There are no super secret (the work is published
http://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.5b00886), I only thought
it would by default reply to the list.
Thank you for your answer. I had the feeling that there was something wrong
coming from OB and different threads, but I wanted to be sure. This
clarifies everything.
Do you know if I will face the same problem if I try with MPI? (I have no
expertise with MPI so the answer may be obvious in one way or another).
Nicolas
2016-11-08 11:16 GMT+01:00 Noel O'Boyle <baoille...@gmail.com>:
> (ccing to list but avoiding scientific details in case they are super
> secret)
>
> Quote: "I don't need OpenMP on the OpenBabel side. My project
> [REDACTED SUPER SECRET DETAILS] so the code is basically a big loop.
> The code uses OpenBabel and for now it runs on a single core. If I
> want to parallelize it on 4 cores I am using:
> ./Run.exe File.input &
> ./Run.exe File.input &
> ./Run.exe File.input &
> ./Run.exe File.input
>
> I would prefer using OpenMP to launch only one instance of the code.
> Regarding the warning, since the code works when I set "export
> OMP_NUM_THREADS=1" I don't think it is the cause of the problem.
>
> Actually, I have a feeling that you are running into a fundamental
> limitation of OB. It's not threadsafe. I can't say for certain that
> this is the cause, but OB has some global variables which will be
> shared between threads in a way that is not good, and it's not trivial
> for us to fix this (though we would certainly like to). I don't know
> of a way around this at the moment, apart from calling it 4 times
> separately. :-/
>
> - Noel
>
> On 8 November 2016 at 09:42, Noel O'Boyle <baoille...@gmail.com> wrote:
> > Sorry - forgot to reply.
> >
> > Do you need OpenMP on the Open Babel side (i.e. if not, turn off it
> > off)? Your original email didn't make it clear whether it was just the
> > client code that needed OpenMP, or you are compiling OB with OpenMP
> > support also.
> >
> > The warning may indicate that your BABEL_DATADIR is not set correctly,
> > though I'm not sure.
> >
> > Regards,
> > - Noel
> >
> > On 8 November 2016 at 07:46, Nicolas Cheron
> > <nicolas.cheron.bou...@gmail.com> wrote:
> >> Dear all,
> >>
> >> Did anyone ever manage to use both openMP and openBabel in the same
> code?
> >>
> >> Thank you.
> >>
> >> Nicolas
> >>
> >>
> >> 2016-10-29 9:11 GMT+02:00 Nicolas Cheron <nicolas.cheron.boulot@gmail.
> com>:
> >>>
> >>> Dear all,
> >>>
> >>> I would like to use OpenMP with a code that uses the Openbabel library,
> >>> and I am facing problems. I have copied an example of a simple code
> below. I
> >>> have tried with Openbabel 2.3.2 and 2.4.1. I am compiling with:
> >>>
> >>> g++ -O3 -Wall -std=c++11 -Wno-uninitialized
> >>> -I/home/nicolas/Programs/Openbabel_2.3.2/include/openbabel-2.0 -lm
> -fopenmp
> >>> -c File.cpp -o File.o
> >>> g++ File.o -o File.exe -rdynamic
> >>> /home/nicolas/Programs/Openbabel_2.3.2/lib/libopenbabel.so
> >>> -Wl,-rpath,/home/nicolas/Programs/Openbabel_2.3.2/lib -fopenmp
> >>>
> >>> When using the following, it works and produces 20 files
> (Ligand_0_x.xyz
> >>> with x from 0 to 19):
> >>> export OMP_NUM_THREADS=1
> >>> ./File.exe
> >>>
> >>> When I set export OMP_NUM_THREADS=4, it fails with:
> >>> ==============================
> >>> *** Open Babel Warning in Translate
> >>> Cannot perform atom type translation: table cannot find requested
> types.
> >>> Erreur de segmentation (core dumped)
> >>>
> >>>
> >>> Can someone please help me fixing it. I am now wondering if it is
> possible
> >>> to mix OpenMP and Openbabel.
> >>>
> >>> Thank you
> >>>
> >>> Nicolas
> >>>
> >>>
> >>>
> >>> ***********************************************
> >>> #include <openbabel/mol.h>
> >>> #include <openbabel/obconversion.h>
> >>> #include <openbabel/forcefield.h>
> >>> #include <openbabel/atom.h>
> >>> #include <omp.h>
> >>>
> >>> using namespace std;
> >>>
> >>> int main(int nbarg, char * argv[])
> >>> {
> >>> #pragma omp parallel for
> >>> for (int x=0 ; x < 20 ; x++) {
> >>> //Convert thread index and x in string
> >>> ostringstream threadFlow;
> >>> threadFlow << omp_get_thread_num();
> >>> string thread = threadFlow.str();
> >>> ostringstream xFlow;
> >>> xFlow << x;
> >>> string counter = xFlow.str();
> >>>
> >>> //Read the input file
> >>> OpenBabel::OBMol obMol;
> >>> OpenBabel::OBConversion obConversion;
> >>> OpenBabel::OBFormat *format =
> >>> obConversion.FormatFromExt("Molecule.pdb");
> >>> obConversion.SetInFormat(format);
> >>> obConversion.ReadFile(&obMol, "Molecule.pdb");
> >>>
> >>> //Convert the object in xyz
> >>> string outputFileName = "Ligand_" + thread + "_" + counter +
> ".xyz";
> >>> obConversion.SetOutFormat("xyz");
> >>> obMol.SetTitle(outputFileName);
> >>> obConversion.WriteFile(&obMol, outputFileName);
> >>> }
> >>> return 0;
> >>> }
> >>>
> >>>
> >>>
> >>>
> >>
> >>
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