OpenMP in a C++ code with Openbabel

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;

}

(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 <[hidden email]> 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
> <[hidden email]> 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 <[hidden email]>:
>>>
>>> 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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