changed function API

hdf5_read/H5Dio_cache.h

@@ -27,7 +27,7 @@ struct H5Dio_mmap {
   hid_t datatype; //
   bool batch_contig;
   vector<int> batch_list;
-  MPI_Datatype buf_type; 
+  MPI_Datatype buf_type;  // we construct a datatype construct
   MPI_Win win;
   pthread_t pthread; 
   pthread_cond_t master_cond;

hdf5_write/H5SSD.c

@@ -211,11 +211,10 @@ hid_t H5Fcreate_cache( const char *name, unsigned flags, hid_t fcpl_id, hid_t fa
 herr_t
 H5Dwrite_cache(hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id,
 	       hid_t file_space_id, hid_t dxpl_id, const void *buf) {
-  //  H5Fwait();
   hsize_t size = get_buf_size(mem_space_id, mem_type_id);
   
   if (H5SSD.mspace_per_rank_left < size) {
-    H5Fwait();
+    H5PthreadWait();
     H5SSD.offset=0;
     H5SSD.mspace_per_rank_left = H5SSD.mspace_per_rank_total;
   }
@@ -248,7 +247,7 @@ H5Dwrite_cache(hid_t dataset_id, hid_t mem_type_id, hid_t mem_space_id,
 /*
   Wait for the pthread to finish all the I/O request
 */
-void H5Fwait() {
+void H5PthreadWait() {
   pthread_mutex_lock(&H5SSD.request_lock);
   while(H5SSD.num_request>0)  {
     pthread_cond_signal(&H5SSD.io_cond);
@@ -260,7 +259,7 @@ void H5Fwait() {
 /*
   Terminate the pthread through joining
  */
-void H5TerminatePthread() {
+void H5PthreadTerminate() {
   pthread_mutex_lock(&H5SSD.request_lock);
   H5SSD.num_request=-1;
   pthread_cond_signal(&H5SSD.io_cond);
@@ -273,8 +272,8 @@ void H5TerminatePthread() {
    and terminate the pthread, remove the files on the SSD. 
  */
 herr_t H5Fclose_cache( hid_t file_id ) {
-  H5Fwait();
-  H5TerminatePthread();
+  H5PthreadWait();
+  H5PthreadTerminate();
   close(H5SSD.fd);
   remove(H5SSD.fname);
   H5SSD.mspace_left = H5SSD.mspace_total;
@@ -285,7 +284,7 @@ herr_t H5Fclose_cache( hid_t file_id ) {
    Wait for pthread to finish the work and close the property
  */
 herr_t H5Pclose_cache(hid_t dxf_id) {
-  H5Fwait();
+  H5PthreadWait();
   return H5Pclose(dxf_id);
 }
 
@@ -293,7 +292,7 @@ herr_t H5Pclose_cache(hid_t dxf_id) {
   Wait for pthread to finish the work and close the dataset 
  */
 herr_t H5Dclose_cache(hid_t dset_id) {
-  H5Fwait();
+  H5PthreadWait();
   return H5Dclose(dset_id);
 }
 
@@ -302,6 +301,6 @@ herr_t H5Dclose_cache(hid_t dset_id) {
   Wait for the pthread to finish the work and close the memory space
  */
 herr_t H5Sclose_cache(hid_t filespace) {
-  H5Fwait();
+  H5PthreadWait();
   return H5Sclose(filespace);
 }

hdf5_write/H5SSD.h

@@ -12,7 +12,7 @@ herr_t H5Dwrite_cache(hid_t dset_id, hid_t mem_type_id,
 herr_t H5Dclose_cache( hid_t id);
 herr_t H5Pclose_cache( hid_t id);
 herr_t H5Sclose_cache( hid_t id);
-void H5Fwait();
+void H5PthreadWait();
 
 void test_mmap_buf();
 

hdf5_write/Makefile

@@ -4,8 +4,8 @@ include make.inc
 
 all: parallel_hdf5
 
-parallel_hdf5: H5SSD.o parallel_hdf5.o
-	$(CXX) $(CFLAGS) -I./ -o parallel_hdf5.x parallel_hdf5.o H5SSD.o $(LIBS)
+parallel_hdf5: H5SSD.o parallel_hdf5.o ../utils/debug.o 
+	$(CXX) $(CFLAGS) -I./ -o parallel_hdf5.x parallel_hdf5.o H5SSD.o ../utils/debug.o $(LIBS)
 parallel_hdf5.o : parallel_hdf5.cpp
 	$(CXX) $(CFLAGS) -o parallel_hdf5.o -c parallel_hdf5.cpp
 H5SSD.o : H5SSD.c

hdf5_write/parallel_hdf5.cpp

@@ -19,6 +19,7 @@
 #include <sys/statvfs.h>
 #include <stdlib.h>
 #include "stat.h"
+#include "debug.h"
 int msleep(long miliseconds)
 {
   struct timespec req, rem;
@@ -45,7 +46,7 @@ int main(int argc, char **argv) {
   if (strcmp(ssd_cache, "yes")==0) {
     cache=true;
   }
-  Timing tt; 
+
   // Assuming that the dataset is a two dimensional array of 8x5 dimension;
   int d1 = 2048; 
   int d2 = 2048; 
@@ -77,6 +78,7 @@ int main(int argc, char **argv) {
   MPI_Init(&argc, &argv);
   MPI_Comm_size(comm, &nproc);
   MPI_Comm_rank(comm, &rank);
+  Timing tt(rank==io_node()); 
   //printf("     MPI: I am rank %d of %d \n", rank, nproc);
   // find local array dimension and offset; 
   hsize_t gdims[2] = {d1*nproc, d2};
@@ -179,7 +181,6 @@ int main(int argc, char **argv) {
   stat(&tt["H5Dwrite"].t_iter[0], niter, avg, std, 'i');
   if (rank==0) printf("  Write rate: %f +/- %f MB/s\n", size*avg/niter/1024/1024, size/niter*std/1024/1024);
 
-  tt.PrintTiming(master); 
   MPI_Finalize();
   return 0;
 }

hdf5_write/run.py

@@ -23,8 +23,8 @@ if hostname.find("theta")!=-1:
     parser.add_argument("--num_nodes", default=int(os.environ['COBALT_JOBSIZE']), type=int)
     parser.add_argument("--ppn", default=32, type=int)
 else:
-#    root="/Users/zhenghh/Documents/Research/ExaHDF5/io_benchmarks/ssd_cache/hdf5/"
-    root="/gpfs/mira-home/hzheng/io_benchmarks/node_local_storage/hdf5/"
+    root="/Users/zhenghh/Documents/Research/ExaHDF5/io_benchmarks/ssd_cache/hdf5/"
+#    root="/gpfs/mira-home/hzheng/io_benchmarks/node_local_storage/hdf5/"
     parser.add_argument("--num_nodes", default=1, type=int)
     parser.add_argument("--SSD", default="SSD")
     parser.add_argument("--ppn", default=2, type=int)