I don't think it's inherently true that multiple mpiruns interfere with each other - we do that routinely, I thought. Any chance that your jobs are doing something like writing to a common directory (like /tmp), and then interfering with each other?
As an aside, you should consider the mpirun argument: -output-filename, --output-filename <filename> Redirect the stdout, stderr, and stddiag of all processes to a process-unique version of the specified file‐ name. Any directories in the filename will automatically be created. Each output file will consist of file‐ name.id<http://name.id>, where the id will be the processes' rank in MPI_COMM_WORLD, left-filled with zero's for correct ordering in listings. A relative path value will be converted to an absolute path based on the cwd where mpirun is executed. Note that this will not work on environments where the file system on compute nodes dif‐ fers from that where mpirun is executed.