VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 17 2023 - 11:04:54 CDT

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://github.com/jvermaas/vmd-packaging-instructions , 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://github.com/jvermaas/vmd-packaging-instructions. 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://vmd.robinbetz.com/) 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) 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 $PYTHONHOME to <prefix>[:<exec_prefix>]
> 'import site' failed; use -v for traceback
> Segmentation fault
>
>
>
> o vmd194 then python: Work, but freeze the display windows until I
> exit. Nothing I do in python has an effect (molecule loading or
> drawing)
> o vmd194 then gopython: same as vmd194 -python
>
> Does someone knows what append and how to fix it ?
>
> Thank you very much,
>
> Dominique MIAS-LUCQUIN.
>
>
>
>
>
> References
>
> Visible links
> 1. https://urldefense.com/v3/__https:/github.com/jvermaas/vmd-packaging-instructions__;!!HXCxUKc!y-YsaM1Sc443dl06e8ZafqT_47Rr8rPUyBMnX2tFZ2RKgvYHXTJSleDm1gnBFTr5TcvbWLn3uv_SBte8EfPQGlvj4TKl$
> 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$ 

-- 
Research Affiliate, NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           
http://www.ks.uiuc.edu/Research/vmd/