Add graph compilation example with holoviews.

darshan-util/pydarshan/examples/darshan-graph/Makefile

+CC=mpicc
+CLFAGS=-g
+
+
+all:
+	${CC} -o app_write -DWRITE app.c
+	${CC} -o app_read -DREAD app.c
+	${CC} -o app_readAB_writeC app_rw_mpiio.c
+
+run: all
+	./run.sh
+
+clean:
+	rm -f ${USER}_*.darshan
+	rm -rf *.o
+	rm -f app_read
+	rm -f app_write
+	rm -f app_readAB_writeC
+	rm -f A B C Z

darshan-util/pydarshan/examples/darshan-graph/app.c

+#define _GNU_SOURCE			// asprintf
+
+#include <mpi.h>
+#include <fcntl.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <unistd.h>
+#include <time.h>
+
+
+
+
+
+int main(int argc, char** argv)
+{
+	int i;
+	int ret = 0;
+
+    // Get the number of processes
+    int world_size;
+    int world_rank;
+    char processor_name[MPI_MAX_PROCESSOR_NAME];
+    int name_len;
+
+    // Initialize the MPI environment
+    MPI_Init(NULL, NULL);
+    MPI_Comm_size(MPI_COMM_WORLD, &world_size);
+    MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
+    MPI_Get_processor_name(processor_name, &name_len);
+
+
+    // Print off a hello world message
+    printf("Hello world from processor %s, rank %d"
+           " out of %d processors\n",
+           processor_name, world_rank, world_size);
+
+
+    char *filename = "A";
+    if (argc > 1) filename = argv[1];
+
+	
+	int size = 10000;
+	int opcount = 10;
+	
+    char* buf = (char*) malloc(sizeof(char) * size);
+#ifdef WRITE 
+    for (i = 0; i < size; i++) {
+        buf[i] = filename[0];
+    }
+#endif
+
+
+
+
+	// write to non existing file
+	int fd = open(filename, O_RDWR | O_CREAT, S_IWUSR | S_IRUSR | S_IWGRP | S_IRGRP | S_IROTH);
+	if ( fd != -1 )
+	{
+
+		for (i = 0; i < opcount; i++)
+		{
+		    int pos =  (size/opcount) * i;
+            int len = size/opcount;
+#ifdef WRITE
+            printf("write(from_pos=%d, len=%d)\n", pos, len);
+			ret = write(fd, buf+pos, len);
+#endif
+#ifdef READ 
+            printf("read(to_pos=%d, len=%d)\n", pos, len);
+			ret = read(fd, buf+pos, len);
+#endif
+		}
+		ret = close(fd);
+	}
+
+
+    for (i = 0; i < size; i++) 
+    {
+        printf("%c", buf[i]);
+    }
+    printf("\n");
+
+
+	MPI_Finalize();
+}
+

darshan-util/pydarshan/examples/darshan-graph/app_rw_mpiio.c

+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ *
+ *  Copyright (C) 2019, Northwestern University
+ *  See COPYRIGHT notice in top-level directory.
+ *
+ * This program shows an example of calling MPI_File_set_view(), which sets
+ * a visible file region to the calling MPI process. With such fileview set,
+ * all successive MPI read and write function calls will read and write only
+ * the visible region. In this example program, the visible region to process
+ * rank i starts from file offset (rank * 10 * sizeof(int)).
+ *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+
+#include <fcntl.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <time.h>
+#include <unistd.h>
+
+#include <mpi.h>
+
+#define CHECK_ERR(func) { \
+    if (err != MPI_SUCCESS) { \
+        int errorStringLen; \
+        char errorString[MPI_MAX_ERROR_STRING]; \
+        MPI_Error_string(err, errorString, &errorStringLen); \
+        printf("Error at line %d: calling %s (%s)\n",__LINE__, #func, errorString); \
+    } \
+}
+
+int main(int argc, char **argv) {
+    char *filename;
+    int i, err, cmode, rank;
+    char buf[10000];
+    MPI_Offset offset;
+    MPI_File fh;
+    MPI_Status status;
+
+    MPI_Init(&argc, &argv);
+
+    err = MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+    CHECK_ERR(MPI_Comm_rank);
+
+
+	// readers
+	int ret = 0;
+	int size = 5000;
+	int opcount = 10;
+	if ( rank % 2 == 1) {
+		filename = "A";
+	} else {
+		filename = "B";
+	}
+	
+	int fd = open(filename, O_RDWR | O_CREAT, S_IWUSR | S_IRUSR | S_IWGRP | S_IRGRP | S_IROTH);
+	if ( fd != -1 )
+	{
+		for (i = 0; i < opcount; i++)
+		{
+			int pos =  (size/opcount) * i;
+			int len = size/opcount;
+			printf("read(to_pos=%d, len=%d)\n", pos, len);
+			ret = read(fd, buf+pos, len);
+		}
+		ret = close(fd);
+	}
+
+
+
+
+	// writers
+    filename = "C";
+    if (argc > 1) filename = argv[1];
+
+    /* open a file (create if the file does not exist) */
+    cmode = MPI_MODE_CREATE | MPI_MODE_RDWR;
+    err = MPI_File_open(MPI_COMM_WORLD, filename, cmode, MPI_INFO_NULL, &fh);
+    CHECK_ERR(MPI_File_open);
+
+
+
+	int data_per_proc = 100;
+
+    /* set file offset for this calling process */
+    offset = (MPI_Offset)rank * data_per_proc * sizeof(char);
+
+    /* initialize write buffer contents */
+    char* abc = "ABCDEFGHIJKLMNOPQRSTUVWXYZ";
+	for (i=0; i<data_per_proc; i++) {
+    	buf[i] = abc[rank];
+	} 
+
+    for (i = 0; i < size; i++) 
+    {
+        printf("%c", buf[i]);
+    }
+    printf("\n");
+
+
+    /* MPI_File_set_view() sets the file visible region to this process starts
+     * at offset. Setting etype argument to MPI_INT means this file will be
+     * accessed in the units of integer size. Setting filetype argument to
+     * MPI_INT means a contiguous 4-byte region (assuming integer size if 4
+     * bytes) is recursively applied to the file to form the visible region to
+     * the calling process, starting from its "offset" set in the offset
+     * argument. In this example, the "file view" of a process is the entire file
+     * starting from its offset.
+     */
+
+
+    err = MPI_File_set_view(fh, offset, MPI_CHAR, MPI_CHAR, "native", MPI_INFO_NULL);
+    CHECK_ERR(MPI_File_set_view);
+
+    /* Each process writes 3 integers to the file region visible to it.
+     * Note the file pointer will advance 3x4 bytes after this call.
+     */
+    err = MPI_File_write_all(fh, &buf[0], 300, MPI_CHAR, &status);
+    CHECK_ERR(MPI_File_set_view);
+
+    /* Each process continues to write next 7 integers to the file region
+     * visible to it, starting from the file pointer updated from the previous
+     * write call.
+     */
+    err = MPI_File_write_all(fh, &buf[3], 700, MPI_CHAR, &status);
+    CHECK_ERR(MPI_File_set_view);
+
+    /* close the file collectively */
+    err = MPI_File_close(&fh);
+    CHECK_ERR(MPI_File_set_view);
+
+    MPI_Finalize();
+    return 0;
+}

darshan-util/pydarshan/examples/darshan-graph/run.sh

+#!/bin/bash
+
+# ensure the sample library libabcxyz.so is found
+export LD_LIBRARY_PATH=.
+
+export darshan_install=$(cd $(dirname $(which darshan-config)); cd ..; pwd -L)
+export darshan_libpath=$darshan_install/lib/libdarshan.so
+
+
+# enable and configure darshan to write logs into current directory
+#export LD_PRELOAD=$PWD/../../darshan-runtime/lib/libdarshan.so
+export LD_PRELOAD=$darshan_libpath
+export DARSHAN_LOG_DIR_PATH=$PWD
+#export DXT_ENABLE_IO_TRACE=4
+
+
+
+mpirun -oversubscribe -np 1 ./app_write A
+mpirun -oversubscribe -np 1 ./app_write B
+mpirun -oversubscribe -np 1 ./app_write Z
+mpirun -oversubscribe -np 1 ./app_read A
+mpirun -oversubscribe -np 4 ./app_readAB_writeC
+mpirun -oversubscribe -np 1 ./app_read C