VMD-L Mailing List

From: He, Xibing (xibing.he_at_pitt.edu)
Date: Tue Feb 06 2024 - 15:28:26 CST

Hi Diego,

Thanks for the hints. I downloaded and tried both of the following:vmd-1.9.4a57.src.tar.gz,vmd-1.9.4a57.src.tar.gz. There is no problem during configuring and making install. However, when execute the install vmd, I got the same problem as before: only the "VMD 1.9.4a55 OpenGL Display" window appears, and the terminal gets stuck:

[xibing_at_qin temp]$ ls
[xibing_at_qin temp]$ tar -xzf ../vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185-RTXRTRT.opengl.tar.gz
[xibing_at_qin temp]$ ls
vmd-1.9.4a55
[xibing_at_qin temp]$ mkdir /home2/xibing/vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185-RTXRTRT.opengl
[xibing_at_qin temp]$ cd vmd-1.9.4a55/
[xibing_at_qin vmd-1.9.4a55]$ ls
Announcement bin configure configure.options data distrib doc lib LICENSE LINUXAMD64 msvc plugins proteins python README scripts shaders src
[xibing_at_qin vmd-1.9.4a55]$ vi configure
[xibing_at_qin vmd-1.9.4a55]$ ./configure
using configure.options: LINUXAMD64 OPENGL OPENGLPBUFFER FLTK TK ACTC CPUDISPATCH CUDA IMD LIBSBALL XINERAMA XINPUT LIBOPTIX LIBOSPRAY LIBTACHYON LIBPNG ZLIB VRPN NETCDF COLVARS TCL PYTHON PTHREADS NUMPY SILENT ICC
[xibing_at_qin vmd-1.9.4a55]$ cd src/
[xibing_at_qin src]$ make install
Make sure /home2/xibing/vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185-RTXRTRT.opengl/bin/vmd is in your path.
VMD installation complete. Enjoy!
[xibing_at_qin src]$ /home2/xibing/vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185-RTXRTRT.opengl/bin/vmd
Info) VMD for LINUXAMD64, version 1.9.4a55 (October 19, 2021)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 64 CPUs, ISA dispatch enabled.
Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 HT
Info) Free system memory: 230GB (91%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator::
Info) [0] GeForce GTX 1080 Ti 28 SM_6.1 1.6 GHz, 11GB RAM SP32 KT AE2 ZC
Info) OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture (4)
OpenGLDisplayDevice) Creating OptiX RTRT context...
OpenGLDisplayDevice) OptiX RTRT context created.
Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info) Compiling OptiX shaders on 1 target GPU...
Info) Dynamically loaded 3 plugins in directory:
Info) /home2/xibing/vmd-1.9.4a55.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185-RTXRTRT.opengl/lib/plugins/LINUXAMD64/molfile

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 4:07 PM
To: He, Xibing <xibing.he_at_pitt.edu>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: unable to open VMD as normal

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<mailto: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<mailto:diego.enry_at_gmail.com>>
Sent: Tuesday, February 6, 2024 1:25 PM
To: Axel Kohlmeyer <akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>>
Cc: He, Xibing <xibing.he_at_pitt.edu<mailto:xibing.he_at_pitt.edu>>; vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu> <vmd-l_at_ks.uiuc.edu<mailto: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<mailto:dgomes_at_auburn.edu>