Thanks for the tips Thomas. I will try and let you know.
João
On Tue, Apr 11, 2017 at 9:12 PM, Thomas Holder <
thomas.hol...@schrodinger.com> wrote:
> Hi João,
>
> Before diving into the hassle of installing additional compilers (which
> probably won't make a difference) I recommend to get familiar with a
> debugger like gdb and obtain a stack trace of the crash.
>
> To compile PyMOL with debug symbols, do
>
> export DEBUG=1
>
> before running setup.py. Then run PyMOL (actually: python) with gdb. There
> is a bit of a learning curve to get familiar with gdb, but considering that
> you already spend time on this problem and are willing to spend more, I
> think it's worthwhile.
>
> Cheers,
> Thomas
>
> On 11 Apr 2017, at 19:08, João M. Damas <jmda...@itqb.unl.pt> wrote:
>
> > Thanks for the feedback, Folmer!
> >
> > I am using CentOS. I already used --use-msgpackc=no and it did not
> improve. gcc --version gives me 4.8.5 (I cannot update more). Do you think
> it would be worth it to install gcc 4.9? On the install page there was said
> that a regression to 4.4 could work, but I don’t know.
> >
> > Anyone else using CentOS having problems with pymol installation?
> >
> > Thanks,
> > João
> >
> >
> > On Wed, Mar 29, 2017 at 10:35 AM, Folmer Fredslund <folm...@gmail.com>
> wrote:
> > Hi João,
> >
> > On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9
> and "--use-msgpackc=no" I get a working pymol with revision 4170.
> >
> > Have you tried creating a new user and test pymol from that account?
> That should help you identify if it is solely a problem with your own
> account.
> >
> > HTH,
> > Folmer
> >
> >
> > On 2017-03-28 03:15, João M. Damas wrote:
> >> Nobody experiencing the same issues? Any tips on what I may be doing
> wrong on the installation?
> >>
> >> João
> >>
> >> On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas <jmda...@itqb.unl.pt>
> wrote:
> >> Dear all,
> >>
> >> I started experiencing segmentation fault on a pymol that I had
> installed through the omnia channel on conda.
> >>
> >> Then, I decided to install from scratch using this recipe:
> https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN
> >>
> >> Still getting the segmentation fault, so maybe something changed in my
> system and it's conflicting with?
> >>
> >> The segmentation fault is not on launching PyMOL, but rather when I do
> stuff: loading a PDB file, building a fragment. Like this:
> >>
> >> ```
> >> ./pymol: line 3: 28505 Segmentation fault "/usr/bin/python2.7"
> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
> >> ```
> >>
> >> Curiously, when I load a 1.740 session (.pse file I had saved), it
> works (no segmentation fault), I can even perform commands like select and
> stuff, and they work. If I load a more recent 1.803 session, it also seg
> faults:
> >>
> >> ```
> >> Executive: Loading version 1.803 session...
> >> ./pymol: line 3: 29221 Segmentation fault "/usr/bin/python2.7"
> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@"
> >> ```
> >>
> >> Any clues? Am I doing something wrong?
> >>
> >> Thanks,
> >> João
> >>
> >> --
> >> João M. Damas
> >> PhD Student
> >> Protein Modelling Group
> >> ITQB-UNL, Oeiras, Portugal
> >> Tel:+351-214469613
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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