changed throttling routine; removed read-only restriction for setting step to existing steps; revised NEWS

.gitattributes

@@ -20,6 +20,7 @@ doc/H5X_File_Format.txt -text
 doc/Makefile.am -text
 doc/doxyfooter -text
 examples/stridedf.F90 -text
+examples/write_setview.c -text
 /install-sh -text
 /license.txt -text
 /missing -text

Makefile.am

@@ -7,6 +7,8 @@ SUBDIRS = \
 	test \
 	tools
 
+EXTRA_DIST = configure-crayxt
+
 MAINTAINERCLEANFILES = \
 	config.h \
 	config.log \

NEWS

@@ -1,3 +1,25 @@
+#### H5PART 1.6.1 ############################################################
+
+All Steps Available on Write
+----------------------------
+
+Previously, existing steps in a file were only accessable in read-only mode.
+Now, all steps are available in all modes, including write-truncate and
+write-append. Thus, it is now possible to overwrite existing data in write
+mode. To help alert the user to this possibility, a warning is issued every
+time an existing dataset is written to. Warnings can be printed by setting
+the verbosity to H5PART_VERB_WARN or higher.
+
+New Throttling Routine
+----------------------
+
+Previously, a throttle factor of N meant that for P processors, the total
+number of P writes were divided into N batchs of P/N writes.
+
+To better accomodate round-robin lustre striping, the new policy is to
+execute P/N batch of N writes. Thus, matching N to the number of stripes
+results in the desirable 1-1 matching of writers to stripes.
+
 #### H5PART 1.6 ##############################################################
 
 Updated Documentation

configure.ac

@@ -1,6 +1,6 @@
 # Every configure script must call AC_INIT before doing anything else.
 # AC_INIT (package, version, [bug-report], [tarname])
-AC_INIT([H5Part], [1.6.0], [h5part@lists.psi.ch], H5Part)
+AC_INIT([H5Part], [1.6.1], [h5part@lists.psi.ch], H5Part)
 
 
 # Ensure that a recent enough version of Autoconf is being used. 

doc/Doxyfile

@@ -4,7 +4,7 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 PROJECT_NAME           = H5Part
-PROJECT_NUMBER         = 1.6.0
+PROJECT_NUMBER         = 1.6.1
 OUTPUT_DIRECTORY       = ./ReferencePages
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English

examples/write_setview.c

@@ -0,0 +1,57 @@
+#include <stdlib.h>
+#include <assert.h>
+#include <mpi.h>
+#include <H5Part.h>
+
+#define DATASIZE 32
+#define ITERS 4
+
+int main(int argc, char** argv)
+{
+    int i, rank, nprocs;
+    h5part_int32_t data[ITERS*DATASIZE];
+    h5part_int64_t stat;
+    h5part_int64_t offset;
+    H5PartFile *file;
+
+    // initialize MPI
+    MPI_Init (&argc, &argv);
+    MPI_Comm_rank (MPI_COMM_WORLD, &rank);
+    MPI_Comm_size (MPI_COMM_WORLD, &nprocs);
+
+    H5PartSetVerbosityLevel(H5PART_VERB_DEBUG);
+
+    file = H5PartOpenFileParallel("test.h5", H5PART_WRITE, MPI_COMM_WORLD);
+    assert (file != NULL);
+
+    stat = H5PartSetStep(file, 0);
+    assert (stat == H5PART_SUCCESS);
+
+    stat = H5PartSetNumParticles(file, ITERS*DATASIZE);
+    assert (stat == H5PART_SUCCESS);
+
+    // create fake data
+    for (i=0; i<ITERS*DATASIZE; i++) {
+        data[i] = i + rank * ITERS * DATASIZE;
+    }
+
+    offset = rank * ITERS * DATASIZE;
+
+    // iterate over arrays
+    for (i=0; i<ITERS; i++) {
+        // set the "view" to select a subset of the dataset
+        stat = H5PartSetView(file,
+                offset + i*DATASIZE,
+                offset + (i+1)*DATASIZE - 1);
+        assert (stat == H5PART_SUCCESS);
+        // write the data
+        stat = H5PartWriteDataInt32(file, "data", data + i*DATASIZE);
+        assert (stat == H5PART_SUCCESS);
+    }
+
+    H5PartCloseFile(file);
+
+    MPI_Finalize();
+    return EXIT_SUCCESS;
+}
+

src/H5Block.c

@@ -1191,6 +1191,11 @@ _H5Block_read_data (
 	herr = _H5Block_select_hyperslab_for_reading ( f, dataset_id );
 	if ( herr < 0 ) return herr;
 
+#ifdef PARALLEL_IO
+	herr = _H5Part_start_throttle ( f );
+	if ( herr < 0 ) return herr;
+#endif
+
 	herr = H5Dread ( 
 		dataset_id,
 		type,
@@ -1200,6 +1205,11 @@ _H5Block_read_data (
 		data );
 	if ( herr < 0 ) return HANDLE_H5D_READ_ERR ( name, f->timestep );
 
+#ifdef PARALLEL_IO
+	herr = _H5Part_end_throttle ( f );
+	if ( herr < 0 ) return herr;
+#endif
+
 	herr = H5Dclose ( dataset_id );
 	if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR;
 
@@ -1448,6 +1458,11 @@ _H5Block_write_data (
 		);
 	if ( dataset < 0 ) return HANDLE_H5D_CREATE_ERR ( name, f->timestep );
 
+#ifdef PARALLEL_IO
+	herr = _H5Part_start_throttle ( f );
+	if ( herr < 0 ) return herr;
+#endif
+
 	herr = H5Dwrite ( 
 		dataset,
 		type,
@@ -1457,6 +1472,11 @@ _H5Block_write_data (
 		data );
 	if ( herr < 0 ) return HANDLE_H5D_WRITE_ERR ( name, f->timestep );
 
+#ifdef PARALLEL_IO
+	herr = _H5Part_end_throttle ( f );
+	if ( herr < 0 ) return herr;
+#endif
+
 	herr = H5Dclose ( dataset );
 	if ( herr < 0 ) return HANDLE_H5D_CLOSE_ERR;
 

src/H5Part.c

@@ -242,7 +242,7 @@ _H5Part_open_file (
 			}
 
 			f->create_prop = H5Pcreate(H5P_FILE_CREATE);
-			H5Pset_istore_k (f->create_prop, H5PART_BTREE_IK);
+			H5Pset_istore_k (f->create_prop, btree_ik);
 
 #ifndef H5_USE_16_API
 			/* defer metadata cache flushing until file close */
@@ -1851,9 +1851,11 @@ _H5Part_set_step (
 	char stepname[H5PART_STEPNAME_LEN];
 	_H5Part_get_step_name(f, step, stepname);
 
+#if H5PART_SET_STEP_READ_ONLY
 	if ( (!(f->flags & H5PART_READ)) && _H5Part_have_group ( f->file, stepname ) ) {
 		return HANDLE_H5PART_STEP_EXISTS_ERR ( step );
 	}
+#endif
 
 	if ( f->timegroup >= 0 ) {
 		herr_t herr = H5Gclose ( f->timegroup );
@@ -1862,6 +1864,9 @@ _H5Part_set_step (
 	f->timegroup = -1;
 	f->timestep = step;
 
+#if H5PART_SET_STEP_READ_ONLY
+	// in this mode, existing steps can be selecting only
+	// for a READ file handle
 	if ( f->flags & H5PART_READ ) {
 		_H5Part_print_debug (
 			"Proc[%d]: Set step to #%lld for file %lld",
@@ -1893,6 +1898,33 @@ _H5Part_set_step (
 			return HANDLE_H5G_CREATE_ERR ( stepname );
 	}
 
+#else // H5PART_SET_STEP_READ_ONLY
+
+	// in this mode, existing steps can be selected for all file
+	// handles: first try to open the step, and create it if it
+	// doesn't exist
+	H5E_BEGIN_TRY
+	f->timegroup = H5Gopen ( f->file, stepname
+#ifndef H5_USE_16_API
+					  , H5P_DEFAULT
+#endif
+					  );
+	H5E_END_TRY
+
+	
+	if ( f->timegroup < 0 )
+	{
+		f->timegroup = H5Gcreate( f->file, stepname, 0
+#ifndef H5_USE_16_API
+					  , H5P_DEFAULT, H5P_DEFAULT
+#endif
+					  );
+		if ( f->timegroup < 0 )
+			return HANDLE_H5G_CREATE_ERR ( stepname );
+	}
+
+#endif // H5PART_SET_STEP_READ_ONLY
+
 	return H5PART_SUCCESS;
 }
 
@@ -3343,12 +3375,14 @@ H5PartSetThrottle (
 
 	if ( f->flags & H5PART_VFD_MPIIO_IND || f->flags & H5PART_VFD_MPIPOSIX ) {
 		f->throttle = factor;
-		_H5Part_print_info (
-			"Throttling set with factor '%d'", f->throttle );
+		if ( f->myproc == 0 )
+			_H5Part_print_info (
+				"Throttling set with factor '%d'", f->throttle );
 	} else {
-		_H5Part_print_warn (
-			"Throttling is only permitted with the MPI-POSIX "
-			"or MPI-IO Independent VFD." );
+		if ( f->myproc == 0 )
+			_H5Part_print_warn (
+				"Throttling is only permitted with the MPI-POSIX "
+				"or MPI-IO Independent VFD." );
 	}
 
 	return H5PART_SUCCESS;
@@ -3366,14 +3400,14 @@ _H5Part_start_throttle (
 			_H5Part_print_info ("Throttling with factor = %d",
 				f->throttle);
 		}
-		if (f->myproc % f->throttle > 0) {
+		if (f->myproc / f->throttle > 0) {
 			_H5Part_print_debug_detail (
 				"[%d] throttle: waiting on token from %d",
-				f->myproc, f->myproc - 1);
+				f->myproc, f->myproc - f->throttle);
 			// wait to receive token before continuing with read
 			ret = MPI_Recv(
 				&token, 1, MPI_INT,
-				f->myproc - 1, // receive from previous proc
+				f->myproc - f->throttle, // receive from previous proc
 				f->myproc, // use this proc id as message tag
 				f->comm,
 				MPI_STATUS_IGNORE
@@ -3393,19 +3427,17 @@ _H5Part_end_throttle (
 	if (f->throttle > 0) {
 		int ret;
 		int token;
-		if (f->myproc % f->throttle < f->throttle - 1) {
+		if (f->myproc + f->throttle < f->nprocs) {
 			// pass token to next proc 
-			if (f->myproc + 1 < f->nprocs) {
-				_H5Part_print_debug_detail (
-					"[%d] throttle: passing token to %d",
-					f->myproc, f->myproc + 1);
-				ret = MPI_Send(
-					&token, 1, MPI_INT,
-					f->myproc + 1, // send to next proc
-					f->myproc + 1, // use the id of the target as tag
-					f->comm
-					);
-			}
+			_H5Part_print_debug_detail (
+				"[%d] throttle: passing token to %d",
+				f->myproc, f->myproc + f->throttle);
+			ret = MPI_Send(
+				&token, 1, MPI_INT,
+				f->myproc + f->throttle, // send to next proc
+				f->myproc + f->throttle, // use the id of the target as tag
+				f->comm
+				);
 			if ( ret != MPI_SUCCESS ) return HANDLE_MPI_SENDRECV_ERR;
 		}
 	}

src/H5Part.h

@@ -16,10 +16,10 @@ extern "C" {
 #include "H5MultiBlock.h"
 #endif
 
-#define H5PART_VER_STRING	"1.6.0"
+#define H5PART_VER_STRING	"1.6.1"
 #define H5PART_VER_MAJOR	1
 #define H5PART_VER_MINOR	6
-#define H5PART_VER_RELEASE	0
+#define H5PART_VER_RELEASE	1
 
 /* error values */
 #define H5PART_SUCCESS		0

src/H5PartPrivate.h

@@ -7,7 +7,7 @@
 
 #define H5PART_GROUPNAME_STEP	"Step"
 
-#define H5PART_BTREE_IK 10000
+#define H5PART_SET_STEP_READ_ONLY 0
 
 h5part_int64_t
 _H5Part_file_is_valid (

test/read.c

@@ -509,7 +509,7 @@ void test_read4(void)
 	status = H5PartSetStep(file2, NTIMESTEPS);
 	RETURN(status, H5PART_SUCCESS, "H5PartSetStep");
 
-	test_read_data64(file2, NPARTICLES, NTIMESTEPS);
+	test_read_data64(file2, NPARTICLES, NTIMESTEPS-2);
 
 	status = H5PartCloseFile(file1);
 	RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");

test/write.c

@@ -65,7 +65,7 @@ static void
 test_write_data64(H5PartFile *file, int nparticles, int step)
 {
 	int i,t;
-	h5part_int64_t status;
+	h5part_int64_t status, val;
 
 	double *x,*y,*z;
 	double *px,*py,*pz;
@@ -108,10 +108,12 @@ test_write_data64(H5PartFile *file, int nparticles, int step)
 			id[i] = i + nparticles*t;
 		}
 
+		val = H5PartHasStep(file, t);
+
 		status = H5PartSetStep(file, t);
 		RETURN(status, H5PART_SUCCESS, "H5PartSetStep");
 
-		test_write_step_attribs(file, t);
+		if (val == 0) test_write_step_attribs(file, t);
 
 		status = H5PartSetNumParticles(file, nparticles);
 		RETURN(status, H5PART_SUCCESS, "H5PartSetNumParticles");
@@ -450,7 +452,7 @@ void test_write4(void)
 	status = H5PartDefineStepName(file2, LONGNAME, 16);
 	RETURN(status, H5PART_SUCCESS, "H5PartDefineStepName");
 
-	test_write_data64(file1, NPARTICLES, NTIMESTEPS);
+	test_write_data64(file1, NPARTICLES, NTIMESTEPS-2);
 	test_write_file_attribs(file1, 1);
 
 	status = H5PartCloseFile(file1);