VMD-L Mailing List

From: Dominique Mias-Lucquin (dominique.mias-lucquin_at_loria.fr)
Date: Tue Apr 18 2023 - 04:46:06 CDT

My mistake, I didn't saw that APT install python3.10-dev didn't worked properly

----- Mail original -----
> De: "Dominique Mias-Lucquin" <dominique.mias-lucquin_at_loria.fr>
> À: "Josh Vermaas" <vermaasj_at_msu.edu>
> Cc: "John Stone" <johns_at_ks.uiuc.edu>, "vmd-l" <vmd-l_at_ks.uiuc.edu>
> Envoyé: Mardi 18 Avril 2023 10:27:39
> Objet: Re: vmd-l: Python crash VMD1.9.4

> 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