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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