VMD-L Mailing List

From: Dominique Mias-Lucquin (dominique.mias-lucquin_at_loria.fr)
Date: Thu Apr 13 2023 - 05:05:45 CDT

Hello and thank you.
I just tried compiling following [ https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!8QZqFDyQucAgwr--8pdhpoHTgrW3ICPmtsy7p_BLRaoFIZhmkFpEcDHu0gUJ5N_R7f7ZlzQx7zgmP-oX4QY0UVuQ8fCQEQ$ | https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!8QZqFDyQucAgwr--8pdhpoHTgrW3ICPmtsy7p_BLRaoFIZhmkFpEcDHu0gUJ5N_R7f7ZlzQx7zgmP-oX4QY0UVuQ8fCQEQ$ ] , 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: [
> https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!8QZqFDyQucAgwr--8pdhpoHTgrW3ICPmtsy7p_BLRaoFIZhmkFpEcDHu0gUJ5N_R7f7ZlzQx7zgmP-oX4QY0UVuQ8fCQEQ$ |
> https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!8QZqFDyQucAgwr--8pdhpoHTgrW3ICPmtsy7p_BLRaoFIZhmkFpEcDHu0gUJ5N_R7f7ZlzQx7zgmP-oX4QY0UVuQ8fCQEQ$ ] . 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 ( [ https://urldefense.com/v3/__https://vmd.robinbetz.com/__;!!DZ3fjg!8QZqFDyQucAgwr--8pdhpoHTgrW3ICPmtsy7p_BLRaoFIZhmkFpEcDHu0gUJ5N_R7f7ZlzQx7zgmP-oX4QY0UVuDt_-74g$ | https://urldefense.com/v3/__https://vmd.robinbetz.com/__;!!DZ3fjg!8QZqFDyQucAgwr--8pdhpoHTgrW3ICPmtsy7p_BLRaoFIZhmkFpEcDHu0gUJ5N_R7f7ZlzQx7zgmP-oX4QY0UVuDt_-74g$ ] ) 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:

> * 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.