Benchmarks: support all MPI libraries (#3412)

Get the number of MPI threads from the cell system. Remove the "mpi" column from the benchmark results.

maintainer/benchmarks/ferrofluid.py

@@ -45,8 +45,6 @@
 args = parser.parse_args()
 
 # process and check arguments
-n_proc = int(os.environ.get("OMPI_COMM_WORLD_SIZE", 1))
-n_part = n_proc * args.particles_per_core
 measurement_steps = int(np.round(5e5 / args.particles_per_core, -2))
 n_iterations = 20
 assert args.volume_fraction > 0, "volume_fraction must be a positive number"
@@ -69,6 +67,10 @@
 
 print(espressomd.features())
 
+# System
+#############################################################
+system = espressomd.System(box_l=[1, 1, 1])
+
 # Interaction parameters (Lennard-Jones)
 #############################################################
 
@@ -79,13 +81,16 @@
 # System parameters
 #############################################################
 
+n_proc = system.cell_system.get_state()['n_nodes']
+n_part = n_proc * args.particles_per_core
 # volume of N spheres with radius r: N * (4/3*pi*r^3)
 box_l = (n_part * 4. / 3. * np.pi * (lj_sig / 2.)**3
          / args.volume_fraction)**(1. / 3.)
 
 # System
 #############################################################
-system = espressomd.System(box_l=3 * (box_l,))
+system.box_l = 3 * (box_l,)
+
 # PRNG seeds
 #############################################################
 system.random_number_generator_state = list(range(
@@ -118,10 +123,7 @@
         id=i,
         pos=np.random.random(3) *
         system.box_l,
-        rotation=(
-            1,
-            1,
-            1),
+        rotation=(1, 1, 1),
         dipm=args.dipole_moment)
 
 #############################################################
@@ -184,13 +186,13 @@
 
     # write report
     cmd = " ".join(x for x in sys.argv[1:] if not x.startswith("--output"))
-    report = ('"{script}","{arguments}",{cores},"{mpi}",{mean:.3e},'
+    report = ('"{script}","{arguments}",{cores},{mean:.3e},'
               '{ci:.3e},{n},{dur:.1f}\n'.format(
                   script=os.path.basename(sys.argv[0]), arguments=cmd,
                   cores=n_proc, dur=main_tock - main_tick, n=measurement_steps,
-                  mpi="OMPI_COMM_WORLD_SIZE" in os.environ, mean=avg, ci=ci))
+                  mean=avg, ci=ci))
     if not os.path.isfile(args.output):
-        report = ('"script","arguments","cores","MPI","mean","ci",'
+        report = ('"script","arguments","cores","mean","ci",'
                   '"nsteps","duration"\n' + report)
     with open(args.output, "a") as f:
         f.write(report)

maintainer/benchmarks/lj.py

@@ -43,8 +43,6 @@
 args = parser.parse_args()
 
 # process and check arguments
-n_proc = int(os.environ.get("OMPI_COMM_WORLD_SIZE", 1))
-n_part = n_proc * args.particles_per_core
 measurement_steps = int(np.round(5e6 / args.particles_per_core, -2))
 n_iterations = 30
 assert args.volume_fraction > 0, "volume_fraction must be a positive number"
@@ -67,6 +65,10 @@
 
 print(espressomd.features())
 
+# System
+#############################################################
+system = espressomd.System(box_l=[1, 1, 1])
+
 # Interaction parameters (Lennard-Jones)
 #############################################################
 
@@ -77,18 +79,22 @@
 # System parameters
 #############################################################
 
+n_proc = system.cell_system.get_state()['n_nodes']
+n_part = n_proc * args.particles_per_core
 # volume of N spheres with radius r: N * (4/3*pi*r^3)
 box_l = (n_part * 4. / 3. * np.pi * (lj_sig / 2.)**3
          / args.volume_fraction)**(1. / 3.)
 
 # System
 #############################################################
-system = espressomd.System(box_l=3 * (box_l,))
+system.box_l = 3 * (box_l,)
+
 # PRNG seeds
 #############################################################
 system.random_number_generator_state = list(range(
     n_proc * (system._get_PRNG_state_size() + 1)))
 # np.random.seed(1)
+
 # Integration parameters
 #############################################################
 system.time_step = 0.01
@@ -183,13 +189,13 @@
 
     # write report
     cmd = " ".join(x for x in sys.argv[1:] if not x.startswith("--output"))
-    report = ('"{script}","{arguments}",{cores},"{mpi}",{mean:.3e},'
+    report = ('"{script}","{arguments}",{cores},{mean:.3e},'
               '{ci:.3e},{n},{dur:.1f}\n'.format(
                   script=os.path.basename(sys.argv[0]), arguments=cmd,
                   cores=n_proc, dur=main_tock - main_tick, n=measurement_steps,
-                  mpi="OMPI_COMM_WORLD_SIZE" in os.environ, mean=avg, ci=ci))
+                  mean=avg, ci=ci))
     if not os.path.isfile(args.output):
-        report = ('"script","arguments","cores","MPI","mean","ci",'
+        report = ('"script","arguments","cores","mean","ci",'
                   '"nsteps","duration"\n' + report)
     with open(args.output, "a") as f:
         f.write(report)

maintainer/benchmarks/p3m.py

@@ -44,8 +44,6 @@
 args = parser.parse_args()
 
 # process and check arguments
-n_proc = int(os.environ.get("OMPI_COMM_WORLD_SIZE", 1))
-n_part = n_proc * args.particles_per_core
 measurement_steps = int(np.round(5e5 / args.particles_per_core, -1))
 n_iterations = 30
 assert args.prefactor > 0, "prefactor must be a positive number"
@@ -67,6 +65,10 @@
 
 print(espressomd.features())
 
+# System
+#############################################################
+system = espressomd.System(box_l=[1, 1, 1])
+
 # Interaction parameters (Lennard-Jones, Coulomb)
 #############################################################
 
@@ -83,15 +85,18 @@
 # System parameters
 #############################################################
 
+n_proc = system.cell_system.get_state()['n_nodes']
+n_part = n_proc * args.particles_per_core
 # volume of N spheres with radius r: N * (4/3*pi*r^3)
 lj_sig = (lj_sigmas["cation"] + lj_sigmas["anion"]) / 2
 box_l = (n_part * 4. / 3. * np.pi * (lj_sig / 2.)**3
          / args.volume_fraction)**(1. / 3.)
 
 # System
 #############################################################
-system = espressomd.System(box_l=3 * (box_l,))
+system.box_l = 3 * (box_l,)
 system.cell_system.set_domain_decomposition(use_verlet_lists=True)
+
 # PRNG seeds
 #############################################################
 system.random_number_generator_state = list(range(
@@ -191,13 +196,13 @@
 
     # write report
     cmd = " ".join(x for x in sys.argv[1:] if not x.startswith("--output"))
-    report = ('"{script}","{arguments}",{cores},"{mpi}",{mean:.3e},'
+    report = ('"{script}","{arguments}",{cores},{mean:.3e},'
               '{ci:.3e},{n},{dur:.1f}\n'.format(
                   script=os.path.basename(sys.argv[0]), arguments=cmd,
                   cores=n_proc, dur=main_tock - main_tick, n=measurement_steps,
-                  mpi="OMPI_COMM_WORLD_SIZE" in os.environ, mean=avg, ci=ci))
+                  mean=avg, ci=ci))
     if not os.path.isfile(args.output):
-        report = ('"script","arguments","cores","MPI","mean","ci",'
+        report = ('"script","arguments","cores","mean","ci",'
                   '"nsteps","duration"\n' + report)
     with open(args.output, "a") as f:
         f.write(report)

maintainer/benchmarks/runner.sh

@@ -36,11 +36,11 @@ for config in ${configs}; do
   # add minimal features for the benchmarks to run
   sed -i '1 i\#define ELECTROSTATICS\n#define LENNARD_JONES\n#define MASS\n' "${config}"
   # remove checks
-  sed -ri "s/#define ADDITIONAL_CHECKS//" "${config}"
+  sed -ri "s/#define\s+ADDITIONAL_CHECKS//" "${config}"
 done
 
 cat > benchmarks.csv << EOF
-"config","script","arguments","cores","MPI","mean","ci","nsteps","duration"
+"config","script","arguments","cores","mean","ci","nsteps","duration"
 EOF
 
 # run benchmarks

maintainer/benchmarks/suite.sh

@@ -63,7 +63,7 @@ cleanup() {
 # prepare output files
 rm -f benchmarks.log
 cat > benchmarks_suite.csv << EOF
-"commit","config","script","arguments","cores","MPI","mean","ci","nsteps","duration"
+"commit","config","script","arguments","cores","mean","ci","nsteps","duration"
 EOF
 
 # run benchmarks