VMD-L Mailing List

From: Dominique Mias-Lucquin (dominique.mias-lucquin_at_loria.fr)
Date: Tue Apr 18 2023 - 03:27:39 CDT

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