allow mpirun to run as root during CI

bin/dorie.in

@@ -25,7 +25,11 @@ MPIEXEC_POSTFLAGS = "@MPIEXEC_POSTFLAGS@"
 DORIE_EXECUTABLE = os.path.join(DORIEDIR, "dune/dorie/dorie")
 PARAMETERDIR = os.path.join(DORIEDIR, "doc/default_files")
 DORIE_PYTHON = os.path.join(DORIEDIR, "dune-env")
-MPIRUN = lambda nproc, exe, *args: [k for k in [MPIEXEC,MPIEXEC_NUMPROC_FLAG,str(nproc),MPIEXEC_PREFLAG,str(exe),MPIEXEC_POSTFLAGS] + list(args) if k]
+def MPIRUN(nproc,exe,*args,mpi_flags=None):
+    mpi_flags = [] if not mpi_flags else list(mpi_flags)
+    return [k for k in [MPIEXEC,MPIEXEC_NUMPROC_FLAG,str(nproc)] \
+                        + mpi_flags + [MPIEXEC_PREFLAG,str(exe),
+                        MPIEXEC_POSTFLAGS] + list(args) if k]
 
 def run(args):
     if not os.path.isfile(args["config"]):
@@ -34,7 +38,8 @@ def run(args):
         if args["parallel"] == 1:
             subprocess.check_call([DORIE_EXECUTABLE, args["config"]])
         else:
-            subprocess.check_call(MPIRUN(args["parallel"],DORIE_EXECUTABLE,args["config"]))
+            subprocess.check_call(MPIRUN(args["parallel"], DORIE_EXECUTABLE,
+                                         args["config"], mpi_flags=args["mpi_flags"]))
     except subprocess.CalledProcessError:
         print("Error while running DORiE")
         sys.exit(1)
@@ -56,7 +61,13 @@ def pfg(args):
         if args["parallel"] == 1:
             subprocess.check_call([DORIE_PYTHON, "pf_from_file.py", args["config"]])
         else:
-            subprocess.check_call([DORIE_PYTHON, "pf_from_file.py", args["config"], "--parallel", str(args["parallel"])])
+            if args["mpi_flags"]:
+                mpi_flags = ["--mpi-flags=" + f for f in args["mpi_flags"]]
+            else:
+                mpi_flags = []
+            subprocess.check_call([DORIE_PYTHON, "pf_from_file.py", args["config"],
+                                  "--parallel", str(args["parallel"]),
+                                  *mpi_flags])
     except subprocess.CalledProcessError:
         print("Error while running DORiE")
         sys.exit(1)
@@ -91,7 +102,7 @@ if __name__ == "__main__": # parse command line and call command handler
 
             parser_pfg = subparsers.add_parser('pfg', help="Start parameter field generator.",
                                                description="Start parameter field generator.",
-                                               usage="%(prog)s <config> [-h] [-p [N]]")
+                                               usage="%(prog)s <config> [-h] [-p [N]] [-m=MPI_FLAGS]")
             parser_pfg.add_argument('config',
                                     help="Configuration file for the parameter field generator. "
                                          "Can be created with 'dorie create'.")
@@ -99,15 +110,21 @@ if __name__ == "__main__": # parse command line and call command handler
                                     const=multiprocessing.cpu_count(), type=int, required=False,
                                     help="Run in parallel on N processes. "
                                          "If N is not specified, run on all available CPU threads.")
+            parser_pfg.add_argument('-m','--mpi-flags', action="append", required=False,
+                                    help="Additional flags that are passed to mpirun when run in parallel. "
+                                         "May be specified multiple times.")
             parser_pfg.set_defaults(func=pfg)
 
             parser_run = subparsers.add_parser('run', help="Run DORiE.", description="Run DORiE.",
-                                               usage="%(prog)s <config> [-h] [-p [N]]")
+                                               usage="%(prog)s <config> [-h] [-p [N]] [-m=MPI_FLAGS]")
             parser_run.add_argument('config',help="DORiE configuration file. Can be created with 'dorie create'.")
             parser_run.add_argument('-p','--parallel', metavar='N', nargs='?', default=1,
                                     const=multiprocessing.cpu_count(), type=int, required=False,
                                     help="Run in parallel on N processes. "
                                          "If N is not specified, run on all available CPU threads.")
+            parser_run.add_argument('-m','--mpi-flags', action="append", required=False,
+                                    help="Additional flags that are passed to mpirun when run in parallel. "
+                                         "May be specified multiple times.")
             parser_run.set_defaults(func=run)
 
             parser_plot = subparsers.add_parser('plot', help="Plot a preview of a VTK file created by DORiE.",

python/parfield/wrapper/pf_from_file.py.in

@@ -23,7 +23,11 @@ MPIEXEC_POSTFLAGS = "@MPIEXEC_POSTFLAGS@"
 #
 
 RFG_EXEC = os.path.join(DORIEDIR, "dune/dorie-rfg/dorie-rfg")
-MPIRUN = lambda nproc, exe, *args: [k for k in [MPIEXEC,MPIEXEC_NUMPROC_FLAG,str(nproc),MPIEXEC_PREFLAG,str(exe),MPIEXEC_POSTFLAGS] + list(args) if k]
+def MPIRUN(nproc,exe,*args,mpi_flags=None):
+    mpi_flags = [] if not mpi_flags else list(mpi_flags)
+    return [k for k in [MPIEXEC,MPIEXEC_NUMPROC_FLAG,str(nproc)] \
+                        + mpi_flags + [MPIEXEC_PREFLAG,str(exe),
+                        MPIEXEC_POSTFLAGS] + list(args) if k]
 
 if __name__ == "__main__":
     try: # catch all exceptions we we can output an error message
@@ -33,6 +37,9 @@ if __name__ == "__main__":
             parser.add_argument('param',help='The configuration file holding all parameterization information')
             parser.add_argument('-p','--parallel', metavar='N', nargs='?', default=1, const=multiprocessing.cpu_count(), type=int, required=False,
                                         help="Run in parallel on N processes. If N is not specified, run on all available CPU threads.")
+            parser.add_argument('-m','--mpi-flags', action="append", required=False,
+                                help="Additional flags that are passed to mpirun when run in parallel. "
+                                     "May be specified multiple times.")
             parser.add_argument('--debug',help='Display warnings',action='store_true',required=False)
             args = vars(parser.parse_args())
 
@@ -55,7 +62,7 @@ if __name__ == "__main__":
                     if args["parallel"] == 1:
                         subprocess.check_call([RFG_EXEC,args["param"]])
                     else:
-                        subprocess.check_call(MPIRUN(args["parallel"], RFG_EXEC, args["param"]))
+                        subprocess.check_call(MPIRUN(args["parallel"], RFG_EXEC, args["param"], mpi_flags=args["mpi_flags"]))
                 except subprocess.CalledProcessError:
                     print("FFT Field generator failed")
                     sys.exit(1)

testing/parfield_parallel.mini.in

@@ -2,7 +2,7 @@ include ${CMAKE_BINARY_DIR}/doc/default_files/parfield.ini
 
 __name = pfg_parallel
 _test_command = pfg
-_test_command_options = --parallel
+_test_command_options = --parallel -m=--allow-run-as-root
 _asset_path = "${CMAKE_CURRENT_LIST_DIR}"
 _data_path = {_asset_path}/parfield-data
 _evaluation = reference