topic If you aren't using mpi then in Intel® MPI Library

OpenMP problem with Threads Number

Rodrigo_Antonio_F_ — Mon, 06 Apr 2015 14:50:26 GMT

Hi,

My program calls a function and it receives two files name that are build in for command. Its goal is read a number of mol2 files and create pdbqt files. Therefore, I create a loop in which each file mol2 file name is created pdbqt file. My part of the code is below:

#pragma omp parallel shared(m,mol2_size) private(path_file_mol2, path_file_pdbqt, file_pdbqt, base_file_name)
{           	
		path_file_mol2 = (char*)malloc(sizeof(char)*MAX_PATH_FILE_NAME);
		path_file_pdbqt = (char*)malloc(sizeof(char)*MAX_PATH_FILE_NAME);
		file_pdbqt = (char*)malloc(sizeof(char)*MAX_FILE_NAME);
		base_file_name  = (char*)malloc(sizeof(char)*MAX_FILE_NAME);     		    	
		#pragma omp for 		
		for (m = 0; m < mol2_size; m++){
			//Obtaing base file name. This is file name without its extension
			set_base_file_name(base_file_name, all_mol2_files.file_name, ex_mol2);
			strcpy(file_pdbqt, base_file_name);
			add_ext_file_name(file_pdbqt, ex_pdbqt);
			//mol2 file
			strcpy(path_file_mol2, param->path_mol2);
			strcat(path_file_mol2, all_mol2_files.file_name);
			//pdbqt files		
			strcpy(path_file_pdbqt, param->path_compounds);
			strcat(path_file_pdbqt, file_pdbqt);
			call_prepare_ligand(param, path_file_mol2, path_file_pdbqt);

		}
		free(base_file_name);
		free(file_pdbqt);
		free(path_file_pdbqt);		
		free(path_file_mol2);		    		
}

I can not understand why my code is working fine when threads number is equal than number of files. In my test, I have 4 mol2 files. When I execute my program with mpirun -np 4 /home/faccioli/workspace/drugdesign/virtualscreening/build/./prepare_ligand config.conf it works fine: 4 pdbq files are created. However, when I execute mpirun -np 2 /home/faccioli/workspace/drugdesign/virtualscreening/build/./prepare_ligand config.conf 2 pdbqt files are created.

I attached my entire code.

I appreciate any help.

Best regards,

Are you running mpi thread

TimP — Sat, 11 Apr 2015 11:51:46 GMT

Are you running mpi thread funneled mode (openmp within each rank under mpi)? Your mpirun np parameter controls number of ranks while omp_num_threads must be set to number of threads per rank.

I hope you're not trying to make each thread of each rank open a file. I'm on a PadFone without internet so can't examine your full example.

Hi,

Rodrigo_Antonio_F_ — Sun, 12 Apr 2015 19:11:57 GMT

Hi,

Thanks for your attention.

I have used OpenMP instead of MPI. In fact I will run it in shared memory.

I understood about mpirun program. Therefore, I have to set omp_num_threads using it as environment variable. I use Debian, export OMP_NUM_THREADS=number, where number means the number of threads that I want to run.

Although I have looked, I could not figure out if it is possible to set omp_num_threads in run time. Is it possible?

Best regards,

If you aren't using mpi then

TimP — Mon, 13 Apr 2015 09:05:35 GMT

If you aren't using mpi then mpirun isn't useful, nor is this forum a good choice.

Besides environment variable, you have the possibilities of omp_set_num_threads function call and num_threads clause in omp parallel.

Hi,

Rodrigo_Antonio_F_ — Mon, 13 Apr 2015 12:13:19 GMT

Hi,

I appreciate your help.

Best regards,