Gajdusek cleaning

docs.it4i/anselm/software/mpi/mpi4py-mpi-for-python.md

@@ -20,7 +20,7 @@ $ ml av Python/
    Python/2.7.11-foss-2016a    Python/3.5.2-foss-2016a    Python/3.5.1
    Python/2.7.9-foss-2015g     Python/3.4.3-intel-2015b   Python/2.7.9
    Python/2.7.11-intel-2015b   Python/3.5.2
-   
+
 $ ml av OpenMPI/
 --------------------------------------- /apps/modules/mpi --------------------------
 OpenMPI/1.8.6-GCC-4.4.7-system   OpenMPI/1.8.8-GNU-4.9.3-2.25  OpenMPI/1.10.1-GCC-4.9.3-2.25
@@ -28,7 +28,8 @@ OpenMPI/1.8.6-GNU-5.1.0-2.25     OpenMPI/1.8.8-GNU-5.1.0-2.25  OpenMPI/1.10.1-GN
     OpenMPI/1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25   OpenMPI/2.0.2-GCC-6.3.0-2.27
 ```
 
-!!! Warning ""
+!!! Warning "Flavours"
+
     * modules Python/x.x.x-intel... - intel MPI
     * modules Python/x.x.x-foss...  - OpenMPI
     * modules Python/x.x.x - without MPI
@@ -37,8 +38,8 @@ OpenMPI/1.8.6-GNU-5.1.0-2.25     OpenMPI/1.8.8-GNU-5.1.0-2.25  OpenMPI/1.10.1-GN
 
 You need to import MPI to your python program. Include the following line to the python script:
 
-```cpp
-    from mpi4py import MPI
+```python
+from mpi4py import MPI
 ```
 
 The MPI4Py enabled python programs [execute as any other OpenMPI](Running_OpenMPI/) code.The simpliest way is to run
@@ -57,43 +58,43 @@ $ mpiexec python hello_world.py
 
 ### Hello World!
 
-```cpp
-    from mpi4py import MPI
+```python
+from mpi4py import MPI
 
-    comm = MPI.COMM_WORLD
+comm = MPI.COMM_WORLD
 
-    print "Hello! I'm rank %d from %d running in total..." % (comm.rank, comm.size)
+print "Hello! I'm rank %d from %d running in total..." % (comm.rank, comm.size)
 
-    comm.Barrier()   # wait for everybody to synchronize
+comm.Barrier()   # wait for everybody to synchronize
 ```
 
 ### Collective Communication With NumPy Arrays
 
-```cpp
-    from mpi4py import MPI
-    from __future__ import division
-    import numpy as np
+```python
+from mpi4py import MPI
+from __future__ import division
+import numpy as np
 
-    comm = MPI.COMM_WORLD
+comm = MPI.COMM_WORLD
 
-    print("-"*78)
-    print(" Running on %d cores" % comm.size)
-    print("-"*78)
+print("-"*78)
+print(" Running on %d cores" % comm.size)
+print("-"*78)
 
-    comm.Barrier()
+comm.Barrier()
 
-    # Prepare a vector of N=5 elements to be broadcasted...
-    N = 5
-    if comm.rank == 0:
-        A = np.arange(N, dtype=np.float64)    # rank 0 has proper data
-    else:
-        A = np.empty(N, dtype=np.float64)     # all other just an empty array
+# Prepare a vector of N=5 elements to be broadcasted...
+N = 5
+if comm.rank == 0:
+    A = np.arange(N, dtype=np.float64)    # rank 0 has proper data
+else:
+    A = np.empty(N, dtype=np.float64)     # all other just an empty array
 
-    # Broadcast A from rank 0 to everybody
-    comm.Bcast( [A, MPI.DOUBLE] )
+# Broadcast A from rank 0 to everybody
+comm.Bcast( [A, MPI.DOUBLE] )
 
-    # Everybody should now have the same...
-    print "[%02d] %s" % (comm.rank, A)
+# Everybody should now have the same...
+print "[%02d] %s" % (comm.rank, A)
 ```
 
 Execute the above code as:
@@ -106,3 +107,64 @@ $ mpiexec -bycore -bind-to-core python hello_world.py
 ```
 
 In this example, we run MPI4Py enabled code on 4 nodes, 16 cores per node (total of 64 processes), each python process is bound to a different core. More examples and documentation can be found on [MPI for Python webpage](https://pypi.python.org/pypi/mpi4py).
+
+###Adding numbers
+
+Task: count sum of numbers from 1 to 1 000 000. (There is an easy formula to count the sum of arithmetic sequence, but we are showing the MPI solution with adding numbers one by one).
+
+
+```python
+#!/usr/bin/python
+
+import numpy
+from mpi4py import MPI
+import time
+
+comm = MPI.COMM_WORLD
+rank = comm.Get_rank()
+size = comm.Get_size()
+
+a = 1
+b = 1000000
+
+perrank = b//size
+summ = numpy.zeros(1)
+
+comm.Barrier()
+start_time = time.time()
+
+temp = 0
+for i in range(a + rank*perrank, a + (rank+1)*perrank):
+    temp = temp + i
+
+summ[0] = temp
+
+if rank == 0:
+    total = numpy.zeros(1)
+else:
+    total = None
+
+comm.Barrier()
+#collect the partial results to total sum
+comm.Reduce(summ, total, op=MPI.SUM, root=0)
+
+stop_time = time.time()
+
+if rank == 0:
+    #add the rest numbers to 1 000 000
+    for i in range(a + (size)*perrank, b+1):
+        total[0] = total[0] + i
+    print ("The sum of numbers from 1 to 1 000 000: ", int(total[0]))
+    print ("time spent with ", size, " threads in milliseconds")
+    print ("-----", int((time.time()-start_time)*1000), "-----")
+```
+
+Execute the code above as:
+```console
+$ qsub -I -q qexp -l select=4:ncpus=16,walltime=00:30:00
+
+$ ml Python/3.5.2-intel-2017.00
+
+$ mpirun -n 2 python myprogram.py
+```
+You can increase n and watch time lowering.