VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Fri Apr 14 2023 - 03:57:24 CDT

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 https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!-CvepFyavsCY-dCnUwf9CPIRvmc3zJfDzNr6kb0X8AnDxQypY0TyRxFnRaFQCl4GJ9EXPyZA389Nj_zPKNo$ <https://urldefense.com/v3/__https:/github.com/jvermaas/vmd-packaging-instructions__;!!HXCxUKc!y-YsaM1Sc443dl06e8ZafqT_47Rr8rPUyBMnX2tFZ2RKgvYHXTJSleDm1gnBFTr5TcvbWLn3uv_SBte8EfPQGlvj4TKl$> , 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!-CvepFyavsCY-dCnUwf9CPIRvmc3zJfDzNr6kb0X8AnDxQypY0TyRxFnRaFQCl4GJ9EXPyZA389Nj_zPKNo$ <https://urldefense.com/v3/__https:/github.com/jvermaas/vmd-packaging-instructions__;!!HXCxUKc!y-YsaM1Sc443dl06e8ZafqT_47Rr8rPUyBMnX2tFZ2RKgvYHXTJSleDm1gnBFTr5TcvbWLn3uv_SBte8EfPQGlvj4TKl$>. When you run vmd with -python, indeed some of the plugins that depend on tcl behave a bit weirdly, but for scripting use, either the user guide or the documentation for vmd-python (https://urldefense.com/v3/__https://vmd.robinbetz.com/__;!!DZ3fjg!-CvepFyavsCY-dCnUwf9CPIRvmc3zJfDzNr6kb0X8AnDxQypY0TyRxFnRaFQCl4GJ9EXPyZA389NLhCFQ1k$ <https://urldefense.com/v3/__https:/vmd.robinbetz.com/__;!!HXCxUKc!y-YsaM1Sc443dl06e8ZafqT_47Rr8rPUyBMnX2tFZ2RKgvYHXTJSleDm1gnBFTr5TcvbWLn3uv_SBte8EfPQGh-0cgPm$>) 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.