From: Dominique Mias-Lucquin (dominique.mias-lucquin_at_loria.fr)
Date: Fri Apr 14 2023 - 02:41:53 CDT

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__;!!HXCxUKc!y-YsaM1Sc443dl06e8ZafqT_47Rr8rPUyBMnX2tFZ2RKgvYHXTJSleDm1gnBFTr5TcvbWLn3uv_SBte8EfPQGlvj4TKl$
> |
> https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!8frIU54xwF6Kb0LJXitQkM-s0c5LbTEyeZj5lbkLXIU0mPiQ05Yki8Np0_4ieB7x6RbM8dKPwA_Q23jDQRgUKknFFcoUnA$ ] , 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__;!!HXCxUKc!y-YsaM1Sc443dl06e8ZafqT_47Rr8rPUyBMnX2tFZ2RKgvYHXTJSleDm1gnBFTr5TcvbWLn3uv_SBte8EfPQGlvj4TKl$
>> |
>> https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!8frIU54xwF6Kb0LJXitQkM-s0c5LbTEyeZj5lbkLXIU0mPiQ05Yki8Np0_4ieB7x6RbM8dKPwA_Q23jDQRgUKknFFcoUnA$ ] . 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/__;!!HXCxUKc!y-YsaM1Sc443dl06e8ZafqT_47Rr8rPUyBMnX2tFZ2RKgvYHXTJSleDm1gnBFTr5TcvbWLn3uv_SBte8EfPQGh-0cgPm$
>> | https://urldefense.com/v3/__https://vmd.robinbetz.com/__;!!DZ3fjg!8frIU54xwF6Kb0LJXitQkM-s0c5LbTEyeZj5lbkLXIU0mPiQ05Yki8Np0_4ieB7x6RbM8dKPwA_Q23jDQRgUKkn43JPPuw$ ] ) 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.