[svn-r12142] Purpose:

change the array size of collective chunking features of parallel tests.

Description:
Previously array size for collective optimization tests
including
cchunk1,
cchunk2,
cchunk3,
cchunk4,
ccontw,
ccontr,
cschunkw,
cschunkr,
ccchunkw,
ccchunkr

are fixed,
They are only valid for some good number of processors(1,2,3,4,6,8,12,16,24,32,48 etc).
Recently there are more requests for parallel tests to be valid on some odd number of processes such as 5,7,11,13 etc.


Solution:
I change the array size to be dynamic rather than static. Now the fastest change array size is a function of mpi_size. dim2 = constant *mpi_size. After some tunings, theoretically the above tests should be valid for any number of processors. However, other parallel tests still need to be tuned.

To verify the correctness of these tests, using mpirun -np 5 ./testphdf5 -b cchunk1 at heping.
Platforms tested:
h5committest(shanti is refused to be connected)
at heping, 5 and 7 processes are used to verify the correctness.

Misc. update:

1 files changed, 77 insertions, 41 deletions

diff --git a/testpar/t_span_tree.c b/testpar/t_span_tree.c
index ca48c17..3ead9d8 100644
--- a/testpar/t_span_tree.c
+++ b/testpar/t_span_tree.c
@@ -225,6 +225,10 @@ void coll_write_test(int chunk_factor)
   hid_t    facc_plist,dxfer_plist,dcrt_plist;
   hid_t    file, datasetc,dataseti;      /* File and dataset identifiers */
   hid_t    mspaceid1, mspaceid, fspaceid,fspaceid1; /* Dataspace identifiers */
+
+  hsize_t mdim1[1],fsdim[2],mdim[2];
+
+#if 0
   hsize_t  mdim1[] = {MSPACE1_DIM};  /* Dimension size of the first dataset
 				      (in memory) */
   hsize_t  fsdim[] = {FSPACE_DIM1, FSPACE_DIM2}; /* Dimension sizes of the dataset
@@ -234,21 +238,27 @@ void coll_write_test(int chunk_factor)
 						  dataset in memory when we
 						  read selection from the
 						  dataset on the disk */
+#endif
 
   hsize_t  start[2];  /* Start of hyperslab */
   hsize_t  stride[2]; /* Stride of hyperslab */
   hsize_t  count[2];  /* Block count */
   hsize_t  block[2];  /* Block sizes */
-  hsize_t  chunk_dims[RANK];
+  hsize_t  chunk_dims[2];
 
   herr_t   ret;
   unsigned i,j;
   int      fillvalue = 0;   /* Fill value for the dataset */
 
+#if 0
   int      matrix_out[MSPACE_DIM1][MSPACE_DIM2];
   int      matrix_out1[MSPACE_DIM1][MSPACE_DIM2];   /* Buffer to read from the
 						       dataset */
   int      vector[MSPACE1_DIM];
+#endif
+
+
+  int      *matrix_out, *matrix_out1, *vector;
 
   hbool_t  use_gpfs = FALSE;
   int      mpi_size,mpi_rank;
@@ -266,8 +276,20 @@ void coll_write_test(int chunk_factor)
   /*
    * Buffers' initialization.
    */
-  vector[0] = vector[MSPACE1_DIM - 1] = -1;
-  for (i = 1; i < MSPACE1_DIM - 1; i++) vector[i] = i;
+
+  mdim1[0] = MSPACE1_DIM *mpi_size;
+  mdim[0]  = MSPACE_DIM1;
+  mdim[1]  = MSPACE_DIM2*mpi_size;
+  fsdim[0] = FSPACE_DIM1;
+  fsdim[1] = FSPACE_DIM2*mpi_size;
+  
+  vector = (int*)HDmalloc(sizeof(int)*mdim1[0]*mpi_size);
+  matrix_out  = (int*)HDmalloc(sizeof(int)*mdim[0]*mdim[1]*mpi_size);
+  matrix_out1 = (int*)HDmalloc(sizeof(int)*mdim[0]*mdim[1]*mpi_size);
+
+  HDmemset(vector,0,sizeof(int)*mdim1[0]*mpi_size);
+  vector[0] = vector[MSPACE1_DIM*mpi_size - 1] = -1;
+  for (i = 1; i < MSPACE1_DIM*mpi_size - 1; i++) vector[i] = i;
 
   /* Grab file access property list */
   facc_plist = create_faccess_plist(comm, info, facc_type, use_gpfs);
@@ -289,8 +311,8 @@ void coll_write_test(int chunk_factor)
   VRFY((ret >= 0),"Fill value creation property list succeeded");
 
   if(chunk_factor != 0) {
-    chunk_dims[0] = FSPACE_DIM1/chunk_factor;
-    chunk_dims[1] = FSPACE_DIM2/chunk_factor;
+    chunk_dims[0] = fsdim[0]/chunk_factor;
+    chunk_dims[1] = fsdim[1]/chunk_factor;
     ret = H5Pset_chunk(dcrt_plist, 2, chunk_dims);
     VRFY((ret >= 0),"chunk creation property list succeeded");
   }
@@ -319,18 +341,18 @@ void coll_write_test(int chunk_factor)
   /* The First selection for FILE
    *
    *  block (3,2)
-   *  stride(4.3) 
+   *  stride(4,3) 
    *  count (1,768/mpi_size)
    *  start (0,1+768*3*mpi_rank/mpi_size)
    *
    */
 
   start[0]  = FHSTART0;
-  start[1]  = FHSTART1+mpi_rank*FHSTRIDE1*FHCOUNT1/mpi_size;
+  start[1]  = FHSTART1+mpi_rank*FHSTRIDE1*FHCOUNT1;
   stride[0] = FHSTRIDE0;
   stride[1] = FHSTRIDE1;
   count[0]  = FHCOUNT0;
-  count[1]  = FHCOUNT1/mpi_size;
+  count[1]  = FHCOUNT1;
   block[0]  = FHBLOCK0;
   block[1]  = FHBLOCK1;
 
@@ -347,13 +369,13 @@ void coll_write_test(int chunk_factor)
    */
 
   start[0]  = SHSTART0;
-  start[1]  = SHSTART1+SHCOUNT1*SHBLOCK1*mpi_rank/mpi_size;
+  start[1]  = SHSTART1+SHCOUNT1*SHBLOCK1*mpi_rank;
   stride[0] = SHSTRIDE0;
   stride[1] = SHSTRIDE1;
   count[0]  = SHCOUNT0;
   count[1]  = SHCOUNT1;
   block[0]  = SHBLOCK0;
-  block[1]  = SHBLOCK1/mpi_size;
+  block[1]  = SHBLOCK1;
 
   ret = H5Sselect_hyperslab(fspaceid, H5S_SELECT_OR, start, stride, count, block);
   VRFY((ret >= 0),"hyperslab selection succeeded");
@@ -377,7 +399,7 @@ void coll_write_test(int chunk_factor)
    */
   start[0]  = MHSTART0;
   stride[0] = MHSTRIDE0;
-  count[0]  = MHCOUNT0/mpi_size;
+  count[0]  = MHCOUNT0;
   block[0]  = MHBLOCK0;
 
   ret = H5Sselect_hyperslab(mspaceid1, H5S_SELECT_SET, start, stride, count, block);
@@ -480,13 +502,13 @@ void coll_write_test(int chunk_factor)
    *
    */
   start[0]  = RFFHSTART0;
-  start[1]  = RFFHSTART1+mpi_rank*RFFHCOUNT1/mpi_size;
+  start[1]  = RFFHSTART1+mpi_rank*RFFHCOUNT1;
   block[0]  = RFFHBLOCK0;
   block[1]  = RFFHBLOCK1;
   stride[0] = RFFHSTRIDE0;
   stride[1] = RFFHSTRIDE1;
   count[0]  = RFFHCOUNT0;
-  count[1]  = RFFHCOUNT1/mpi_size;
+  count[1]  = RFFHCOUNT1;
 
 
   /* The first selection of the dataset generated by collective write */
@@ -507,13 +529,13 @@ void coll_write_test(int chunk_factor)
    */
 
   start[0] = RFSHSTART0;
-  start[1] = RFSHSTART1+RFSHCOUNT1*mpi_rank/mpi_size;
+  start[1] = RFSHSTART1+RFSHCOUNT1*mpi_rank;
   block[0] = RFSHBLOCK0;
   block[1] = RFSHBLOCK1;
   stride[0] = RFSHSTRIDE0;
   stride[1] = RFSHSTRIDE0;
   count[0]  = RFSHCOUNT0;
-  count[1]  = RFSHCOUNT1/mpi_size;
+  count[1]  = RFSHCOUNT1;
 
   /* The second selection of the dataset generated by collective write */
   ret = H5Sselect_hyperslab(fspaceid, H5S_SELECT_OR, start, stride, count, block);
@@ -546,13 +568,13 @@ void coll_write_test(int chunk_factor)
 
 
   start[0]  = RMFHSTART0;
-  start[1]  = RMFHSTART1+mpi_rank*RMFHCOUNT1/mpi_size;
+  start[1]  = RMFHSTART1+mpi_rank*RMFHCOUNT1;
   block[0]  = RMFHBLOCK0;
   block[1]  = RMFHBLOCK1;
   stride[0] = RMFHSTRIDE0;
   stride[1] = RMFHSTRIDE1;
   count[0]  = RMFHCOUNT0;
-  count[1]  = RMFHCOUNT1/mpi_size;
+  count[1]  = RMFHCOUNT1;
 
   ret = H5Sselect_hyperslab(mspaceid, H5S_SELECT_SET, start, stride, count, block);
   VRFY((ret >= 0),"hyperslab selection succeeded");
@@ -569,13 +591,13 @@ void coll_write_test(int chunk_factor)
    *
    */
   start[0]  = RMSHSTART0;
-  start[1]  = RMSHSTART1+mpi_rank*RMSHCOUNT1/mpi_size;
+  start[1]  = RMSHSTART1+mpi_rank*RMSHCOUNT1;
   block[0]  = RMSHBLOCK0;
   block[1]  = RMSHBLOCK1;
   stride[0] = RMSHSTRIDE0;
   stride[1] = RMSHSTRIDE1;
   count[0]  = RMSHCOUNT0;
-  count[1]  = RMSHCOUNT1/mpi_size;
+  count[1]  = RMSHCOUNT1;
 
   ret = H5Sselect_hyperslab(mspaceid, H5S_SELECT_OR, start, stride, count, block);
   VRFY((ret >= 0),"hyperslab selection succeeded");
@@ -584,8 +606,8 @@ void coll_write_test(int chunk_factor)
    * Initialize data buffer.
    */
 
-  HDmemset(matrix_out,0,sizeof(int)*MSPACE_DIM1*MSPACE_DIM2);
-  HDmemset(matrix_out1,0,sizeof(int)*MSPACE_DIM1*MSPACE_DIM2);
+  HDmemset(matrix_out,0,sizeof(int)*MSPACE_DIM1*MSPACE_DIM2*mpi_size);
+  HDmemset(matrix_out1,0,sizeof(int)*MSPACE_DIM1*MSPACE_DIM2*mpi_size);
   /*
    * Read data back to the buffer matrix_out.
    */
@@ -601,12 +623,11 @@ void coll_write_test(int chunk_factor)
 
   ret = 0;
 
-  for (i = 0; i < MSPACE_DIM1; i++){
-    for (j = 0; j < MSPACE_DIM2; j++){
-      if(matrix_out[i][j]!=matrix_out1[i][j]) ret = -1;
+  for (i = 0; i < MSPACE_DIM1*MSPACE_DIM2*mpi_size; i++){
+         if(matrix_out[i]!=matrix_out1[i]) ret = -1;
       if(ret < 0) break;
     }
-  }
+  
   VRFY((ret >= 0),"H5D irregular collective write succeed");
 
   /*
@@ -670,13 +691,16 @@ void coll_read_test(int chunk_factor)
   hid_t   file, dataseti;           /* File and dataset identifiers */
   hid_t   mspaceid, fspaceid1;      /* Dataspace identifiers */
 
+
   /* Dimension sizes of the dataset (on disk) */
+#if 0
   hsize_t mdim[] = {MSPACE_DIM1, MSPACE_DIM2}; /* Dimension sizes of the
 						  dataset in memory when we
 						  read selection from the
 						  dataset on the disk */
 
-  
+#endif
+  hsize_t mdim[2];  
   hsize_t  start[2];  /* Start of hyperslab */
   hsize_t  stride[2]; /* Stride of hyperslab */
   hsize_t  count[2];  /* Block count */
@@ -684,9 +708,15 @@ void coll_read_test(int chunk_factor)
   herr_t   ret;
 
   unsigned i,j;
+
+  int     *matrix_out;
+  int     *matrix_out1;
+#if 0
   int      matrix_out[MSPACE_DIM1][MSPACE_DIM2];
   int      matrix_out1[MSPACE_DIM1][MSPACE_DIM2];   /* Buffer to read from the
 						       dataset */
+
+#endif
   hbool_t  use_gpfs = FALSE;
   int      mpi_size,mpi_rank;
 
@@ -700,7 +730,15 @@ void coll_read_test(int chunk_factor)
 
   /* Obtain file name */
   filename = GetTestParameters();
- 
+
+
+  /* Initialize the buffer */
+   
+  mdim[0] = MSPACE_DIM1;
+  mdim[1] = MSPACE_DIM2*mpi_size;
+  matrix_out =(int*)HDmalloc(sizeof(int)*MSPACE_DIM1*MSPACE_DIM2*mpi_size);
+  matrix_out1=(int*)HDmalloc(sizeof(int)*MSPACE_DIM1*MSPACE_DIM2*mpi_size);
+
   /*** For testing collective hyperslab selection read ***/
 
   /* Obtain file access property list */
@@ -734,13 +772,13 @@ void coll_read_test(int chunk_factor)
    *
    */
   start[0]  = RFFHSTART0;
-  start[1]  = RFFHSTART1+mpi_rank*RFFHCOUNT1/mpi_size;
+  start[1]  = RFFHSTART1+mpi_rank*RFFHCOUNT1;
   block[0]  = RFFHBLOCK0;
   block[1]  = RFFHBLOCK1;
   stride[0] = RFFHSTRIDE0;
   stride[1] = RFFHSTRIDE1;
   count[0]  = RFFHCOUNT0;
-  count[1]  = RFFHCOUNT1/mpi_size;
+  count[1]  = RFFHCOUNT1;
 
   ret = H5Sselect_hyperslab(fspaceid1, H5S_SELECT_SET, start, stride, count, block);
   VRFY((ret >= 0),"hyperslab selection succeeded");
@@ -754,13 +792,13 @@ void coll_read_test(int chunk_factor)
    *
    */
   start[0]  = RFSHSTART0;
-  start[1]  = RFSHSTART1+RFSHCOUNT1*mpi_rank/mpi_size;
+  start[1]  = RFSHSTART1+RFSHCOUNT1*mpi_rank;
   block[0]  = RFSHBLOCK0;
   block[1]  = RFSHBLOCK1;
   stride[0] = RFSHSTRIDE0;
   stride[1] = RFSHSTRIDE0;
   count[0]  = RFSHCOUNT0;
-  count[1]  = RFSHCOUNT1/mpi_size;
+  count[1]  = RFSHCOUNT1;
 
   ret = H5Sselect_hyperslab(fspaceid1, H5S_SELECT_OR, start, stride, count, block);
   VRFY((ret >= 0),"hyperslab selection succeeded");
@@ -784,13 +822,13 @@ void coll_read_test(int chunk_factor)
    */
 
   start[0]  = RMFHSTART0;
-  start[1]  = RMFHSTART1+mpi_rank*RMFHCOUNT1/mpi_size;
+  start[1]  = RMFHSTART1+mpi_rank*RMFHCOUNT1;
   block[0]  = RMFHBLOCK0;
   block[1]  = RMFHBLOCK1;
   stride[0] = RMFHSTRIDE0;
   stride[1] = RMFHSTRIDE1;
   count[0]  = RMFHCOUNT0;
-  count[1]  = RMFHCOUNT1/mpi_size;
+  count[1]  = RMFHCOUNT1;
   ret = H5Sselect_hyperslab(mspaceid, H5S_SELECT_SET, start, stride, count, block);
   VRFY((ret >= 0),"hyperslab selection succeeded");
 
@@ -806,13 +844,13 @@ void coll_read_test(int chunk_factor)
    *
    */
   start[0]  = RMSHSTART0;
-  start[1]  = RMSHSTART1+mpi_rank*RMSHCOUNT1/mpi_size;
+  start[1]  = RMSHSTART1+mpi_rank*RMSHCOUNT1;
   block[0]  = RMSHBLOCK0;
   block[1]  = RMSHBLOCK1;
   stride[0] = RMSHSTRIDE0;
   stride[1] = RMSHSTRIDE1;
   count[0]  = RMSHCOUNT0;
-  count[1]  = RMSHCOUNT1/mpi_size;
+  count[1]  = RMSHCOUNT1;
   ret = H5Sselect_hyperslab(mspaceid, H5S_SELECT_OR, start, stride, count, block);
   VRFY((ret >= 0),"hyperslab selection succeeded");
 
@@ -821,8 +859,8 @@ void coll_read_test(int chunk_factor)
    * Initialize data buffer.
    */
 
-  HDmemset(matrix_out,0,sizeof(int)*MSPACE_DIM1*MSPACE_DIM2);
-  HDmemset(matrix_out1,0,sizeof(int)*MSPACE_DIM1*MSPACE_DIM2);
+  HDmemset(matrix_out,0,sizeof(int)*MSPACE_DIM1*MSPACE_DIM2*mpi_size);
+  HDmemset(matrix_out1,0,sizeof(int)*MSPACE_DIM1*MSPACE_DIM2*mpi_size);
 
   /*
    * Read data back to the buffer matrix_out.
@@ -848,11 +886,9 @@ void coll_read_test(int chunk_factor)
   VRFY((ret >= 0),"H5D independent read succeed");
 
   ret = 0;
-  for (i = 0; i < MSPACE_DIM1; i++){
-    for (j = 0; j < MSPACE_DIM2; j++){
-      if(matrix_out[i][j]!=matrix_out1[i][j])ret = -1;
+  for (i = 0; i < MSPACE_DIM1*MSPACE_DIM2*mpi_size; i++){
+      if(matrix_out[i]!=matrix_out1[i])ret = -1;
       if(ret < 0) break;
-    }
   }
   VRFY((ret >= 0),"H5D contiguous irregular collective read succeed");