Yes, it was on the same machine (stack was 8192kb)
2017-04-27 17:24 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>:
> Nice digging down. I presume that this was on the same machine?
>
> It could be something to do with changes in string handling (in the
> compiler), particularly if you are a fan of flags for recent
> standards.
>
> We should definitely try to streamline our handling of large molecules
> though, and we should be aware of what the largest SMILES string/PDB
> file/etc we can currently handle and try to push back on those sizes.
> Roger talks about "Dalke marks", which is the longest linear alkane a
> toolkit can handle (from Andrew Dalke's use of "C"*LARGE_NUMBER to
> stress test from Python). There's a limit of course, and we don't want
> to trade off too much speed for the common case (e.g. by allocating
> everything on the heap), but it's good to keep an eye on it.
>
> On 26 April 2017 at 18:49, Nicolas Cheron
> <nicolas.cheron.bou...@gmail.com> wrote:
> > After digging a little bit, I found the cause of the problem, and it is
> not
> > (directly) linked to OpenBabel. I have found that a code as simple as:
> > #include <iostream>
> > using namespace std;
> > int main(int nbarg, char * argv[])
> > {
> > string List[400000];
> > return 0;
> > }
> > can compile with g++5.4 but returns a segmentation fault during execution
> > (on Ubuntu 16.04 in VirtualBox). After setting "ulimit -s unlimited", the
> > problem disappears. I don't find any problem with g++4.8. It works with
> an
> > array of 40000 and fails with 400000, I didn't look for the exact
> threshold.
> >
> > One consequence is that if I want to load a protein.pdb file with more
> than
> > 45000 atoms in an obMol object, it can compile but crashes with
> segmentation
> > fault (and again, this can be solved with "ulimit -s unlimited"). If
> there
> > is a way, in future versions, to change the stack limit in OpenBabel, I
> > think it could be useful.
> >
> > Nicolas
> >
> >
> >
> > 2017-04-22 18:17 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>:
> >>
> >> No known problems. Could you file a bug?
> >>
> >> On 22 Apr 2017 1:51 p.m., "Nicolas Cheron"
> >> <nicolas.cheron.bou...@gmail.com> wrote:
> >>>
> >>> Dear all,
> >>>
> >>> I have a code in C++ that uses the OpenBabel library. Everything is
> >>> working smoothly with gcc4.8 or 4.9 (used to compile both OpenBabel
> and my
> >>> code). However, when I am using gcc5 and above (I tried 5.4 and 6.3) I
> found
> >>> some problems. For example, one of them seemed to be that I can not
> load pdb
> >>> files larger than 40,000 atoms as an OBMol (segmentation fault). I am
> using
> >>> v2.4.1 of OpenBabel and tried with Ubuntu 16.04 and 17.04 as well as
> Fedora
> >>> 25.
> >>>
> >>> Is there known problems with gcc5 and above?
> >>>
> >>> Thank you.
> >>>
> >>> Nicolas
> >>>
> >>>
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> >
>
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