added cluster tree timer

tests/cluster_tree_timer.py

@@ -0,0 +1,51 @@
+import argparse
+import math
+from timeit import default_timer as timer
+import numpy as np
+from memory_profiler import profile
+
+from HierMat import *
+
+
+def main(limit, dimension):
+    lim = limit
+    if dimension == 1:
+        points = [((i + 0.5) / lim,) for i in xrange(lim)]
+        supports = {points[i]: (points[i][0] - 0.5/lim, points[i][0] + 0.5/lim) for i in xrange(lim)}
+    elif dimension == 2:
+        points = [(math.sin(float(i)/lim), math.cos(float(j)/lim)) for i in xrange(lim) for j in xrange(lim)]
+        supports = {points[k]: (points[k-1], points[k+1]) for k in xrange(lim * lim - 1)}
+        supports[points[lim*lim-1]] = (points[lim*lim-2], points[0])
+    else:
+        points = [(float(i) / lim, float(j) / lim, float(k) / lim) for i in xrange(lim) for j in
+                  xrange(lim) for k in xrange(lim)]
+        supports = {points[k]: (points[k - 1], points[k + 1]) for k in xrange(lim * lim * lim - 1)}
+        supports[points[lim * lim * lim - 1]] = (points[lim * lim * lim - 2], points[0])
+    grid = Grid(points, supports)
+    cluster = Cluster(grid)
+    rc = RegularCuboid(cluster)
+    start = timer()
+    ct_rc = build_cluster_tree(rc, 1)
+    end = timer()
+    print "ClusterTree build-up with RegularCuboid took {0} seconds.".format(end - start)
+    start = timer()
+    bct_rc_rc = build_block_cluster_tree(ct_rc, ct_rc)
+    end = timer()
+    print "BlockClusterTree build-up with RegularCuboid took {0} seconds." .format(end - start)
+    file_str = '/compute/nem/bct_{0}'.format(limit)
+    export(bct_rc_rc, form='bin', out_file=file_str)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser("HMatrix Profiler")
+    parser.add_argument("dimension", type=int, choices=[1, 2, 3])
+    parser.add_argument("limit", type=int)
+    try:
+        args = parser.parse_args()
+        print '\n' + '*' * 74 + '\n'
+        print 'Starting run with n={0}'.format(args.limit) + '\n'
+        main(args.limit, args.dimension)
+        print '\n' + 'Finished run with n={0}'.format(args.limit)
+        print '\n' + '*' * 74 + '\n'
+    except SystemExit:
+        main(20, 2)

tests/cluster_tree_timer.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+OUTFILE=/compute/nem/cluster_tree_timer.out
+if [ -f ${OUTFILE} ];
+then
+    rm -f ${OUTFILE}
+fi
+for e in `seq 2 20`;
+do
+    python cluster_tree_timer.py 1 $(( 2**${e} )) >> ${OUTFILE}
+done