Allow the python script to run in MPMD mode.

Added a plotting script that does not write BP output.

Author: pnorbert

Tutorial/heat2d/python/decomp.py

@@ -29,7 +29,8 @@ def __init__(self, args):
 
             from mpi4py import MPI
 
-            self.comm_world = MPI.COMM_WORLD
+            color = 3
+            self.comm_world = MPI.COMM_WORLD.Split(color, MPI.COMM_WORLD.Get_rank()) 
             self.size = self.comm_world.Get_size()
             self.rank['world'] = self.comm_world.Get_rank()
             if self.size != (self.nx * self.ny):

Tutorial/heat2d/python/heat_all.py

@@ -36,13 +36,15 @@ def SetupArgs():
 
 
 
-def Plot2D(args, fullshape, step, fontsize, displaysec):
+def Plot2D(args, fr, fullshape, step, fontsize, displaysec):
     data = fr.read(args.varname, [0, 0], fullshape, step, 1)
     gs = gridspec.GridSpec(1, 1)
     fig = plt.figure(1, figsize=(8,10))
     ax = fig.add_subplot(gs[0, 0])
 
-    ax.imshow(data, origin='lower', extent=[0, fullshape[1], 0, fullshape[0]] )
+    print ("data size:", fullshape[0],"x",fullshape[1])
+    print (data.shape)
+    ax.imshow(data[0, :, :], origin='lower', extent=[0, fullshape[1], 0, fullshape[0]] )
 
     for i in range(args.ny):
         y = fullshape[0] / args.ny * i
@@ -69,7 +71,7 @@ def Plot2D(args, fullshape, step, fontsize, displaysec):
 
     # fontsize on plot
     fontsize = 22
-    displaysec = 3
+    displaysec = 0.5
 
     # Parse command line arguments
     args = SetupArgs()
@@ -79,10 +81,10 @@ def Plot2D(args, fullshape, step, fontsize, displaysec):
 
 
     # Read the data from this object
-    fr = adios2.open(args.infile, "r", *mpi.readargs)
+    fr = adios2.open(args.infile, "r", mpi.comm_world, "adios2.xml", "VizInput")
 
     # Calculate difference between steps, and write to this object
-    fw = adios2.open(args.outfile, "w", *mpi.readargs)
+    fw = adios2.open(args.outfile, "w", mpi.comm_world)
 
 
     # Get the ADIOS selections -- equally partition the data if parallelization is requested
@@ -106,7 +108,7 @@ def Plot2D(args, fullshape, step, fontsize, displaysec):
 
 
         if (mpi.rank['world'] == 0) and (args.plot):
-            Plot2D(args, fullshape, step, fontsize, displaysec)
+            Plot2D(args, fr, fullshape, step, fontsize, displaysec)
 
 
         if (step > 0):

Tutorial/heat2d/python/heat_plot.py

@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+from __future__ import absolute_import, division, print_function, unicode_literals
+
+"""
+Example:
+
+$ mpirun -n 1 python ./heat_transfer.py -f inputstream -o outputstream -v varname
+"""
+
+import adios2
+import argparse
+
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.gridspec as gridspec
+import decomp
+
+
+def SetupArgs():
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument("--instream", "-i", help="Name of the input stream", required=True)
+    parser.add_argument("--outfile", "-o", help="Name of the output file", default="screen")
+    parser.add_argument("--varname", "-v", help="Name of variable read", default="T")
+    parser.add_argument("--nompi", "-nompi", help="ADIOS was installed without MPI", action="store_true")
+
+    args = parser.parse_args()
+    args.nx = 1
+    args.ny = 1
+    return args
+
+
+
+def Plot2D(args, fr, data, fullshape, step, fontsize, displaysec):
+    gs = gridspec.GridSpec(1, 1)
+    fig = plt.figure(1, figsize=(8,10))
+    ax = fig.add_subplot(gs[0, 0])
+    ax.imshow(data, origin='lower', extent=[0, fullshape[1], 0, fullshape[0]] )
+
+    for i in range(args.ny):
+        y = fullshape[0] / args.ny * i
+        ax.plot([0, fullshape[1]], [y, y], color='black')
+
+    for i in range(args.nx):
+        x = fullshape[1] / args.nx * i
+        ax.plot([x, x], [0, fullshape[0]], color='black')
+
+    ax.set_title("Timestep = {0}".format(step), fontsize=fontsize)
+    ax.set_xlabel("x")
+    ax.set_ylabel("y")
+
+    plt.ion()
+    if (args.outfile == "screen"):
+        plt.show()
+        plt.pause(displaysec)
+    else:
+        imgfile = args.outfile+str(step)+".png"
+        fig.savefig(imgfile)
+
+    plt.clf()
+
+
+if __name__ == "__main__":
+
+    # fontsize on plot
+    fontsize = 22
+    displaysec = 0.01
+
+    # Parse command line arguments
+    args = SetupArgs()
+
+    # Setup up 2D communicators if MPI is installed
+    mpi = decomp.MPISetup(args)
+
+
+    # Read the data from this object
+    fr = adios2.open(args.instream, "r", mpi.comm_world, "adios2.xml", "VizInput")
+
+    # Get the ADIOS selections -- equally partition the data if parallelization is requested
+    start, size, fullshape = mpi.Partition(fr, args)
+
+    # Read through the steps, one at a time
+    step = 0
+    while (not fr.eof()):
+        data = fr.read(args.varname, start, size, endl=True)
+
+        # Print a couple simple diagnostics
+        avg = np.average(data)
+        std = np.std(data)
+        print("step:{0}, rank: {1}, avg: {2:.3f}, std: {3:.3f}".format(step, mpi.rank['world'], avg, std))
+        Plot2D(args, fr, data, fullshape, step, fontsize, displaysec)
+
+        step += 1
+
+    fr.close()
+