VMD-L Mailing List

From: Dominique Mias-Lucquin (dominique.mias-lucquin_at_loria.fr)
Date: Tue Apr 18 2023 - 08:10:33 CDT

So, i successfully compile my VMD, thank you very much for the help.
Three notes : 1)When using Josh guide, be careful to switch to a57 branch.
2) I had some difficulties installing numpy for python 3.10, so I made the changes necessary to use python 3.8
3) cuda-version compiling had a version issue that I didn't tried to solve, but instead commented CUDA target in the makefile.

Thank you again very much,
Dominique MIAS-LUCQUIN.

----- 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 11:46:06
> Objet: Re: vmd-l: Python crash VMD1.9.4

> 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