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.boulot@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
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
