VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Tue Apr 18 2023 - 09:20:51 CDT

Thanks Dominique for your feedback! Now that 3 people have tested this,
I think I've gotten this sorted for a57. For future people who stumble
across this on the internet, I've brought in the a57 branch into main,
and made a release for the instructions.

-Josh

On 4/18/23 9:10 AM, Dominique Mias-Lucquin wrote:
> 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 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io