add python client example

tests/Python/example/build.sh

@@ -0,0 +1,6 @@
+#!/bin/bash 
+
+module load python/3.6.3
+module unload openmpi/1.10.1
+module load mpich
+make

tests/Python/example/example.c

@@ -0,0 +1,20 @@
+#define MPICH_SKIP_MPICXX 1
+#define OMPI_SKIP_MPICXX  1
+
+#include <mpi.h>
+#include <stdio.h>
+
+void sayhello(MPI_Comm comm) {
+  int size, rank;
+  char pname[MPI_MAX_PROCESSOR_NAME]; int len;
+  if (comm == MPI_COMM_NULL) {
+    printf("You passed MPI_COMM_NULL !!!\n");
+    return;
+  }
+  MPI_Comm_size(comm, &size);
+  MPI_Comm_rank(comm, &rank);
+  MPI_Get_processor_name(pname, &len);
+  pname[len] = 0;
+  printf("Hello, World! I am process %d of %d on %s.\n",
+         rank, size, pname);
+}

tests/Python/example/example.i

@@ -0,0 +1,18 @@
+%module example
+
+%{
+#include <mpi.h>
+#include "example.c"
+%}
+
+%include mpi4py/mpi4py.i
+
+%mpi4py_typemap(Comm, MPI_Comm);
+
+void sayhello(MPI_Comm comm);
+
+/*
+ * Local Variables:
+ * mode: C
+ * End:
+ */

tests/Python/example/makefile

@@ -0,0 +1,36 @@
+.PHONY: default
+default: build example clean
+
+PYTHON = python
+PYTHON_CONFIG = ${PYTHON} ../python-config
+MPI4PY_INCLUDE = ${shell ${PYTHON} -c 'import mpi4py; print( mpi4py.get_include() )'}
+
+
+SWIG = swig
+SWIG_PY = ${SWIG} -python
+.PHONY: src
+src: example_wrap.c
+example_wrap.c: example.i
+	${SWIG_PY} -I${MPI4PY_INCLUDE} -o $@ $<
+
+MPICC = mpicc
+CFLAGS = -fPIC ${shell ${PYTHON_CONFIG} --includes}
+LDFLAGS = -shared ${shell ${PYTHON_CONFIG} --libs}
+SO = ${shell ${PYTHON_CONFIG} --extension-suffix}
+.PHONY: build
+build: _example${SO}
+_example${SO}: example_wrap.c
+	${MPICC} ${CFLAGS} -I${MPI4PY_INCLUDE} -o $@ $< ${LDFLAGS}
+
+
+MPIEXEC = mpiexec
+NP_FLAG = -n
+NP = 5
+.PHONY: example
+example: build
+	${MPIEXEC} ${NP_FLAG} ${NP} ${PYTHON} testexample.py
+
+
+.PHONY: clean
+clean:
+	${RM} example_wrap.c example.py* _example${SO}

tests/Python/example/testexample.py

@@ -0,0 +1,8 @@
+from mpi4py import MPI
+import example as ex
+
+null = MPI.COMM_NULL
+ex.sayhello(null)
+
+comm = MPI.COMM_WORLD
+ex.sayhello(comm)

tests/Python/getdata.c

@@ -0,0 +1,93 @@
+/* put.c : Example 1: DataSpaces put tutorial 
+ * This example will show you the simplest way 
+ * to put a 1D array of 3 elements into the DataSpace.
+ * */
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include "dataspaces.h"
+#include "mpi.h"
+
+int get_data_test(double *data, int n)
+{
+    int i = 0;
+    for (i = 0; i < n; i++)
+    {
+        data[i] = i * 0.1;
+    }
+    return 0;
+}
+
+int get_data(MPI_Comm pgcomm, int pndim, double *data, int n)
+{
+
+    int err;
+    int nprocs, rank;
+
+    MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
+    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+    MPI_Comm gcomm = MPI_COMM_WORLD;
+    MPI_Barrier(gcomm);
+
+    printf("in c file nprocs %d rank %d\n", nprocs, rank);
+    printf("curr ndim is %d\n", pndim);
+
+    // Initalize DataSpaces
+    // # of Peers, Application ID, ptr MPI comm, additional parameters
+    // # Peers: Number of connecting clients to the DS server
+    // Application ID: Unique idenitifier (integer) for application
+    // Pointer to the MPI Communicator, allows DS Layer to use MPI barrier func
+    // Addt'l parameters: Placeholder for future arguments, currently NULL.
+    // the first parameter should be same with the number of threads to access server (namely -n after mpiexec)
+    // we use -n 2 (defined at run.sh)for this example
+    // the second parameter is used to label current application, one application/program should have unique appid
+    // use 1 for putdata and 2 for get data
+    dspaces_init(2, 2, &gcomm, NULL);
+
+    sleep(1);
+
+    int timestep = 0;
+
+    // DataSpaces: Lock Mechanism
+    // Usage: Prevent other process from modifying
+    //        data at the same time as ours
+    //dspaces_lock_on_write("my_test_lock", &gcomm);
+
+    //Name the Data that will be writen
+    char var_name[128];
+    sprintf(var_name, "ex1_sample_data");
+
+    // Create integer array, size 3
+    // We will store the data we get out of the DataSpace
+    // in this array.
+    // instead of using malloc to get new data, using data array sent from python
+    //double *getdata = malloc(3 * sizeof(int));
+
+    // Define the dimensionality of the data to be received
+    int ndim = 1;
+
+    // Prepare LOWER and UPPER bound dimensions
+    uint64_t lb[1] = {0}, ub[1] = {0};
+
+    // DataSpaces: Get data array from the space
+    // Usage: dspaces_get(Name of variable, version num,
+    // size (in bytes of each element), dimensions for bounding box,
+    // lower bound coordinates, upper bound coordinates,
+    // ptr to data buffer
+    dspaces_get(var_name, timestep, 3 * sizeof(double), ndim,
+                lb, ub, data);
+
+    printf("Timestep %d: get data %lf %lf %lf\n",
+           timestep, data[0], data[1], data[2]);
+
+    // DataSpaces: Release our lock on the data
+    dspaces_unlock_on_read("my_test_lock", &gcomm);
+
+    // DataSpaces: Finalize and clean up DS process
+    common_finalize();
+
+    MPI_Barrier(gcomm);
+    MPI_Finalize;
+
+    return 0;
+}

tests/Python/getdata.i

@@ -0,0 +1,30 @@
+%module getdata
+
+%{
+#define SWIG_FILE_WITH_INIT
+#include "mpi.h"
+#include "getdata.c"
+%}
+
+%include mpi4py/mpi4py.i
+%include "numpy.i"
+
+%init %{
+    import_array();
+%}
+
+%mpi4py_typemap(Comm, MPI_Comm);
+
+%apply (double* INPLACE_ARRAY1, int DIM1) {(double* data, int n)}; 
+
+int get_data_test(double *data, int n);
+int get_data(MPI_Comm gcomm, int pndim, double *data, int n);
+
+
+/*
+ * Local Variables:
+ * mode: C
+ * End:
+ * refer to http://numpy-discussion.10968.n7.nabble.com/Numpy-SWIG-with-arrays-in-input-and-output-of-a-function-td29411.html
+ * refer to https://docs.scipy.org/doc/numpy/reference/swig.interface-file.html?highlight=array
+ */

tests/Python/makefile

@@ -0,0 +1,52 @@
+.PHONY: default
+default: buildput buildget runtest
+
+PYTHON = python
+PYTHON_CONFIG = ${PYTHON} ./python-config
+MPI4PY_INCLUDE = ${shell ${PYTHON} -c 'import mpi4py; print( mpi4py.get_include() )'}
+NUMPY_INCLUDE = ${shell ${PYTHON} -c 'import numpy; print( numpy.get_include() )'}
+PREFIX = /home1/zw241/dataspaces
+INCLUDES = -I$(PREFIX)/include
+DSCOMMON = ../C/common.o
+LFLAG = -L/home1/zw241/dataspaces/install/lib -ldspaces -ldart -ldscommon -ldspacesf -lpthread -lm -lrt -libverbs -lrdmacm
+CFLAGS = -Wall -g
+
+SWIG = swig
+SWIG_PY = ${SWIG} -python
+.PHONY: src
+src: putdata_wrap.c
+putdata_wrap.c: putdata.i
+	[ -f ./numpy.i ] && echo "numpy.i already here, good" || wget https://raw.githubusercontent.com/numpy/numpy/master/tools/swig/numpy.i
+	${SWIG_PY} -I${MPI4PY_INCLUDE} -I${NUMPY_INCLUDE} $(INCLUDES) -o $@ $<
+
+src: getdata_wrap.c
+getdata_wrap.c: getdata.i
+	[ -f ./numpy.i ] && echo "numpy.i already here, good" || wget https://raw.githubusercontent.com/numpy/numpy/master/tools/swig/numpy.i
+	${SWIG_PY} -I${MPI4PY_INCLUDE} -I${NUMPY_INCLUDE} $(INCLUDES) -o $@ $<
+
+
+MPICC = mpicc
+CFLAGS = -fPIC ${shell ${PYTHON_CONFIG} --includes}
+LDFLAGS = -shared ${shell ${PYTHON_CONFIG} --libs}
+SO = ${shell ${PYTHON_CONFIG} --extension-suffix}
+
+.PHONY: buildput
+buildput: _putdata${SO} 
+_putdata${SO}:  putdata_wrap.c 
+	${MPICC} ${CFLAGS} -I${MPI4PY_INCLUDE} -I${NUMPY_INCLUDE} $(INCLUDES) $(DSCOMMON) $(LFLAG) -o $@ $< ${LDFLAGS}
+
+.PHONY: buildget
+buildget: _getdata${SO} 
+_getdata${SO}:  getdata_wrap.c 
+	${MPICC} ${CFLAGS} -I${MPI4PY_INCLUDE} -I${NUMPY_INCLUDE} $(INCLUDES) $(DSCOMMON) $(LFLAG) -o $@ $< ${LDFLAGS}
+
+
+.PHONY: runtest 
+runtest: buildget buildput
+	/bin/bash ./run.sh
+
+
+.PHONY: clean
+clean:
+	${RM} putdata_wrap.c putdata.py* _putdata${SO} *.o
+	${RM} getdata_wrap.c getdata.py* _getdata${SO} *.o

tests/Python/putdata.c

@@ -0,0 +1,83 @@
+/* put.c : Example 1: DataSpaces put tutorial 
+ * This example will show you the simplest way 
+ * to put a 1D array of 3 elements into the DataSpace.
+ * */
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdint.h>
+#include "dataspaces.h"
+#include "mpi.h"
+
+int put_data(MPI_Comm pgcomm, int pndim , double *data, int n)
+{
+        printf("array len %d\n", n);
+        int i = 0;
+        for (i = 0; i < n; i++)
+        {
+        printf("index %d value %lf\n", data[i]);
+        }
+        int err;
+        int nprocs, rank;
+
+        MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
+        MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+        MPI_Comm gcomm = MPI_COMM_WORLD;
+        MPI_Barrier(gcomm);
+
+        printf("in c file nprocs %d rank %d\n", nprocs, rank);
+        printf("curr ndim is %d\n", pndim);
+
+        // Initalize DataSpaces
+        // # of Peers, Application ID, ptr MPI comm, additional parameters
+        // # Peers: Number of connecting clients to the DS server
+        // Application ID: Unique idenitifier (integer) for application
+        // Pointer to the MPI Communicator, allows DS Layer to use MPI barrier func
+        // Addt'l parameters: Placeholder for future arguments, currently NULL.
+        // the first parameter should be same with the number of threads to access server (namely -n after mpiexec)
+        // the second parameter is used to label current application, one application/program should have unique appid
+        // init is only needed to call once for multiple timesteps
+        dspaces_init(2, 1, &gcomm, NULL);
+
+        int timestep=0;
+
+        sleep(1);
+
+        // DataSpaces: Lock Mechanism
+        // Usage: Prevent other process from modifying
+        //        data at the same time as ours
+        //dspaces_lock_on_write("my_test_lock", &gcomm);
+
+        //Name the Data that will be writen
+        char var_name[128];
+        sprintf(var_name, "ex1_sample_data");
+
+        printf("Timestep %d: put data %lf %lf %lf\n",
+               timestep, data[0], data[1], data[2]);
+
+        // ndim: Dimensions for application data domain
+        // In this case, our data array is 1 dimensional
+        int ndim = pndim;
+
+        // Prepare LOWER and UPPER bound dimensions
+        // In this example, we will put all data into a
+        // one dimention array lb=(0) up=(2)
+        uint64_t lb[1] = {0}, ub[1] = {2};
+
+        // DataSpaces: Put data array into the space
+        // Usage: dspaces_put(Name of variable, version num,
+        // size (in bytes of each element), dimensions for bounding box,
+        // lower bound coordinates, upper bound coordinates,
+        // ptr to data buffer
+        dspaces_put(var_name, timestep, 3 * sizeof(double), ndim, lb, ub, data);
+
+        // DataSpaces: Release our lock on the data
+        dspaces_unlock_on_write("my_test_lock", &gcomm);
+
+        // DataSpaces: Finalize and clean up DS process
+        common_finalize();
+
+        MPI_Barrier(gcomm);
+        MPI_Finalize;
+
+        return 0;
+}

tests/Python/putdata.i

@@ -0,0 +1,32 @@
+%module putdata
+
+%{
+#define SWIG_FILE_WITH_INIT
+#include "mpi.h"
+#include "putdata.c"
+%}
+
+%include mpi4py/mpi4py.i
+%include "numpy.i"
+
+%init %{
+    import_array();
+%}
+
+%mpi4py_typemap(Comm, MPI_Comm);
+
+/*
+refer to https://docs.scipy.org/doc/numpy/reference/swig.interface-file.html 
+for 2d and 3d array
+*/
+%apply (double* IN_ARRAY1, int DIM1) {(double* data, int n)};
+
+
+int put_data(MPI_Comm gcomm, int pndim, double *data, int n);
+
+
+/*
+ * Local Variables:
+ * mode: C
+ * End:
+ */