing.he_at_pitt.edu> wrote:

> Hi Diego, Axel, and all,
>
> I downloaded vmd-1.9.4a57.src.tar.gz, untared it, configured and installed
> it under my home directory, but unfortunately encountered errors as shown
> below:
>
> [xibing_at_qin temp]$ tar -xzf ../vmd-1.9.4a57.src.tar.gz
> [xibing_at_qin temp]$ ls
> plugins vmd-1.9.4a57
> [xibing_at_qin temp]$ mv plugins vmd-1.9.4a57/
> [xibing_at_qin temp]$ cd vmd-1.9.4a57/
> [xibing_at_qin vmd-1.9.4a57]$ ls
> Announcement bin configure configure.options data distrib doc lib
> LICENSE make_distrib Makefile msvc plugins proteins python README
> scripts shaders src
> [xibing_at_qin vmd-1.9.4a57]$ ls /home2/xibing/softwares/vmd-1.9.4a57
> ls: cannot access /home2/xibing/softwares/vmd-1.9.4a57: No such file or
> directory
> [xibing_at_qin vmd-1.9.4a57]$ mkdir /home2/xibing/softwares/vmd-1.9.4a57
> [xibing_at_qin vmd-1.9.4a57]$ vi configure
> [xibing_at_qin vmd-1.9.4a57]$ ./configure
> using configure.options: LINUXAMD64 OPENGL OPENGLPBUFFER FLTK TK ACTC CUDA
> CXX11 IMD LIBSBALL XINERAMA XINPUT LIBOPTIX LIBOSPRAY LIBTACHYON LIBPNG
> ZLIB VRPN NETCDF COLVARS TCL PYTHON PTHREADS NUMPY SILENT ICC
> [xibing_at_qin vmd-1.9.4a57]$ cd src/
> [xibing_at_qin src]$ make install
> cp: cannot stat ‘../LINUXAMD64/vmd_LINUXAMD64’: No such file or directory
> cp: cannot stat ‘../lib/stride/stride_LINUXAMD64’: No such file or
> directory
> cp: cannot stat ‘../lib/surf/surf_LINUXAMD64’: No such file or directory
> cp: cannot stat ‘../lib/tachyon/tachyon_LINUXAMD64’: No such file or
> directory
> Make sure /home2/xibing/softwares/vmd-1.9.4a57/bin/vmd is in your path.
> VMD installation complete. Enjoy!
> [xibing_at_qin src]$ ls /home2/xibing/softwares/vmd-1.9.4a57/bin/
> vmd
> [xibing_at_qin src]$ /home2/xibing/softwares/vmd-1.9.4a57/bin/vmd
> /home2/xibing/softwares/vmd-1.9.4a57/lib/vmd_LINUX: Command not found.
>
> (1) First of all, after untarring vmd-1.9.4a57.src.tar.gz, why is the
> directory "plugins" is outside of the directory "vmd-1.9.4a57"? It is
> supposed to be inside of vmd-1.9.4a57. I have to manually "mv plugins
> vmd-1.9.4a57/". This is really confusing and will bring troubles to new
> users. It's lucky for me to do the untarring under an empty "temp"
> directory so that I could easily notice this situation. Hope this issue can
> get attention from VMD developers (the web master).
> (2) after doing "make install", I got several error messages about cannot
> copy some files. (as show above)
> (3) the output executable file "vmd" cannot be executed.
> (4) The latest version I see from the VMD download web page is 1.9.4a57,
> so Diego where did you get VMD 1.9.4a58 as shown in your email?
>
> 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:* Tuesday, February 6, 2024 1:25 PM
> *To:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *Cc:* He, Xibing <xibing.he_at_pitt.edu>; vmd-l_at_ks.uiuc.edu <
> vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: unable to open VMD as normal
>
> To complement Axel's comments...
> I wonder what happens if you use the terminal & type "menu main on" after
> opening VMD.
>
> What happened after removing .vmdrc ?
>
> About changing the install path, you may edit the "configure" file. Then
> run:
> ./configure
> cd src
> make install
>
> Here's how I like to edit my "configure" file :
>
> ##############################################################################
> # User modifiable installation parameters, can be overridden by env
> variables
>
> ##############################################################################
>
> # Name of shell script used to start program; this is the name used by
> users
> $install_name = "vmd";
>
> # Directory where VMD startup script is installed, should be in users'
> paths.
> $install_bin_dir="/home/dgomes/software/vmd-1.9.4.58/bin";
>
> # Directory where VMD files and executables are installed
> $install_library_dir="/home/dgomes/software/vmd-1.9.4.58/lib/";
>
> 

-- 
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu