VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Tue Jan 21 2025 - 10:53:25 CST

Hi Stipe,

Based on the log you attached, you want to look for compiler errors. I
see this in the log you attached:

src/qcschemaplugin.c: In function ‘open_qcschema_read’:
src/qcschemaplugin.c:162:29: error: assignment to ‘int’ from ‘struct
_json_value *’ makes integer from pointer without a cast [-Wint-conversion]
   162 |           data->totalcharge = aux_value->u.object.values[j].value;
       |                             ^
src/qcschemaplugin.c:165:30: error: assignment to ‘int’ from ‘struct
_json_value *’ makes integer from pointer without a cast [-Wint-conversion]
   165 |           data->multiplicity = aux_value->u.object.values[j].value;

To me, this looks like your compiler is pickier than mine, and is
treating something that used to be a warning into a full-blown error.
See https://urldefense.com/v3/__https://gcc.gnu.org/bugzilla/show_bug.cgi?id=106416__;!!DZ3fjg!5GLnwLPtjyTg-CT5k7yY3R-r9_uy2OCAAJZ_NADHJ_Tec_oMZ-UtutjloRTRtbwS4R1C_vcPMMFZXy-rwxM$ which makes this
look like the intended behavior nowadays, which is unfortunate since
this particular plugin hasn't been changed in YEARS. I think you could
make the compiler happy by adding in the cast there:

data->totalcharge = (int) aux_value->u.object.values[j].value;
data->multiplicity = (int) aux_value->u.object.values[j].value;

Or alternatively changing the compiler flags to make that error a
warning again.

-Josh

On 1/21/25 11:18 AM, Stipe Mustać wrote:
> Hello Josh!
>
> Thank you very much for the links you provided. I used them all and I
> can compile nothing. Neither vmd nor vmd-python. I actually realized
> later i have to compile vmd from source and that is what i am trying
> to do the entire day today. I was mostly referring to the guide posted
> by Robin Betz. Unfortunately I can‘t even compile the plugins. The
> error I get when compiling plugins is:
>
> make[2]: *** [Makefile:556:
> ../compile/lib_LINUXAMD64/molfile/qcschemaplugin.o] Error 1
> make[2]: Leaving directory
> '/home/stipe/downloads/vmdpackaging/plugins/molfile_plugin'
> make[1]: *** [Makefile:164: molfilelibs] Error 1
> make[1]: Leaving directory '/home/stipe/downloads/vmdpackaging/plugins'
> make: *** [Make-arch:338: LINUXAMD64] Error 2
>
> I applied that sed command you provided in your guide to switch from
> tcl 8.5 to 8.6. I am sending the entire make output in the attachment.
> I haven’t still installed surf, stride or tachyon. My os is arch linux
> and it uses python 3.13.
>
> Thank you once again.
> Sincerely,
> Stipe Mustac
>
>
> > Am 21.01.2025 um 16:23 schrieb Josh Vermaas <vermaasj_at_msu.edu>:
> >
> > Hi Stipe,
> >
> > How did you install VMD? The default VMD installations that you can
> download from the ks.uiuc.edu website don't come with a python
> interpreter built-in. Instead, if you want python and graphics, you
> end up needing to compile VMD yourself.
> https://urldefense.com/v3/__https://robinbetz.com/blog/2015/01/08/compiling-vmd-with-python-support/__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKLeSGKjP8$
> has a blogpost describing the process, and she's also got a way of
> installing VMD as a python package
> (https://urldefense.com/v3/__https://vmd.robinbetz.com/__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKLw_8HEtI$
> ). I've got packaging instructions for alpha versions of VMD that I
> use within my lab as well.
> https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKL8qbMb2s$
> > Hope this helps!
> >
> > -Josh
> >
> >
> >> On 1/20/25 2:18 PM, Stipe Mustać wrote:
> >> Hello! I am trying to use python interpreter in vmd. The error
> message I keep getting is:
> >>
> >> Info) Starting Python...
> >> 'import site' failed; use -v for traceback
> >> rlwrap: warning: vmd crashed, killed by SIGSEGV (core dumped).
> >> rlwrap itself has not crashed, but for transparency,
> >> it will now kill itself with the same signal
> >>
> >> warnings can be silenced by the --no-warnings (-n) option
> >> Segmentation fault (core dumped)
> >>
> >> I saw a person who posted in this mailing list having the same
> issue in 2023, tried to reproduce all the tutorials and guides, but
> without any success. I would appreciate any help.
> >>
> >> Sincerely,
> >> Stipe Mustac
> >>
> >
> > --
> > 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