VMD-L Mailing List

From: Daipayan Sarkar (sdaipayan_at_gmail.com)
Date: Tue Apr 18 2023 - 10:25:23 CDT

Hi,

Thanks Josh for working on this and updating the instructions. I was
successfully able to compile vmd-1.9.4a57 on my personal workstation
running Ubuntu 22.04 with some minor tweaks. At the time I was testing
this, the git repository Josh prepared, the debian control commit is not
most recent. Perhaps this is why for you Dominique, the 1.9.4a55 compiles.
Here, is the summary of changes I made:

First, I modified debian/control. Note, here I changed the line
Build-depends where python3.8-dev is replaced with python3.10-dev. Next,
in all lines corresponding to Architecture, I removed i386 and only kept
amd64 which is probably why it was defaulting to the intel icpc compiler.
Here is how my debian control looks like:

Section: science
Priority: extra
Maintainer: Josh Vermaas <vermaas2_at_illinois.edu>
Build-Depends: debhelper (>= 10.0.0), libtachyon-mt-0-dev (>=0.99~b6),
python3.10-dev, tcl8.6-dev, tk8.6-dev, libnetcdf-dev, libpng-dev,
python3-numpy, mesa-common-dev,
libglu1-mesa-dev, actc-dev, libxinerama-dev, libfltk1.3-dev, coreutils (>=
8.5), sed (>= 4.2.1)
Standards-Version: 3.9.7
Homepage: http://www.ks.uiuc.edu/Research/vmd/
#Vcs-Git: git://git.debian.org/collab-maint/vmd.git
#Vcs-Browser: https://urldefense.com/v3/__http://git.debian.org/?p=collab-maint*vmd.git;a=summary__;Lw!!DZ3fjg!_KBe2ieM9J82a4bu1SiCWhGAvoHr8nFg7x8IHGcjeaZJOYNY6nn3kbrpodOWAaidGw8BB7w5A3PctLs3a8c$

Package: vmd-plugins
Architecture: amd64
Depends: ${shlibs:Depends}, ${misc:Depends}, vmd | vmd-cuda
Description: The plugins for VMD
 An assortment of plugins to VMD that extend the scope of questions VMD
 can answer. STAMP structural alignment is one thing. CATDCD is another.

Package: vmd
Architecture: amd64
Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
${perl:Depends}
Recommends: vmd-plugins, surf, msms, tachyon, stride, tcllib
Suggests: openbabel
Conflicts: vmd-cuda
Description: Visual Molecular Dynamics
 This is the standard VMD binary, without CUDA.

Package: vmd-cuda
Architecture: amd64
Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
${perl:Depends}
Recommends: vmd-plugins, surf, msms, tachyon, stride, liboptix, libospray,
tcllib
Suggests: openbabel
Conflicts: vmd
Description: Visual Molecular Dynamics
 This is the standard VMD binary, with CUDA. Needs the binary nvidia
drivers.

This should be sufficient for most people running on newer GPU hardware.
But my personal workstation still uses an old graphic card (upgrade long
overdue) which runs on PASCAL architecture. Hence, this step was only
relevant for me, where I modified (commented) the newer compute environment
so that nvcc doesn't complain. These were the changes made to the
vmd/configure script (again this is specific to the old GPU hardware on my
personal workstation)

$arch_nvccflags = "-lineinfo --ptxas-options=-v " .

    "-gencode arch=compute_50,code=compute_50 " .

    "-gencode arch=compute_50,code=sm_50 " .

    "-gencode arch=compute_52,code=sm_52 " .

    "-gencode arch=compute_60,code=compute_60 " .

    "-gencode arch=compute_60,code=sm_60 " .

    #"-gencode arch=compute_70,code=compute_70 " .

    #"-gencode arch=compute_70,code=sm_70 " .

    #"-gencode arch=compute_75,code=sm_75 " .

    #"-gencode arch=compute_80,code=compute_80 " .

    #"-gencode arch=compute_80,code=sm_80 " .

    #"-gencode arch=compute_86,code=sm_86 " .

    #"-gencode arch=compute_89,code=sm_89 " .

    "--ftz=true ";

I hope this helps.

Best,
Daipayan

On Tue, Apr 18, 2023 at 9:58 AM Josh Vermaas <vermaasj_at_msu.edu> wrote:

> Thanks Dominique for your feedback! Now that 3 people have tested this,
> I think I've gotten this sorted for a57. For future people who stumble
> across this on the internet, I've brought in the a57 branch into main,
> and made a release for the instructions.
>
> -Josh
>
> On 4/18/23 9:10 AM, Dominique Mias-Lucquin wrote:
> > So, i successfully compile my VMD, thank you very much for the help.
> > Three notes : 1)When using Josh guide, be careful to switch to a57
> branch.
> > 2) I had some difficulties installing numpy for python 3.10, so I made
> the changes necessary to use python 3.8
> > 3) cuda-version compiling had a version issue that I didn't tried to
> solve, but instead commented CUDA target in the makefile.
> >
> > Thank you again very much,
> > Dominique MIAS-LUCQUIN.
> >
> >
> > ----- Mail original -----
> >> De: "Dominique Mias-Lucquin" <dominique.mias-lucquin_at_loria.fr>
> >> À: "Josh Vermaas" <vermaasj_at_msu.edu>
> >> Cc: "John Stone" <johns_at_ks.uiuc.edu>, "vmd-l" <vmd-l_at_ks.uiuc.edu>
> >> Envoyé: Mardi 18 Avril 2023 11:46:06
> >> Objet: Re: vmd-l: Python crash VMD1.9.4
> >> My mistake, I didn't saw that APT install python3.10-dev didn't worked
> properly
> >>
> >> ----- Mail original -----
> >>> De: "Dominique Mias-Lucquin" <dominique.mias-lucquin_at_loria.fr>
> >>> À: "Josh Vermaas" <vermaasj_at_msu.edu>
> >>> Cc: "John Stone" <johns_at_ks.uiuc.edu>, "vmd-l" <vmd-l_at_ks.uiuc.edu>
> >>> Envoyé: Mardi 18 Avril 2023 10:27:39
> >>> Objet: Re: vmd-l: Python crash VMD1.9.4
> >>> Thank both of you, I making progress !
> >>> Now, it seems that it doesn't find the Python.h file:
> >>>
> >>> compilation terminated.
> >>> make[2]: *** [Makefile:631 : PythonTextInterp.o] Erreur 1
> >>> make[2]: *** Attente des tâches non terminées....
> >>> make[2]: *** [Makefile:631 : VMDTkinterMenu.o] Erreur 1
> >>> Compiling py_selection.C --> py_selection.o ...
> >>> make[2]: *** [Makefile:631 : py_animate.o] Erreur 1
> >>> In file included from py_atomsel.C:19:
> >>> py_commands.h:24:10: fatal error: Python.h: Aucun fichier ou dossier
> de ce type
> >>> 24 | #include "Python.h"
> >>> | ^~~~~~~~~~
> >>> compilation terminated.
> >>> make[2]: *** [Makefile:631 : py_atomsel.o] Erreur 1
> >>> In file included from py_selection.C:20:
> >>> py_commands.h:24:10: fatal error: Python.h: Aucun fichier ou dossier
> de ce type
> >>> 24 | #include "Python.h"
> >>> | ^~~~~~~~~~
> >>> compilation terminated.
> >>> make[2]: *** [Makefile:631 : py_selection.o] Erreur 1
> >>> make[2] : on quitte le répertoire «
> >>> /home/dominique/utils/vmdpackaging/vmd-1.9.4a57/vmd/src »
> >>> make[1]: *** [Makefile:31 : compilevmd] Erreur 2
> >>> make[1] : on quitte le répertoire «
> >>> /home/dominique/utils/vmdpackaging/vmd-1.9.4a57 »
> >>> dh_auto_build: error: make -j1 returned exit code 2
> >>> make: *** [debian/rules:20 : build] Erreur 25
> >>> dpkg-buildpackage: erreur: debian/rules build subprocess returned exit
> status 2
> >>> debuild: fatal error at line 1182:
> >>> dpkg-buildpackage -us -uc -ui -b failed
> >>>
> >>> D.
> >>>
> >>> ----- Mail original -----
> >>>> De: "Josh Vermaas" <vermaasj_at_msu.edu>
> >>>> À: "John Stone" <johns_at_ks.uiuc.edu>, "Dominique Mias-Lucquin"
> >>>> <dominique.mias-lucquin_at_loria.fr>, "vmd-l"
> >>>> <vmd-l_at_ks.uiuc.edu>
> >>>> Envoyé: Lundi 17 Avril 2023 19:59:42
> >>>> Objet: Re: vmd-l: Python crash VMD1.9.4
> >>>> Hi Dominique,
> >>>>
> >>>> I think I found the issue. I've updated my instructions to a57
> >>>> (
> https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions/tree/a57__;!!DZ3fjg!47mI1Y1UommVkU4z8I7tcC8d58kUmVxIeRDX4nTTwpROqYxe8Zmo48MvFatC5IqBxLcr4FEfpDRmCJsML7s$
> >>>> ). The
> >>>> icpc errors crop up in some shells when you have "" in the overall
> >>>> makefile, which means configure fails, which means that the
> >>>> configure.options that ships with VMD (and uses icpc) is the
> >>>> configuration options used. I think now it ought to point you towards
> gcc.
> >>>>
> >>>> -Josh
> >>>>
> >>>> On 4/17/23 12:04 PM, John Stone wrote:
> >>>>> Hi,
> >>>>> "icpc" is the Intel C++ compiler.
> >>>>> You can of course simply compile VMD with GCC ("gcc", "g++", and/or
> "cc", "c++"
> >>>>> on most Linux distributions). If you ensure that "ICC" isn't listed
> in the
> >>>>> flags passed to the VMD configure script, then at least the VMD
> compilations
> >>>>> won't need "icpc" etc.
> >>>>>
> >>>>> Best,
> >>>>> John
> >>>>>
> >>>>>
> >>>>> On Fri, Apr 14, 2023 at 08:57:24AM +0000, Vermaas, Josh wrote:
> >>>>>> Thanks for the feedback. One of my postdocs ran into this too
> recently, so
> >>>>>> I'm looking into it. I hope to have the guide updated to a57
> soon.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> -Josh
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> From: Dominique Mias-Lucquin <dominique.mias-lucquin_at_loria.fr>
> >>>>>> Date: Friday, April 14, 2023 at 3:42 AM
> >>>>>> To: "Vermaas, Josh" <vermaasj_at_msu.edu>
> >>>>>> Cc: vmd-l <vmd-l_at_ks.uiuc.edu>
> >>>>>> Subject: Re: vmd-l: Python crash VMD1.9.4
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> Maybe the issue was from me trying to apply your instructions
> with vmd a57
> >>>>>> instead of a55...
> >>>>>>
> >>>>>> Using a55 sources, it works better, but it fail on a "icpc:
> not found"
> >>>>>> error, icpc for which I dont find any information on the
> guide...
> >>>>>>
> >>>>>> Best regards,
> >>>>>>
> >>>>>> Dominique.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> --------------------------------------------------------------------------
> >>>>>>
> >>>>>> De: "Josh Vermaas" <vermaasj_at_msu.edu>
> >>>>>> À: "Dominique Mias-Lucquin" <dominique.mias-lucquin_at_loria.fr
> >
> >>>>>> Cc: "vmd-l" <vmd-l_at_ks.uiuc.edu>
> >>>>>> Envoyé: Jeudi 13 Avril 2023 15:11:14
> >>>>>> Objet: Re: vmd-l: Python crash VMD1.9.4
> >>>>>>
> >>>>>> Hi Dominique,
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> The line that is failing is this one: dh_auto_configure
> >>>>>> ./configure --build=x86_64-linux-gnu --prefix=/usr
> >>>>>> --includedir=\${prefix}/include --mandir=\${prefix}/share/man
> >>>>>> --infodir=\${prefix}/share/info --sysconfdir=/etc
> --localstatedir=/var
> >>>>>> --disable-silent-rules
> --libdir=\${prefix}/lib/x86_64-linux-gnu
> >>>>>> --libexecdir=\${prefix}/lib/x86_64-linux-gnu
> --disable-maintainer-mode
> >>>>>> --disable-dependency-tracking
> >>>>>> Architecture --build=x86_64-linux-gnu not supported (AIX6_64
> >>>>>> ANDROIDARMV7A BLUEGENEQ BLUEWATERS CRAY_XC CRAY_XK FREEBSD
> FREEBSDAMD64
> >>>>>> LINUX LINUXAMD64 LINUXARM64 LINUXCARMA LINUXPPC64 MACOSX
> MACOSXARM64
> >>>>>> MACOSXX86 MACOSXX86_64 OPENPOWER SUMMIT SUMMITDEV SOLARIS2
> SOLARIS2_64
> >>>>>> SOLARISX86 SOLARISX86_64 WIN32 WIN64)
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> Did you copy over the overarching Makefile? This one has
> >>>>>> "compileplugins" and "compilevmd" as targets. Something
> isn't right,
> >>>>>> since the correct configure line should be something like
> this:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> ./configure LINUXAMD64 OPENGL TK FLTK IMD ACTC XINERAMA
> LIBTACHYON ZLIB
> >>>>>> LIBPNG NETCDF TCL PYTHON PTHREADS NUMPY COLVARS
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> I'm guessing that either that makefile is missing, or that
> you ran
> >>>>>> debuild from a different directory than I intended.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> -Josh
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> From: Dominique Mias-Lucquin <
> dominique.mias-lucquin_at_loria.fr>
> >>>>>> Date: Thursday, April 13, 2023 at 6:05 AM
> >>>>>> To: "Vermaas, Josh" <vermaasj_at_msu.edu>
> >>>>>> Cc: vmd-l <vmd-l_at_ks.uiuc.edu>
> >>>>>> Subject: Re: vmd-l: Python crash VMD1.9.4
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> Hello and thank you.
> >>>>>>
> >>>>>> I just tried compiling following
> >>>>>> [1]
> https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!HXCxUKc!3M8emn8n6V3KuiNsUUtCgwBvqTTmJTnUPUKy4tvMrTTJmYAybfhYhT6TQremjlnjKxogVIvmhVXPoxsn$
> >>>>>> , but i get
> >>>>>> this error that I cant identify
> >>>>>>
> >>>>>> (base) dominique_at_godel>~/utils/vmdpackaging/vmd-1.9.4a57:
> debuild -b
> >>>>>> dpkg-buildpackage -us -uc -ui -b
> >>>>>> dpkg-buildpackage: info: paquet source vmd
> >>>>>> dpkg-buildpackage: info: version source 1.9.4a57-3
> >>>>>> dpkg-buildpackage: info: distribution source focal
> >>>>>> dpkg-buildpackage: info: source changé par Josh Vermaas
> >>>>>> <vermaas2_at_illinois.edu>
> >>>>>> dpkg-source --before-build .
> >>>>>> dpkg-buildpackage: info: architecture hôte amd64
> >>>>>> fakeroot debian/rules clean
> >>>>>> dh clean
> >>>>>> dh_auto_clean
> >>>>>> make -j1 clean
> >>>>>> make[1] : on entre dans le répertoire
> >>>>>> « /home/dominique/utils/vmdpackaging/vmd-1.9.4a57 »
> >>>>>> cd plugins; make clean ; cd ../vmd ; rm -rf plugins; cd src;
> make
> >>>>>> veryclean ; \
> >>>>>> cd ../.. ; rm -rf vmd-cuda
> >>>>>> make[2] : on entre dans le répertoire
> >>>>>> « /home/dominique/utils/vmdpackaging/vmd-1.9.4a57/plugins »
> >>>>>> make[2] : on quitte le répertoire
> >>>>>> « /home/dominique/utils/vmdpackaging/vmd-1.9.4a57/plugins »
> >>>>>> make[2] : on entre dans le répertoire
> >>>>>> « /home/dominique/utils/vmdpackaging/vmd-1.9.4a57/vmd/src »
> >>>>>> /bin/sh: 1: cd: can't cd to ../LINUXAMD64
> >>>>>> /bin/sh: 1: cd: can't cd to ../LINUXAMD64
> >>>>>> make[2] : on quitte le répertoire
> >>>>>> « /home/dominique/utils/vmdpackaging/vmd-1.9.4a57/vmd/src »
> >>>>>> make[1] : on quitte le répertoire
> >>>>>> « /home/dominique/utils/vmdpackaging/vmd-1.9.4a57 »
> >>>>>> dh_clean
> >>>>>> rm -f debian/debhelper-build-stamp
> >>>>>> rm -rf debian/.debhelper/
> >>>>>> rm -f debian/vmd-cuda.debhelper.log
> >>>>>> debian/vmd-plugins.debhelper.log debian/vmd.debhelper.log
> >>>>>> rm -f -- debian/vmd-plugins.substvars
> debian/vmd.substvars
> >>>>>> debian/vmd-cuda.substvars debian/files
> >>>>>> rm -fr -- debian/vmd-plugins/ debian/tmp/ debian/vmd/
> >>>>>> debian/vmd-cuda/
> >>>>>> find . \( \( \
> >>>>>> \( -path .\*/.git -o -path .\*/.svn -o -path
> .\*/.bzr -o
> >>>>>> -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path
> .\*/_darcs \)
> >>>>>> -prune -o -type f -a \
> >>>>>> \( -name '#*#' -o -name '.*~' -o -name '*~'
> -o -name
> >>>>>> DEADJOE \
> >>>>>> -o -name '*.orig' -o -name '*.rej' -o -name
> '*.bak' \
> >>>>>> -o -name '.*.orig' -o -name .*.rej -o -name
> '.SUMS' \
> >>>>>> -o -name TAGS -o \( -path '*/.deps/*' -a
> -name '*.P' \)
> >>>>>> \
> >>>>>> \) -exec rm -f {} + \) -o \
> >>>>>> \( -type d -a -name autom4te.cache -prune
> -exec rm -rf
> >>>>>> {} + \) \)
> >>>>>> debian/rules build
> >>>>>> dh build
> >>>>>> dh_update_autotools_config
> >>>>>> dh_auto_configure
> >>>>>> ./configure --build=x86_64-linux-gnu --prefix=/usr
> >>>>>> --includedir=\${prefix}/include --mandir=\${prefix}/share/man
> >>>>>> --infodir=\${prefix}/share/info --sysconfdir=/etc
> --localstatedir=/var
> >>>>>> --disable-silent-rules
> --libdir=\${prefix}/lib/x86_64-linux-gnu
> >>>>>> --libexecdir=\${prefix}/lib/x86_64-linux-gnu
> --disable-maintainer-mode
> >>>>>> --disable-dependency-tracking
> >>>>>> Architecture --build=x86_64-linux-gnu not supported (AIX6_64
> >>>>>> ANDROIDARMV7A BLUEGENEQ BLUEWATERS CRAY_XC CRAY_XK FREEBSD
> FREEBSDAMD64
> >>>>>> LINUX LINUXAMD64 LINUXARM64 LINUXCARMA LINUXPPC64 MACOSX
> MACOSXARM64
> >>>>>> MACOSXX86 MACOSXX86_64 OPENPOWER SUMMIT SUMMITDEV SOLARIS2
> SOLARIS2_64
> >>>>>> SOLARISX86 SOLARISX86_64 WIN32 WIN64)
> >>>>>> Current working directory:
> >>>>>> /home/dominique/utils/vmdpackaging/vmd-1.9.4a57
> >>>>>> vmd
> >>>>>> dh_auto_configure: error: ./configure
> --build=x86_64-linux-gnu
> >>>>>> --prefix=/usr --includedir=\${prefix}/include
> >>>>>> --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info
> >>>>>> --sysconfdir=/etc --localstatedir=/var --disable-silent-rules
> >>>>>> --libdir=\${prefix}/lib/x86_64-linux-gnu
> >>>>>> --libexecdir=\${prefix}/lib/x86_64-linux-gnu
> --disable-maintainer-mode
> >>>>>> --disable-dependency-tracking returned exit code 255
> >>>>>> make: *** [debian/rules:20 : build] Erreur 2
> >>>>>> dpkg-buildpackage: erreur: debian/rules build subprocess
> returned exit
> >>>>>> status 2
> >>>>>> debuild: fatal error at line 1182:
> >>>>>> dpkg-buildpackage -us -uc -ui -b failed
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> --------------------------------------------------------------------------
> >>>>>>
> >>>>>> De: "Josh Vermaas" <vermaasj_at_msu.edu>
> >>>>>> À: "Dominique Mias-Lucquin" <
> dominique.mias-lucquin_at_loria.fr>, "vmd-l"
> >>>>>> <vmd-l_at_ks.uiuc.edu>
> >>>>>> Envoyé: Mercredi 12 Avril 2023 16:30:56
> >>>>>> Objet: Re: vmd-l: Python crash VMD1.9.4
> >>>>>>
> >>>>>> Hi Dominique,
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> Is this the standard precompiled VMD downloaded from the
> UIUC site? If
> >>>>>> so, that usually ends poorly in my experience. In my lab,
> we compile
> >>>>>> VMD ourselves to use system python, with the rough outline
> of how to
> >>>>>> do this for newer Ubuntu versions (we use 22.04 in the
> lab) here:
> >>>>>> [2]
> https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!HXCxUKc!3M8emn8n6V3KuiNsUUtCgwBvqTTmJTnUPUKy4tvMrTTJmYAybfhYhT6TQremjlnjKxogVIvmhVXPoxsn$
> >>>>>> . When you
> >>>>>> run vmd with -python, indeed some of the plugins that
> depend on tcl
> >>>>>> behave a bit weirdly, but for scripting use, either the
> user guide or
> >>>>>> the documentation for vmd-python
> >>>>>> ([3]
> https://urldefense.com/v3/__https://vmd.robinbetz.com/__;!!HXCxUKc!3M8emn8n6V3KuiNsUUtCgwBvqTTmJTnUPUKy4tvMrTTJmYAybfhYhT6TQremjlnjKxogVIvmhbaK7NUf$
> >>>>>> ) are
> >>>>>> usually pretty good for figuring out what you want to do.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> -Josh
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Dominique
> Mias-Lucquin
> >>>>>> <dominique.mias-lucquin_at_loria.fr>
> >>>>>> Date: Wednesday, April 12, 2023 at 9:58 AM
> >>>>>> To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> >>>>>> Subject: vmd-l: Python crash VMD1.9.4
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> Hello,
> >>>>>>
> >>>>>> I'm trying to use the 1.9.4 version of VMD with python in
> Ubuntu
> >>>>>> 18.04.
> >>>>>>
> >>>>>> I encountered several case:
> >>>>>>
> >>>>>> o vmd194 -python :
> >>>>>>
> >>>>>> Info) VMD for LINUXAMD64, version 1.9.4a55 (October 18,
> 2021)
> >>>>>> Info)
> >>>>>>
> https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!!HXCxUKc!3M8emn8n6V3KuiNsUUtCgwBvqTTmJTnUPUKy4tvMrTTJmYAybfhYhT6TQremjlnjKxogVIvmhQf0XerO$
> >>>>>> 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 $PYTHONHOME to <prefix>[:<exec_prefix>]
> >>>>>> 'import site' failed; use -v for traceback
> >>>>>> Segmentation fault
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> o vmd194 then python: Work, but freeze the display
> windows until I
> >>>>>> exit. Nothing I do in python has an effect (molecule
> loading or
> >>>>>> drawing)
> >>>>>> o vmd194 then gopython: same as vmd194 -python
> >>>>>>
> >>>>>> Does someone knows what append and how to fix it ?
> >>>>>>
> >>>>>> Thank you very much,
> >>>>>>
> >>>>>> Dominique MIAS-LUCQUIN.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> References
> >>>>>>
> >>>>>> Visible links
> >>>>>> 1.
> >>>>>>
> https://urldefense.com/v3/__https:/github.com/jvermaas/vmd-packaging-instructions__;!!HXCxUKc!y-YsaM1Sc443dl06e8ZafqT_47Rr8rPUyBMnX2tFZ2RKgvYHXTJSleDm1gnBFTr5TcvbWLn3uv_SBte8EfPQGlvj4TKl$
> >>>>>> 2.
> >>>>>>
> https://urldefense.com/v3/__https:/github.com/jvermaas/vmd-packaging-instructions__;!!HXCxUKc!y-YsaM1Sc443dl06e8ZafqT_47Rr8rPUyBMnX2tFZ2RKgvYHXTJSleDm1gnBFTr5TcvbWLn3uv_SBte8EfPQGlvj4TKl$
> >>>>>> 3.
> >>>>>>
> https://urldefense.com/v3/__https:/vmd.robinbetz.com/__;!!HXCxUKc!y-YsaM1Sc443dl06e8ZafqT_47Rr8rPUyBMnX2tFZ2RKgvYHXTJSleDm1gnBFTr5TcvbWLn3uv_SBte8EfPQGh-0cgPm$
> >>>> --
> >>>> Josh Vermaas
> >>>>
> >>>> vermaasj_at_msu.edu
> >>>> Assistant Professor, Plant Research Laboratory and Biochemistry and
> Molecular
> >>>> Biology
> >>>> Michigan State University
> >>>> vermaaslab.github.io
>
> --
> Josh Vermaas
>
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and
> Molecular Biology
> Michigan State University
> vermaaslab.github.io
>
>