VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Apr 12 2023 - 09:57:28 CDT

In the first and third case you are missing the python runtime files that
match the VMD binary.
In the second case, VMD just executed your standard "python" binary (the
VMD/Tcl command prompt will try to execute commands as shell commands, if
there is no equivalent command within the interpreter) and while that is
running, VMD is suspended.

In the past, those python files were occasionally made available for
download, but I suspect that is no longer the case.
As far as I remember, these days you would have to compile VMD from source
to get a VMD binary that can use the python interface.

Axel.

On Wed, Apr 12, 2023 at 9:41 AM Dominique Mias-Lucquin <
dominique.mias-lucquin_at_loria.fr> wrote:

> Hello,
> I'm trying to use the 1.9.4 version of VMD with python in Ubuntu 18.04.
> I encountered several case:
>
> - vmd194 -python :
>
> Info) VMD for LINUXAMD64, version 1.9.4a55 (October 18, 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, 40 CPUs, ISA dispatch enabled.
> Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 AVX512F AVX512CD HT
> Info) Free system memory: 7183MB (22%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator::
> Info) [0] Quadro P620 4 SM_6.1 1.4 GHz, 2.0GB RAM SP32 KT AE2 ZC
> Info) OpenGL renderer: Quadro P620/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)
> 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) /home/dominique/utils/vmd-1.9.4a55/bin/plugins/LINUXAMD64/molfile
> after#0
> Info) Starting Python...
> Could not find platform independent libraries <prefix>
> Could not find platform dependent libraries <exec_prefix>
> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
> 'import site' failed; use -v for traceback
> Segmentation fault
>
>
> - vmd194 then python: Work, but freeze the display windows until I
> exit. Nothing I do in python has an effect (molecule loading or drawing)
> - vmd194 then gopython: same as vmd194 -python
>
> Does someone knows what append and how to fix it ?
> Thank you very much,
> Dominique MIAS-LUCQUIN.
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!4SqhnyesgraKQheVUzbkwVgSKk0hc49vmpZT_y5LHpN0PtvdVj-kDDvFxdJKPg_G4VdsLhaDxGEthFCuTw$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.