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-rw-r--r--MANIFEST1
-rw-r--r--fortran/src/H5Aff.F903
-rw-r--r--fortran/src/H5Dff.F909
-rw-r--r--fortran/src/H5Pff.F908
-rw-r--r--fortran/src/H5Rff.F906
-rw-r--r--fortran/src/H5Tff.F902
-rw-r--r--fortran/src/H5_buildiface.F90194
-rw-r--r--java/test/TestH5Z.java34
-rw-r--r--release_docs/RELEASE.txt14
-rw-r--r--src/H5Dchunk.c22
-rw-r--r--src/H5FDlog.c16
-rw-r--r--src/H5FDsec2.c16
-rw-r--r--src/H5Fprivate.h2
-rw-r--r--src/H5Pfapl.c15
-rw-r--r--tools/src/misc/h5repart.c45
-rw-r--r--tools/test/misc/CMakeTestsRepart.cmake5
-rw-r--r--tools/test/misc/repart_test.c21
-rw-r--r--tools/test/misc/testh5repart.sh.in6
-rw-r--r--tools/test/perform/CMakeLists.txt10
-rw-r--r--tools/test/perform/Makefile.am4
-rw-r--r--tools/test/perform/chunk_cache.c405
21 files changed, 716 insertions, 122 deletions
diff --git a/MANIFEST b/MANIFEST
index f2c36a3..00f16fc 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -2616,6 +2616,7 @@
./tools/test/perform/build_h5perf_alone.sh
./tools/test/perform/build_h5perf_serial_alone.sh
./tools/test/perform/chunk.c
+./tools/test/perform/chunk_cache.c
./tools/test/perform/direct_write_perf.c
./tools/test/perform/gen_report.pl
./tools/test/perform/iopipe.c
diff --git a/fortran/src/H5Aff.F90 b/fortran/src/H5Aff.F90
index 827b803..a728f2d 100644
--- a/fortran/src/H5Aff.F90
+++ b/fortran/src/H5Aff.F90
@@ -76,6 +76,9 @@ MODULE H5A
USE H5GLOBAL
+ PRIVATE h5awrite_char_scalar, h5awrite_ptr
+ PRIVATE h5aread_char_scalar, h5aread_ptr
+
INTERFACE h5awrite_f
MODULE PROCEDURE h5awrite_char_scalar
! This is the preferred way to call h5awrite
diff --git a/fortran/src/H5Dff.F90 b/fortran/src/H5Dff.F90
index 3915f72..77f0a15 100644
--- a/fortran/src/H5Dff.F90
+++ b/fortran/src/H5Dff.F90
@@ -90,6 +90,15 @@ MODULE H5D
USE, INTRINSIC :: ISO_C_BINDING
USE H5GLOBAL
+ PRIVATE h5dread_vl_integer, h5dread_vl_real, h5dread_vl_string
+ PRIVATE h5dwrite_vl_integer, h5dwrite_vl_real, h5dwrite_vl_string
+ PRIVATE h5dwrite_reference_obj, h5dwrite_reference_dsetreg, h5dwrite_char_scalar, h5dwrite_ptr
+ PRIVATE h5dread_reference_obj, h5dread_reference_dsetreg, h5dread_char_scalar, h5dread_ptr
+ PRIVATE h5dfill_integer, h5dfill_c_float, h5dfill_c_double, h5dfill_char
+#if H5_FORTRAN_C_LONG_DOUBLE_IS_UNIQUE!=0
+ PRIVATE h5dfill_c_long_double
+#endif
+
INTERFACE h5dextend_f
MODULE PROCEDURE h5dset_extent_f
END INTERFACE
diff --git a/fortran/src/H5Pff.F90 b/fortran/src/H5Pff.F90
index afb9136..455c72e 100644
--- a/fortran/src/H5Pff.F90
+++ b/fortran/src/H5Pff.F90
@@ -42,6 +42,14 @@ MODULE H5P
USE H5GLOBAL
USE H5fortkit
+ PRIVATE h5pset_fapl_multi_l, h5pset_fapl_multi_s
+ PRIVATE h5pset_fill_value_integer, h5pset_fill_value_char, h5pset_fill_value_ptr
+ PRIVATE h5pget_fill_value_integer, h5pget_fill_value_char, h5pget_fill_value_ptr
+ PRIVATE h5pset_integer, h5pset_char, h5pset_ptr
+ PRIVATE h5pget_integer, h5pget_char, h5pget_ptr
+ PRIVATE h5pregister_integer, h5pregister_ptr
+ PRIVATE h5pinsert_integer, h5pinsert_char, h5pinsert_ptr
+
INTERFACE h5pset_fapl_multi_f
MODULE PROCEDURE h5pset_fapl_multi_l
MODULE PROCEDURE h5pset_fapl_multi_s
diff --git a/fortran/src/H5Rff.F90 b/fortran/src/H5Rff.F90
index f5a9c6e..6c2ba28 100644
--- a/fortran/src/H5Rff.F90
+++ b/fortran/src/H5Rff.F90
@@ -56,6 +56,12 @@ MODULE H5R
! END TYPE
!
+ PRIVATE h5rget_object_type_obj_f
+ PRIVATE h5rget_region_region_f, h5rget_region_ptr_f
+ PRIVATE h5rcreate_object_f, h5rcreate_region_f, h5rcreate_ptr_f
+ PRIVATE h5rdereference_object_f, h5rdereference_region_f, h5rdereference_ptr_f
+ PRIVATE h5rget_name_object_f, h5rget_name_region_f, h5rget_name_ptr_f
+
INTERFACE h5rget_object_type_f
MODULE PROCEDURE h5rget_object_type_obj_f
diff --git a/fortran/src/H5Tff.F90 b/fortran/src/H5Tff.F90
index b63c61d..46c8f39 100644
--- a/fortran/src/H5Tff.F90
+++ b/fortran/src/H5Tff.F90
@@ -41,6 +41,8 @@ MODULE H5T
USE H5GLOBAL
IMPLICIT NONE
+ PRIVATE h5tenum_insert_f03, h5tenum_insert_f90
+
!****t* H5T/hvl_t
! Fortran2003 Derived Type:
TYPE hvl_t
diff --git a/fortran/src/H5_buildiface.F90 b/fortran/src/H5_buildiface.F90
index d4ebdd3..f793b7f 100644
--- a/fortran/src/H5_buildiface.F90
+++ b/fortran/src/H5_buildiface.F90
@@ -135,162 +135,268 @@ PROGRAM H5_buildiface
WRITE(11,'(A)') "MODULE H5_GEN"
- WRITE(11,'(A)') ' USE, INTRINSIC :: ISO_C_BINDING'
- WRITE(11,'(A)') ' USE H5GLOBAL'
+ WRITE(11,'(2X,A)') 'USE, INTRINSIC :: ISO_C_BINDING'
+ WRITE(11,'(2X,A)') 'USE H5GLOBAL'
+
+ WRITE(11,'(2X,A)') 'USE H5A'
+ WRITE(11,'(2X,A)') 'USE H5D'
+ WRITE(11,'(2X,A)') 'USE H5P'
+ WRITE(11,'(2X,A)') 'IMPLICIT NONE'
+
+!******************************
+! DECLARE PRIVATE INTERFACES
+!******************************
+
+ DO i = 1, num_rkinds
+ j = rkind(i)
+ WRITE(chr2,'(I2)') j
+ DO k = 1, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5awrite_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ ENDDO
+ END DO
+ DO i = 1, num_ikinds
+ j = ikind(i)
+ WRITE(chr2,'(I2)') j
+ DO k = 1, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5awrite_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ ENDDO
+ END DO
+ DO k = 2, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5awrite_ckind_rank"//chr_rank(k)
+ ENDDO
+ DO i = 1, num_rkinds
+ j = rkind(i)
+ WRITE(chr2,'(I2)') j
+ DO k = 1, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5aread_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ ENDDO
+ END DO
+ DO i = 1, num_ikinds
+ j = ikind(i)
+ WRITE(chr2,'(I2)') j
+ DO k = 1, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5aread_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ ENDDO
+ END DO
+ DO k = 2, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5aread_ckind_rank"//chr_rank(k)
+ ENDDO
+
+ DO i = 1, num_rkinds
+ j = rkind(i)
+ WRITE(chr2,'(I2)') j
+ DO k = 1, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5dwrite_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ ENDDO
+ END DO
+ DO i = 1, num_ikinds
+ j = ikind(i)
+ WRITE(chr2,'(I2)') j
+ DO k = 1, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5dwrite_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ ENDDO
+ END DO
+ DO k = 2, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5dwrite_ckind_rank"//chr_rank(k)
+ END DO
+ DO i = 1, num_rkinds
+ j = rkind(i)
+ WRITE(chr2,'(I2)') j
+ DO k = 1, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5dread_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ ENDDO
+ END DO
+ DO i = 1, num_ikinds
+ j = ikind(i)
+ WRITE(chr2,'(I2)') j
+ DO k = 1, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5dread_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ ENDDO
+ END DO
+ DO k = 2, 8
+ WRITE(11,'(2X,A)') "PRIVATE h5dread_ckind_rank"//chr_rank(k)
+ ENDDO
+
+ DO i = 1, num_rkinds
+ j = rkind(i)
+ WRITE(chr2,'(I2)') j
+ WRITE(11,'(2X,A)') "PRIVATE h5pset_fill_value_kind_"//TRIM(ADJUSTL(chr2))
+ END DO
+ DO i = 1, num_rkinds
+ j = rkind(i)
+ WRITE(chr2,'(I2)') j
+ WRITE(11,'(2X,A)') "PRIVATE h5pget_fill_value_kind_"//TRIM(ADJUSTL(chr2))
+ END DO
+ DO i = 1, num_rkinds
+ j = rkind(i)
+ WRITE(chr2,'(I2)') j
+ WRITE(11,'(2X,A)') "PRIVATE h5pset_kind_"//TRIM(ADJUSTL(chr2))
+ END DO
+ DO i = 1, num_rkinds
+ j = rkind(i)
+ WRITE(chr2,'(I2)') j
+ WRITE(11,'(2X,A)') "PRIVATE h5pget_kind_"//TRIM(ADJUSTL(chr2))
+ END DO
+ DO i = 1, num_rkinds
+ j = rkind(i)
+ WRITE(chr2,'(I2)') j
+ WRITE(11,'(2X,A)') "PRIVATE h5pregister_kind_"//TRIM(ADJUSTL(chr2))
+ END DO
+ DO i = 1, num_rkinds
+ j = rkind(i)
+ WRITE(chr2,'(I2)') j
+ WRITE(11,'(2X,A)') "PRIVATE h5pinsert_kind_"//TRIM(ADJUSTL(chr2))
+ END DO
- WRITE(11,'(A)') ' USE H5A'
- WRITE(11,'(A)') ' USE H5D'
- WRITE(11,'(A)') ' USE H5P'
- WRITE(11,'(A)') ' IMPLICIT NONE'
!***************
! H5A INTERFACES
!***************
!
! H5Awrite_f
!
- WRITE(11,'(A)') " INTERFACE h5awrite_f"
+ WRITE(11,'(2X,A)') "INTERFACE h5awrite_f"
DO i = 1, num_rkinds
j = rkind(i)
WRITE(chr2,'(I2)') j
DO k = 1, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5awrite_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5awrite_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
ENDDO
END DO
DO i = 1, num_ikinds
j = ikind(i)
WRITE(chr2,'(I2)') j
DO k = 1, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5awrite_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5awrite_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
ENDDO
END DO
DO k = 2, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5awrite_ckind_rank"//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5awrite_ckind_rank"//chr_rank(k)
ENDDO
- WRITE(11,'(A)') " END INTERFACE"
+ WRITE(11,'(2X,A)') "END INTERFACE"
! H5Aread_f
- WRITE(11,'(A)') " INTERFACE h5aread_f"
+ WRITE(11,'(2X,A)') "INTERFACE h5aread_f"
DO i = 1, num_rkinds
j = rkind(i)
WRITE(chr2,'(I2)') j
DO k = 1, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5aread_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5aread_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
ENDDO
END DO
DO i = 1, num_ikinds
j = ikind(i)
WRITE(chr2,'(I2)') j
DO k = 1, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5aread_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5aread_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
ENDDO
END DO
DO k = 2, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5aread_ckind_rank"//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5aread_ckind_rank"//chr_rank(k)
ENDDO
- WRITE(11,'(A)') " END INTERFACE"
+ WRITE(11,'(2X,A)') "END INTERFACE"
!***************
! H5D INTERFACES
!***************
!
! H5Dwrite_f
- WRITE(11,'(A)') " INTERFACE h5dwrite_f"
+ WRITE(11,'(2X,A)') "INTERFACE h5dwrite_f"
DO i = 1, num_rkinds
j = rkind(i)
WRITE(chr2,'(I2)') j
DO k = 1, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5dwrite_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5dwrite_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
ENDDO
END DO
DO i = 1, num_ikinds
j = ikind(i)
WRITE(chr2,'(I2)') j
DO k = 1, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5dwrite_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5dwrite_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
ENDDO
END DO
DO k = 2, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5dwrite_ckind_rank"//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5dwrite_ckind_rank"//chr_rank(k)
END DO
- WRITE(11,'(A)') " END INTERFACE"
+ WRITE(11,'(2X,A)') "END INTERFACE"
! H5Dread_f
- WRITE(11,'(A)') " INTERFACE h5dread_f"
+ WRITE(11,'(2X,A)') "INTERFACE h5dread_f"
DO i = 1, num_rkinds
j = rkind(i)
WRITE(chr2,'(I2)') j
DO k = 1, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5dread_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5dread_rkind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
ENDDO
END DO
DO i = 1, num_ikinds
j = ikind(i)
WRITE(chr2,'(I2)') j
DO k = 1, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5dread_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5dread_ikind_"//TRIM(ADJUSTL(chr2))//'_rank'//chr_rank(k)
ENDDO
END DO
DO k = 2, 8
- WRITE(11,'(A)') " MODULE PROCEDURE h5dread_ckind_rank"//chr_rank(k)
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5dread_ckind_rank"//chr_rank(k)
ENDDO
- WRITE(11,'(A)') " END INTERFACE"
+ WRITE(11,'(2X,A)') "END INTERFACE"
!***************
! H5P INTERFACES
!***************
!
! H5Pset_fill_value_f
- WRITE(11,'(A)') " INTERFACE h5pset_fill_value_f"
+ WRITE(11,'(2X,A)') "INTERFACE h5pset_fill_value_f"
DO i = 1, num_rkinds
j = rkind(i)
WRITE(chr2,'(I2)') j
- WRITE(11,'(A)') " MODULE PROCEDURE h5pset_fill_value_kind_"//TRIM(ADJUSTL(chr2))
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5pset_fill_value_kind_"//TRIM(ADJUSTL(chr2))
END DO
- WRITE(11,'(A)') " END INTERFACE"
+ WRITE(11,'(2X,A)') "END INTERFACE"
! H5Pget_fill_value_f
- WRITE(11,'(A)') " INTERFACE h5pget_fill_value_f"
+ WRITE(11,'(2X,A)') "INTERFACE h5pget_fill_value_f"
DO i = 1, num_rkinds
j = rkind(i)
WRITE(chr2,'(I2)') j
- WRITE(11,'(A)') " MODULE PROCEDURE h5pget_fill_value_kind_"//TRIM(ADJUSTL(chr2))
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5pget_fill_value_kind_"//TRIM(ADJUSTL(chr2))
END DO
- WRITE(11,'(A)') " END INTERFACE"
+ WRITE(11,'(2X,A)') "END INTERFACE"
! H5Pset_f
- WRITE(11,'(A)') " INTERFACE h5pset_f"
+ WRITE(11,'(2X,A)') "INTERFACE h5pset_f"
DO i = 1, num_rkinds
j = rkind(i)
WRITE(chr2,'(I2)') j
- WRITE(11,'(A)') " MODULE PROCEDURE h5pset_kind_"//TRIM(ADJUSTL(chr2))
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5pset_kind_"//TRIM(ADJUSTL(chr2))
END DO
- WRITE(11,'(A)') " END INTERFACE"
+ WRITE(11,'(2X,A)') "END INTERFACE"
! H5Pget_f
- WRITE(11,'(A)') " INTERFACE h5pget_f"
+ WRITE(11,'(2X,A)') "INTERFACE h5pget_f"
DO i = 1, num_rkinds
j = rkind(i)
WRITE(chr2,'(I2)') j
- WRITE(11,'(A)') " MODULE PROCEDURE h5pget_kind_"//TRIM(ADJUSTL(chr2))
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5pget_kind_"//TRIM(ADJUSTL(chr2))
END DO
- WRITE(11,'(A)') " END INTERFACE"
+ WRITE(11,'(2X,A)') "END INTERFACE"
! H5Pregister_f
- WRITE(11,'(A)') " INTERFACE h5pregister_f"
+ WRITE(11,'(2X,A)') "INTERFACE h5pregister_f"
DO i = 1, num_rkinds
j = rkind(i)
WRITE(chr2,'(I2)') j
- WRITE(11,'(A)') " MODULE PROCEDURE h5pregister_kind_"//TRIM(ADJUSTL(chr2))
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5pregister_kind_"//TRIM(ADJUSTL(chr2))
END DO
- WRITE(11,'(A)') " END INTERFACE"
+ WRITE(11,'(2X,A)') "END INTERFACE"
! H5Pinsert_f
- WRITE(11,'(A)') " INTERFACE h5pinsert_f"
+ WRITE(11,'(2X,A)') "INTERFACE h5pinsert_f"
DO i = 1, num_rkinds
j = rkind(i)
WRITE(chr2,'(I2)') j
- WRITE(11,'(A)') " MODULE PROCEDURE h5pinsert_kind_"//TRIM(ADJUSTL(chr2))
+ WRITE(11,'(5X,A)') "MODULE PROCEDURE h5pinsert_kind_"//TRIM(ADJUSTL(chr2))
END DO
- WRITE(11,'(A)') " END INTERFACE"
+ WRITE(11,'(2X,A)') "END INTERFACE"
WRITE(11,'(A)') 'CONTAINS'
diff --git a/java/test/TestH5Z.java b/java/test/TestH5Z.java
index 31adf22..f3049ed 100644
--- a/java/test/TestH5Z.java
+++ b/java/test/TestH5Z.java
@@ -41,8 +41,8 @@ public class TestH5Z {
@Test
public void testH5Zfilter_avail() {
try {
- int filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE);
- assertTrue("H5.H5Zfilter_avail_DEFLATE", filter_found > 0);
+ int filter_found;
+
filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_FLETCHER32);
assertTrue("H5.H5Zfilter_avail_FLETCHER32", filter_found > 0);
filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_NBIT);
@@ -51,8 +51,12 @@ public class TestH5Z {
assertTrue("H5.H5Zfilter_avail_SCALEOFFSET", filter_found > 0);
filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SHUFFLE);
assertTrue("H5.H5Zfilter_avail_SHUFFLE", filter_found > 0);
-// filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SZIP);
-// assertTrue("H5.H5Zfilter_avail_SZIP", filter_found > 0);
+
+ // Just make sure H5Zfilter_avail() doesn't fail with szip/zlib
+ // since there is no way for us to determine if they should be present
+ // or not.
+ filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE);
+ filter_found = H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SZIP);
}
catch (Throwable err) {
err.printStackTrace();
@@ -63,9 +67,8 @@ public class TestH5Z {
@Test
public void testH5Zget_filter_info() {
try {
- int filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_DEFLATE);
- assertTrue("H5.H5Zget_filter_info_DEFLATE_DECODE_ENABLED", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
- assertTrue("H5.H5Zget_filter_info_DEFLATE_ENCODE_ENABLED", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
+ int filter_flag;
+
filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_FLETCHER32);
assertTrue("H5.H5Zget_filter_info_FLETCHER32_DECODE_ENABLED", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
assertTrue("H5.H5Zget_filter_info_FLETCHER32_ENCODE_ENABLED", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
@@ -78,9 +81,19 @@ public class TestH5Z {
filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SHUFFLE);
assertTrue("H5.H5Zget_filter_info_DECODE_SHUFFLE_ENABLED", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
assertTrue("H5.H5Zget_filter_info_ENCODE_SHUFFLE_ENABLED", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
-// filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SZIP);
-// assertTrue("H5.H5Zget_filter_info_DECODE_SZIP_ENABLED", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
-// assertTrue("H5.H5Zget_filter_info_ENCODE_SZIP_ENABLED", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
+
+ if(1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_DEFLATE)) {
+ filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_DEFLATE);
+ assertTrue("H5.H5Zget_filter_info_DEFLATE_DECODE_ENABLED", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
+ assertTrue("H5.H5Zget_filter_info_DEFLATE_ENCODE_ENABLED", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_ENCODE_ENABLED) > 0);
+ }
+
+ if(1 == H5.H5Zfilter_avail(HDF5Constants.H5Z_FILTER_SZIP)) {
+ filter_flag = H5.H5Zget_filter_info(HDF5Constants.H5Z_FILTER_SZIP);
+ // Decode should always be available, but we have no way of determining
+ // if encode is so don't assert on that.
+ assertTrue("H5.H5Zget_filter_info_DECODE_SZIP_ENABLED", (filter_flag & HDF5Constants.H5Z_FILTER_CONFIG_DECODE_ENABLED) > 0);
+ }
}
catch (Throwable err) {
err.printStackTrace();
@@ -96,3 +109,4 @@ public class TestH5Z {
H5.H5Zunregister(HDF5Constants.H5Z_FILTER_SHUFFLE);
}
}
+
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index dcc9892..4661b59 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -170,7 +170,7 @@ New Features
(DER - 2018/10/26, HDFFV-10614)
- Parallel Library:
+ Parallel Library:
-----------------
-
@@ -233,7 +233,17 @@ New Features
Tools:
------
- -
+ - The h5repart -family-to-sec2 argument was changed to -family-to-single
+
+ In order to better support other single-file VFDs which could work with
+ h5repart, the -family-to-sec2 argument was renamed to -family-to-single.
+ This is just a name change and the functionality of the argument has not
+ changed.
+
+ The -family-to-sec2 argument has been kept for backwards-compatibility.
+ This argument should be considered deprecated.
+
+ (DER - 2018/11/14, HDFFV-10633)
High-Level APIs:
---------------
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 22dc05a..cb6b925 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -949,7 +949,10 @@ H5D__chunk_init(H5F_t *f, const H5D_t *dset, hid_t dapl_id)
/* Initial scaled dimension sizes */
if(dset->shared->layout.u.chunk.dim[u] == 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", u)
- rdcc->scaled_dims[u] = dset->shared->curr_dims[u] / dset->shared->layout.u.chunk.dim[u];
+
+ /* Round up to the next integer # of chunks, to accommodate partial chunks */
+ rdcc->scaled_dims[u] = (dset->shared->curr_dims[u] + dset->shared->layout.u.chunk.dim[u] - 1) /
+ dset->shared->layout.u.chunk.dim[u];
if( !(scaled_power2up = H5VM_power2up(rdcc->scaled_dims[u])) )
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get the next power of 2")
@@ -2799,6 +2802,7 @@ H5D__chunk_hash_val(const H5D_shared_t *shared, const hsize_t *scaled)
hsize_t val; /* Intermediate value */
unsigned ndims = shared->ndims; /* Rank of dataset */
unsigned ret = 0; /* Value to return */
+ unsigned u; /* Local index variable */
FUNC_ENTER_STATIC_NOERR
@@ -2809,17 +2813,11 @@ H5D__chunk_hash_val(const H5D_shared_t *shared, const hsize_t *scaled)
/* If the fastest changing dimension doesn't have enough entropy, use
* other dimensions too
*/
- if(ndims > 1 && shared->cache.chunk.scaled_dims[ndims - 1] <= shared->cache.chunk.nslots) {
- unsigned u; /* Local index variable */
-
- val = scaled[0];
- for(u = 1; u < ndims; u++) {
- val <<= shared->cache.chunk.scaled_encode_bits[u];
- val ^= scaled[u];
- } /* end for */
- } /* end if */
- else
- val = scaled[ndims - 1];
+ val = scaled[0];
+ for(u = 1; u < ndims; u++) {
+ val <<= shared->cache.chunk.scaled_encode_bits[u];
+ val ^= scaled[u];
+ } /* end for */
/* Modulo value against the number of array slots */
ret = (unsigned)(val % shared->cache.chunk.nslots);
diff --git a/src/H5FDlog.c b/src/H5FDlog.c
index 7c2297a..3dcd7f5 100644
--- a/src/H5FDlog.c
+++ b/src/H5FDlog.c
@@ -117,7 +117,7 @@ typedef struct H5FD_log_t {
* Whether to eliminate the family driver info and convert this file to
* a single file
*/
- hbool_t fam_to_sec2;
+ hbool_t fam_to_single;
/* Fields for tracking I/O operations */
unsigned char *nread; /* Number of reads from a file location */
@@ -635,13 +635,13 @@ H5FD_log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
/* Check for non-default FAPL */
if(H5P_FILE_ACCESS_DEFAULT != fapl_id) {
/* This step is for h5repart tool only. If user wants to change file driver from
- * family to sec2 while using h5repart, this private property should be set so that
- * in the later step, the library can ignore the family driver information saved
- * in the superblock.
+ * family to one that uses single files (sec2, etc.) while using h5repart, this
+ * private property should be set so that in the later step, the library can ignore
+ * the family driver information saved in the superblock.
*/
- if(H5P_exist_plist(plist, H5F_ACS_FAMILY_TO_SEC2_NAME) > 0)
- if(H5P_get(plist, H5F_ACS_FAMILY_TO_SEC2_NAME, &file->fam_to_sec2) < 0)
- HGOTO_ERROR(H5E_VFL, H5E_CANTGET, NULL, "can't get property of changing family to sec2")
+ if(H5P_exist_plist(plist, H5F_ACS_FAMILY_TO_SINGLE_NAME) > 0)
+ if(H5P_get(plist, H5F_ACS_FAMILY_TO_SINGLE_NAME, &file->fam_to_single) < 0)
+ HGOTO_ERROR(H5E_VFL, H5E_CANTGET, NULL, "can't get property of changing family to single")
} /* end if */
/* Set return value */
@@ -900,7 +900,7 @@ H5FD_log_query(const H5FD_t *_file, unsigned long *flags /* out */)
*flags |= H5FD_FEAT_DEFAULT_VFD_COMPATIBLE; /* VFD creates a file which can be opened with the default VFD */
/* Check for flags that are set by h5repart */
- if(file && file->fam_to_sec2)
+ if(file && file->fam_to_single)
*flags |= H5FD_FEAT_IGNORE_DRVRINFO; /* Ignore the driver info when file is opened (which eliminates it) */
} /* end if */
diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c
index 32aff0f..06c008d 100644
--- a/src/H5FDsec2.c
+++ b/src/H5FDsec2.c
@@ -94,7 +94,7 @@ typedef struct H5FD_sec2_t {
* Whether to eliminate the family driver info and convert this file to
* a single file.
*/
- hbool_t fam_to_sec2;
+ hbool_t fam_to_single;
} H5FD_sec2_t;
@@ -386,13 +386,13 @@ H5FD_sec2_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
HGOTO_ERROR(H5E_VFL, H5E_BADTYPE, NULL, "not a file access property list")
/* This step is for h5repart tool only. If user wants to change file driver from
- * family to sec2 while using h5repart, this private property should be set so that
- * in the later step, the library can ignore the family driver information saved
- * in the superblock.
+ * family to one that uses single files (sec2, etc.) while using h5repart, this
+ * private property should be set so that in the later step, the library can ignore
+ * the family driver information saved in the superblock.
*/
- if(H5P_exist_plist(plist, H5F_ACS_FAMILY_TO_SEC2_NAME) > 0)
- if(H5P_get(plist, H5F_ACS_FAMILY_TO_SEC2_NAME, &file->fam_to_sec2) < 0)
- HGOTO_ERROR(H5E_VFL, H5E_CANTGET, NULL, "can't get property of changing family to sec2")
+ if(H5P_exist_plist(plist, H5F_ACS_FAMILY_TO_SINGLE_NAME) > 0)
+ if(H5P_get(plist, H5F_ACS_FAMILY_TO_SINGLE_NAME, &file->fam_to_single) < 0)
+ HGOTO_ERROR(H5E_VFL, H5E_CANTGET, NULL, "can't get property of changing family to single")
} /* end if */
/* Set return value */
@@ -532,7 +532,7 @@ H5FD_sec2_query(const H5FD_t *_file, unsigned long *flags /* out */)
*flags |= H5FD_FEAT_DEFAULT_VFD_COMPATIBLE; /* VFD creates a file which can be opened with the default VFD */
/* Check for flags that are set by h5repart */
- if(file && file->fam_to_sec2)
+ if(file && file->fam_to_single)
*flags |= H5FD_FEAT_IGNORE_DRVRINFO; /* Ignore the driver info when file is opened (which eliminates it) */
} /* end if */
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index 00aefa0..83513a5 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -483,7 +483,7 @@ typedef struct H5F_t H5F_t;
#define H5F_ACS_CLOSE_DEGREE_NAME "close_degree" /* File close degree */
#define H5F_ACS_FAMILY_OFFSET_NAME "family_offset" /* Offset position in file for family file driver */
#define H5F_ACS_FAMILY_NEWSIZE_NAME "family_newsize" /* New member size of family driver. (private property only used by h5repart) */
-#define H5F_ACS_FAMILY_TO_SEC2_NAME "family_to_sec2" /* Whether to convert family to sec2 driver. (private property only used by h5repart) */
+#define H5F_ACS_FAMILY_TO_SINGLE_NAME "family_to_single" /* Whether to convert family to a single-file driver. (private property only used by h5repart) */
#define H5F_ACS_MULTI_TYPE_NAME "multi_type" /* Data type in multi file driver */
#define H5F_ACS_LIBVER_LOW_BOUND_NAME "libver_low_bound" /* 'low' bound of library format versions */
#define H5F_ACS_LIBVER_HIGH_BOUND_NAME "libver_high_bound" /* 'high' bound of library format versions */
diff --git a/src/H5Pfapl.c b/src/H5Pfapl.c
index f4dbd0a..a792e57 100644
--- a/src/H5Pfapl.c
+++ b/src/H5Pfapl.c
@@ -135,10 +135,11 @@
* property only used by h5repart */
#define H5F_ACS_FAMILY_NEWSIZE_SIZE sizeof(hsize_t)
#define H5F_ACS_FAMILY_NEWSIZE_DEF 0
-/* Definition for whether to convert family to sec2 driver. It's private
- * property only used by h5repart */
-#define H5F_ACS_FAMILY_TO_SEC2_SIZE sizeof(hbool_t)
-#define H5F_ACS_FAMILY_TO_SEC2_DEF FALSE
+/* Definition for whether to convert family to a single-file driver.
+ * It's a private property only used by h5repart.
+ */
+#define H5F_ACS_FAMILY_TO_SINGLE_SIZE sizeof(hbool_t)
+#define H5F_ACS_FAMILY_TO_SINGLE_DEF FALSE
/* Definition for data type in multi file driver */
#define H5F_ACS_MULTI_TYPE_SIZE sizeof(H5FD_mem_t)
#define H5F_ACS_MULTI_TYPE_DEF H5FD_MEM_DEFAULT
@@ -391,7 +392,7 @@ static const unsigned H5F_def_gc_ref_g = H5F_ACS_GARBG_COLCT_REF_DEF;
static const H5F_close_degree_t H5F_def_close_degree_g = H5F_CLOSE_DEGREE_DEF; /* Default file close degree */
static const hsize_t H5F_def_family_offset_g = H5F_ACS_FAMILY_OFFSET_DEF; /* Default offset for family VFD */
static const hsize_t H5F_def_family_newsize_g = H5F_ACS_FAMILY_NEWSIZE_DEF; /* Default size of new files for family VFD */
-static const hbool_t H5F_def_family_to_sec2_g = H5F_ACS_FAMILY_TO_SEC2_DEF; /* Default ?? for family VFD */
+static const hbool_t H5F_def_family_to_single_g = H5F_ACS_FAMILY_TO_SINGLE_DEF; /* Default ?? for family VFD */
static const H5FD_mem_t H5F_def_mem_type_g = H5F_ACS_MULTI_TYPE_DEF; /* Default file space type for multi VFD */
static const H5F_libver_t H5F_def_libver_low_bound_g = H5F_ACS_LIBVER_LOW_BOUND_DEF; /* Default setting for "low" bound of format version */
@@ -527,9 +528,9 @@ H5P__facc_reg_prop(H5P_genclass_t *pclass)
NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
- /* Register the private property of whether convert family to sec2 driver. It's used by h5repart only. */
+ /* Register the private property of whether convert family to a single-file driver. It's used by h5repart only. */
/* (Note: this property should not have an encode/decode callback -QAK) */
- if(H5P__register_real(pclass, H5F_ACS_FAMILY_TO_SEC2_NAME, H5F_ACS_FAMILY_TO_SEC2_SIZE, &H5F_def_family_to_sec2_g,
+ if(H5P__register_real(pclass, H5F_ACS_FAMILY_TO_SINGLE_NAME, H5F_ACS_FAMILY_TO_SINGLE_SIZE, &H5F_def_family_to_single_g,
NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
diff --git a/tools/src/misc/h5repart.c b/tools/src/misc/h5repart.c
index cdc554f..2f4d93e 100644
--- a/tools/src/misc/h5repart.c
+++ b/tools/src/misc/h5repart.c
@@ -29,11 +29,12 @@
#define NAMELEN 4096
#define GB *1024*1024*1024
-/*Make these 2 private properties(defined in H5Fprivate.h) available to h5repart.
- *The first one updates the member file size in the superblock. The second one
- *change file driver from family to sec2. */
+/* Make these 2 private properties(defined in H5Fprivate.h) available to h5repart.
+ * The first one updates the member file size in the superblock. The second one
+ * change file driver from family to a single file driver.
+ */
#define H5F_ACS_FAMILY_NEWSIZE_NAME "family_newsize"
-#define H5F_ACS_FAMILY_TO_SEC2_NAME "family_to_sec2"
+#define H5F_ACS_FAMILY_TO_SINGLE_NAME "family_to_single"
/*-------------------------------------------------------------------------
@@ -53,13 +54,14 @@
static void
usage (const char *progname)
{
- fprintf(stderr, "usage: %s [-v] [-V] [-[b|m] N[g|m|k]] [-family_to_sec2] SRC DST\n",
+ fprintf(stderr, "usage: %s [-v] [-V] [-[b|m] N[g|m|k]] [-family_to_sec2|-family_to_single] SRC DST\n",
progname);
fprintf(stderr, " -v Produce verbose output\n");
fprintf(stderr, " -V Print a version number and exit\n");
fprintf(stderr, " -b N The I/O block size, defaults to 1kB\n");
fprintf(stderr, " -m N The destination member size or 1GB\n");
- fprintf(stderr, " -family_to_sec2 Change file driver from family to sec2\n");
+ fprintf(stderr, " -family_to_sec2 Deprecated version of -family_to_single (below)\n");
+ fprintf(stderr, " -family_to_single Change file driver from family to the default single-file VFD (windows or sec2)\n");
fprintf(stderr, " SRC The name of the source file\n");
fprintf(stderr, " DST The name of the destination files\n");
fprintf(stderr, "Sizes may be suffixed with `g' for GB, `m' for MB or "
@@ -186,7 +188,7 @@ main (int argc, char *argv[])
hid_t fapl; /*file access property list */
hid_t file;
hsize_t hdsize; /*destination logical memb size */
- hbool_t family_to_sec2=FALSE; /*change family to sec2 driver? */
+ hbool_t family_to_single = FALSE; /*change family to single file driver? */
/*
* Get the program name from argv[0]. Use only the last component.
@@ -206,7 +208,10 @@ main (int argc, char *argv[])
prog_name, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE);
exit(EXIT_SUCCESS);
} else if (!strcmp (argv[argno], "-family_to_sec2")) {
- family_to_sec2 = TRUE;
+ family_to_single = TRUE;
+ argno++;
+ } else if (!strcmp (argv[argno], "-family_to_single")) {
+ family_to_single = TRUE;
argno++;
} else if ('b'==argv[argno][1]) {
blk_size = (size_t)get_size (prog_name, &argno, argc, argv);
@@ -422,11 +427,12 @@ main (int argc, char *argv[])
exit (EXIT_FAILURE);
}
- if(family_to_sec2) {
- /* The user wants to change file driver from family to sec2. Open the file
- * with sec2 driver. This property signals the library to ignore the family
- * driver information saved in the superblock. */
- if(H5Pset(fapl, H5F_ACS_FAMILY_TO_SEC2_NAME, &family_to_sec2) < 0) {
+ if(family_to_single) {
+ /* The user wants to change file driver from family to a single-file VFD.
+ * Open the file with the sec2, windows, etc. driver. This property signals
+ * the library to ignore the family driver information saved in the superblock.
+ */
+ if(H5Pset(fapl, H5F_ACS_FAMILY_TO_SINGLE_NAME, &family_to_single) < 0) {
perror ("H5Pset");
exit (EXIT_FAILURE);
}
@@ -449,13 +455,14 @@ main (int argc, char *argv[])
/* If the new file is a family file, try to open file for "read and write" to
* flush metadata. Flushing metadata will update the superblock to the new
- * member size. If the original file is a family file and the new file is a sec2
- * file, the property FAMILY_TO_SEC2 will signal the library to switch to sec2
- * driver when the new file is opened. If the original file is a sec2 file and the
- * new file can only be a sec2 file, reopen the new file should fail. There's
- * nothing to do in this case. */
+ * member size. If the original file is a family file and the new file is a single
+ * file, the property FAMILY_TO_SINGLE will signal the library to switch to default
+ * single-file driver when the new file is opened. If the original file is a single
+ * file and the new file can only be a single file, reopen the new file should fail.
+ * There's nothing to do in this case.
+ */
H5E_BEGIN_TRY {
- file=H5Fopen(dst_gen_name, H5F_ACC_RDWR, fapl);
+ file = H5Fopen(dst_gen_name, H5F_ACC_RDWR, fapl);
} H5E_END_TRY;
if(file>=0) {
diff --git a/tools/test/misc/CMakeTestsRepart.cmake b/tools/test/misc/CMakeTestsRepart.cmake
index 37da903..830de11 100644
--- a/tools/test/misc/CMakeTestsRepart.cmake
+++ b/tools/test/misc/CMakeTestsRepart.cmake
@@ -68,6 +68,7 @@
scd_family00001.h5
scd_family00002.h5
scd_family00003.h5
+ family_to_single.h5
family_to_sec2.h5
)
if (NOT "${last_test}" STREQUAL "")
@@ -84,6 +85,10 @@
set_tests_properties (H5REPART-h5repart_5K PROPERTIES DEPENDS H5REPART-clearall-objects)
# convert family file to sec2 file of 20,000 bytes
+ add_test (NAME H5REPART-h5repart_single COMMAND $<TARGET_FILE:h5repart> -m 20000 -family_to_single family_file%05d.h5 family_to_single.h5)
+ set_tests_properties (H5REPART-h5repart_single PROPERTIES DEPENDS H5REPART-clearall-objects)
+
+ # convert family file to sec2 file of 20,000 bytes (old argument)
add_test (NAME H5REPART-h5repart_sec2 COMMAND $<TARGET_FILE:h5repart> -m 20000 -family_to_sec2 family_file%05d.h5 family_to_sec2.h5)
set_tests_properties (H5REPART-h5repart_sec2 PROPERTIES DEPENDS H5REPART-clearall-objects)
diff --git a/tools/test/misc/repart_test.c b/tools/test/misc/repart_test.c
index 4016ee8..b8e0292 100644
--- a/tools/test/misc/repart_test.c
+++ b/tools/test/misc/repart_test.c
@@ -26,12 +26,13 @@
const char *FILENAME[] = {
"fst_family%05d.h5",
"scd_family%05d.h5",
+ "family_to_single.h5",
"family_to_sec2.h5",
NULL
};
herr_t test_family_h5repart_opens(void);
-herr_t test_sec2_h5repart_opens(void);
+herr_t test_single_h5repart_opens(void);
/*-------------------------------------------------------------------------
@@ -90,23 +91,28 @@ error:
/*-------------------------------------------------------------------------
- * Function: test_sec2_h5repart_opens
+ * Function: test_single_h5repart_opens
*
- * Purpose: Tries to reopen a sec2 file.
+ * Purpose: Tries to reopen a single file.
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
herr_t
-test_sec2_h5repart_opens(void)
+test_single_h5repart_opens(void)
{
hid_t fid = -1;
- /* open the sec2 file */
+ /* open the single file */
if ((fid = H5Fopen(FILENAME[2], H5F_ACC_RDWR, H5P_DEFAULT)) < 0)
goto error;
+ if (H5Fclose(fid) < 0)
+ goto error;
+ /* open the single file (created using the old argument) */
+ if ((fid = H5Fopen(FILENAME[3], H5F_ACC_RDWR, H5P_DEFAULT)) < 0)
+ goto error;
if (H5Fclose(fid) < 0)
goto error;
@@ -119,7 +125,7 @@ error:
return FAIL;
-} /* end test_sec2_h5repart_opens() */
+} /* end test_single_h5repart_opens() */
/*-------------------------------------------------------------------------
@@ -137,7 +143,7 @@ main(void)
int nerrors = 0;
nerrors += test_family_h5repart_opens() < 0 ? 1 : 0;
- nerrors += test_sec2_h5repart_opens() < 0 ? 1 : 0;
+ nerrors += test_single_h5repart_opens() < 0 ? 1 : 0;
if (nerrors)
goto error;
@@ -150,3 +156,4 @@ error:
nerrors, 1 == nerrors ? "" : "S");
HDexit(EXIT_FAILURE);
} /* end main() */
+
diff --git a/tools/test/misc/testh5repart.sh.in b/tools/test/misc/testh5repart.sh.in
index 594d37e..143f607 100644
--- a/tools/test/misc/testh5repart.sh.in
+++ b/tools/test/misc/testh5repart.sh.in
@@ -171,7 +171,9 @@ COPY_TESTFILES_TO_TESTDIR
TOOLTEST -m 20000 family_file%05d.h5 fst_family%05d.h5
# repartition family member size to 5 KB.
TOOLTEST -m 5k family_file%05d.h5 scd_family%05d.h5
-# convert family file to sec2 file of 20,000 bytes
+# convert family file to single file of 20,000 bytes
+TOOLTEST -m 20000 -family_to_single family_file%05d.h5 family_to_single.h5
+# convert family file to single file of 20,000 bytes (old argument)
TOOLTEST -m 20000 -family_to_sec2 family_file%05d.h5 family_to_sec2.h5
# test the output files repartitioned above.
@@ -183,7 +185,7 @@ CLEAN_TESTFILES_AND_TESTDIR
if test -z "$HDF5_NOCLEANUP"; then
cd $actual_dir
- rm -f fst_family*.h5 scd_family*.h5 family_to_sec2.h5
+ rm -f fst_family*.h5 scd_family*.h5 family_to_single.h5 family_to_sec2.h5
fi
if test $nerrors -eq 0 ; then
diff --git a/tools/test/perform/CMakeLists.txt b/tools/test/perform/CMakeLists.txt
index fa41608..14abdec 100644
--- a/tools/test/perform/CMakeLists.txt
+++ b/tools/test/perform/CMakeLists.txt
@@ -51,6 +51,16 @@ TARGET_C_PROPERTIES (iopipe STATIC)
target_link_libraries (iopipe PRIVATE ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
set_target_properties (iopipe PROPERTIES FOLDER perform)
+#-- Adding test for chunk_cache
+set (chunk_cache_SOURCES
+ ${HDF5_TOOLS_TEST_PERFORM_SOURCE_DIR}/chunk_cache.c
+)
+add_executable (chunk_cache ${chunk_cache_SOURCES})
+target_include_directories(chunk_cache PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+TARGET_C_PROPERTIES (chunk_cache STATIC)
+target_link_libraries (chunk_cache PRIVATE ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
+set_target_properties (chunk_cache PROPERTIES FOLDER perform)
+
#-- Adding test for overhead
set (overhead_SOURCES
${HDF5_TOOLS_TEST_PERFORM_SOURCE_DIR}/overhead.c
diff --git a/tools/test/perform/Makefile.am b/tools/test/perform/Makefile.am
index 5a89a66..39800d7 100644
--- a/tools/test/perform/Makefile.am
+++ b/tools/test/perform/Makefile.am
@@ -50,12 +50,12 @@ if BUILD_PARALLEL_CONDITIONAL
TEST_PROG_PARA=h5perf perf
endif
# Serial test programs.
-TEST_PROG = iopipe chunk overhead zip_perf perf_meta h5perf_serial $(BUILD_ALL_PROGS)
+TEST_PROG = iopipe chunk chunk_cache overhead zip_perf perf_meta h5perf_serial $(BUILD_ALL_PROGS)
# check_PROGRAMS will be built but not installed. Do not any executable
# that is in bin_PROGRAMS already. Otherwise, it will be removed twice in
# "make clean" and some systems, e.g., AIX, do not like it.
-check_PROGRAMS= iopipe chunk overhead zip_perf perf_meta $(BUILD_ALL_PROGS) perf
+check_PROGRAMS= iopipe chunk chunk_cache overhead zip_perf perf_meta $(BUILD_ALL_PROGS) perf
h5perf_SOURCES=pio_perf.c pio_engine.c
h5perf_serial_SOURCES=sio_perf.c sio_engine.c
diff --git a/tools/test/perform/chunk_cache.c b/tools/test/perform/chunk_cache.c
new file mode 100644
index 0000000..429f70a
--- /dev/null
+++ b/tools/test/perform/chunk_cache.c
@@ -0,0 +1,405 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Purpose: check the performance of chunk cache in these two cases (HDFFV-10601):
+ * 1. partial chunks exist along any dimension.
+ * 2. number of slots in chunk cache is smaller than the number of chunks
+ * in the fastest-growing dimension.
+ */
+#include "hdf5.h"
+#include "H5private.h"
+
+#define FILENAME "chunk_cache_perf.h5"
+
+#define RANK 2
+
+#define DSET1_NAME "partial_chunks"
+#define DSET1_DIM1 9 * 1000
+#define DSET1_DIM2 9
+#define CHUNK1_DIM1 2 * 1000
+#define CHUNK1_DIM2 2
+
+#define DSET2_NAME "hash_value"
+#define DSET2_DIM1 300
+#define DSET2_DIM2 600
+#define CHUNK2_DIM1 100
+#define CHUNK2_DIM2 100
+
+#define RDCC_NSLOTS 5
+#define RDCC_NBYTES 1024 * 1024 * 10
+#define RDCC_W0 0.75F
+
+#define FILTER_COUNTER 306
+static size_t nbytes_global;
+
+typedef struct test_time_t {
+ long tv_sec;
+ long tv_usec;
+} test_time_t;
+
+/* Local function prototypes for the dummy filter */
+static size_t
+counter (unsigned flags, size_t cd_nelmts,
+ const unsigned *cd_values, size_t nbytes,
+ size_t *buf_size, void **buf);
+
+/* This message derives from H5Z */
+const H5Z_class2_t H5Z_COUNTER[1] = {{
+ H5Z_CLASS_T_VERS, /* H5Z_class_t version */
+ FILTER_COUNTER, /* Filter id number */
+ 1, 1, /* Encoding and decoding enabled */
+ "counter", /* Filter name for debugging */
+ NULL, /* The "can apply" callback */
+ NULL, /* The "set local" callback */
+ counter, /* The actual filter function */
+}};
+
+/*-------------------------------------------------------------------------
+ * Count number of bytes but don't do anything else. Keep
+ * track of the data of chunks being read from file into memory.
+ */
+static size_t
+counter (unsigned flags, size_t cd_nelmts,
+ const unsigned *cd_values, size_t nbytes,
+ size_t *buf_size, void **buf)
+{
+ nbytes_global += nbytes;
+ return nbytes;
+}
+
+/*---------------------------------------------------------------------------*/
+double retrieve_time(void)
+{
+#ifdef H5_HAVE_GETTIMEOFDAY
+ struct timeval t;
+ HDgettimeofday(&t, NULL);
+ return ((double)t.tv_sec + (double)t.tv_usec / 1000000);
+#else
+ return 0.0;
+#endif
+}
+
+/*---------------------------------------------------------------------------*/
+static void
+cleanup (void)
+{
+ if (!getenv ("HDF5_NOCLEANUP")) {
+ remove (FILENAME);
+ }
+}
+
+/*-------------------------------------------------------------------------------
+ * Create a chunked dataset with partial chunks along either dimensions:
+ * dataset dimension: 9000 x 9
+ * chunk dimension: 2000 x 2
+ */
+static int create_dset1(hid_t file)
+{
+ hid_t dataspace, dataset;
+ hid_t dcpl;
+ hsize_t dims[RANK] = {DSET1_DIM1, DSET1_DIM2};
+ hsize_t chunk_dims[RANK] = {CHUNK1_DIM1, CHUNK1_DIM2};
+ int data[DSET1_DIM1][DSET1_DIM2]; /* data for writing */
+ int i, j;
+
+ /* Create the data space. */
+ if((dataspace = H5Screate_simple (RANK, dims, NULL)) < 0)
+ goto error;
+
+ /* Modify dataset creation properties, i.e. enable chunking */
+ if((dcpl = H5Pcreate (H5P_DATASET_CREATE)) < 0)
+ goto error;
+ if(H5Pset_chunk (dcpl, RANK, chunk_dims) < 0)
+ goto error;
+
+ /* Set the dummy filter simply for counting the number of bytes being read into the memory */
+ if(H5Zregister(H5Z_COUNTER) < 0)
+ goto error;
+
+ if(H5Pset_filter(dcpl, FILTER_COUNTER, 0, 0, NULL) < 0)
+ goto error;
+
+ /* Create a new dataset within the file using chunk creation properties. */
+ if((dataset = H5Dcreate2 (file, DSET1_NAME, H5T_NATIVE_INT, dataspace,
+ H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
+ goto error;
+
+ for (i = 0; i < DSET1_DIM1; i++)
+ for (j = 0; j < DSET1_DIM2; j++)
+ data[i][j] = i+j;
+
+ /* Write data to dataset */
+ if(H5Dwrite (dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, data) < 0)
+ goto error;
+
+ /* Close resources */
+ H5Dclose (dataset);
+ H5Pclose (dcpl);
+ H5Sclose (dataspace);
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose (dataset);
+ H5Pclose (dcpl);
+ H5Sclose (dataspace);
+ } H5E_END_TRY;
+
+ return 1;
+}
+
+/*---------------------------------------------------------------------------
+ * Create a chunked dataset for testing hash values:
+ * dataset dimensions: 300 x 600
+ * chunk dimensions: 100 x 100
+ */
+static int create_dset2(hid_t file)
+{
+ hid_t dataspace, dataset;
+ hid_t dcpl;
+ hsize_t dims[RANK] = {DSET2_DIM1, DSET2_DIM2};
+ hsize_t chunk_dims[RANK] = {CHUNK2_DIM1, CHUNK2_DIM2};
+ int data[DSET2_DIM1][DSET2_DIM2]; /* data for writing */
+ int i, j;
+
+ /* Create the data space. */
+ if((dataspace = H5Screate_simple (RANK, dims, NULL)) < 0)
+ goto error;
+
+ /* Modify dataset creation properties, i.e. enable chunking */
+ if((dcpl = H5Pcreate (H5P_DATASET_CREATE)) < 0)
+ goto error;
+ if(H5Pset_chunk (dcpl, RANK, chunk_dims) < 0)
+ goto error;
+
+ /* Set the dummy filter simply for counting the number of bytes being read into the memory */
+ if(H5Zregister(H5Z_COUNTER) < 0)
+ goto error;
+ if(H5Pset_filter(dcpl, FILTER_COUNTER, 0, 0, NULL) < 0)
+ goto error;
+
+ /* Create a new dataset within the file using chunk creation properties. */
+ if((dataset = H5Dcreate2 (file, DSET2_NAME, H5T_NATIVE_INT, dataspace,
+ H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
+ goto error;
+
+ for (i = 0; i < DSET2_DIM1; i++)
+ for (j = 0; j < DSET2_DIM2; j++)
+ data[i][j] = i+j;
+
+ /* Write data to dataset */
+ if(H5Dwrite (dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, data) < 0)
+ goto error;
+
+ /* Close resources */
+ H5Dclose (dataset);
+ H5Pclose (dcpl);
+ H5Sclose (dataspace);
+
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose (dataset);
+ H5Pclose (dcpl);
+ H5Sclose (dataspace);
+ } H5E_END_TRY;
+
+ return 1;
+}
+/*---------------------------------------------------------------------------
+ * Check the performance of the chunk cache when partial chunks exist
+ * along the dataset dimensions.
+ */
+static int check_partial_chunks_perf(hid_t file)
+{
+ hid_t dataset;
+ hid_t filespace;
+ hid_t memspace;
+ hid_t dapl;
+
+ int rdata[DSET1_DIM2]; /* data for reading */
+ int i;
+
+ hsize_t row_rank = 1;
+ hsize_t row_dim[1] = {DSET1_DIM2};
+ hsize_t start[RANK] = {0, 0};
+ hsize_t count[RANK] = {1, DSET1_DIM2};
+ double start_t, end_t;
+
+ if((dapl = H5Pcreate(H5P_DATASET_ACCESS)) < 0)
+ goto error;
+ if(H5Pset_chunk_cache (dapl, RDCC_NSLOTS, RDCC_NBYTES, RDCC_W0) < 0)
+ goto error;
+
+ dataset = H5Dopen2 (file, DSET1_NAME, dapl);
+
+ memspace = H5Screate_simple(row_rank, row_dim, NULL);
+ filespace = H5Dget_space(dataset);
+
+ nbytes_global = 0;
+
+ start_t = retrieve_time();
+
+ /* Read the data row by row */
+ for(i = 0; i < DSET1_DIM1; i++) {
+ start[0] = i;
+ if(H5Sselect_hyperslab(filespace, H5S_SELECT_SET,
+ start, NULL, count, NULL) < 0)
+ goto error;
+
+ if(H5Dread (dataset, H5T_NATIVE_INT, memspace, filespace,
+ H5P_DEFAULT, rdata) < 0)
+ goto error;
+ }
+
+ end_t = retrieve_time();
+
+#ifdef H5_HAVE_GETTIMEOFDAY
+ printf("1. Partial chunks: total read time is %lf; number of bytes being read from file is %lu\n", (end_t -start_t), nbytes_global);
+#else
+ printf("1. Partial chunks: no total read time because gettimeofday() is not available; number of bytes being read from file is %lu\n", nbytes_global);
+#endif
+
+ H5Dclose (dataset);
+ H5Sclose (filespace);
+ H5Sclose (memspace);
+ H5Pclose (dapl);
+
+ return 0;
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose (dataset);
+ H5Sclose (filespace);
+ H5Sclose (memspace);
+ H5Pclose (dapl);
+ } H5E_END_TRY;
+ return 1;
+}
+
+/*---------------------------------------------------------------------------
+ * Check the performance of chunk cache when the number of cache slots
+ * is smaller than the number of chunks along the fastest-growing
+ * dimension of the dataset.
+ */
+static int check_hash_value_perf(hid_t file)
+{
+ hid_t dataset;
+ hid_t filespace;
+ hid_t memspace;
+ hid_t dapl;
+
+ int rdata[DSET2_DIM1]; /* data for reading */
+ int i;
+
+ hsize_t column_rank = 1;
+ hsize_t column_dim[1] = {DSET2_DIM1};
+ hsize_t start[RANK] = {0, 0};
+ hsize_t count[RANK] = {DSET2_DIM1, 1};
+ double start_t, end_t;
+
+ if((dapl = H5Pcreate(H5P_DATASET_ACCESS)) < 0)
+ goto error;
+ if(H5Pset_chunk_cache (dapl, RDCC_NSLOTS, RDCC_NBYTES, RDCC_W0) < 0)
+ goto error;
+
+ if((dataset = H5Dopen2 (file, DSET2_NAME, dapl)) < 0)
+ goto error;
+ if((memspace = H5Screate_simple(column_rank, column_dim, NULL)) < 0)
+ goto error;
+ if((filespace = H5Dget_space(dataset)) < 0)
+ goto error;
+
+ nbytes_global = 0;
+
+ start_t = retrieve_time();
+
+ /* Read the data column by column */
+ for(i = 0; i < DSET2_DIM2; i++) {
+ start[1] = i;
+ if(H5Sselect_hyperslab(filespace, H5S_SELECT_SET,
+ start, NULL, count, NULL) < 0)
+ goto error;
+
+ if(H5Dread (dataset, H5T_NATIVE_INT, memspace, filespace,
+ H5P_DEFAULT, rdata) < 0)
+ goto error;
+ }
+
+ end_t = retrieve_time();
+
+#ifdef H5_HAVE_GETTIMEOFDAY
+ printf("2. Hash value: total read time is %lf; number of bytes being read from file is %lu\n", (end_t -start_t), nbytes_global);
+#else
+ printf("2. Hash value: no total read time because gettimeofday() is not available; number of bytes being read from file is %lu\n", nbytes_global);
+#endif
+
+ H5Dclose (dataset);
+ H5Sclose (filespace);
+ H5Sclose (memspace);
+ H5Pclose (dapl);
+ return 0;
+
+error:
+ H5E_BEGIN_TRY {
+ H5Dclose (dataset);
+ H5Sclose (filespace);
+ H5Sclose (memspace);
+ H5Pclose (dapl);
+ } H5E_END_TRY;
+ return 1;
+}
+
+/*-------------------------------------------------------------------------------------
+ * Purpose: check the performance of chunk cache in these two cases (HDFFV-10601):
+ * 1. partial chunks exist along any dimension.
+ * 2. number of slots in chunk cache is smaller than the number of chunks
+ * in the fastest-growing dimension.
+ *-------------------------------------------------------------------------------------*/
+int
+main (void)
+{
+ hid_t file; /* handles */
+ int nerrors = 0;
+
+ /* Create a new file. If file exists its contents will be overwritten. */
+ if((file = H5Fcreate (FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+ goto error;
+
+ nerrors += create_dset1(file);
+ nerrors += create_dset2(file);
+
+ if(H5Fclose (file) < 0)
+ goto error;
+
+ /* Re-open the file for testing performance. */
+ if((file = H5Fopen (FILENAME, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
+ goto error;
+
+ nerrors += check_partial_chunks_perf(file);
+ nerrors += check_hash_value_perf(file);
+
+ if(H5Fclose (file) < 0)
+ goto error;
+
+ if (nerrors>0) goto error;
+ cleanup();
+ return 0;
+
+error:
+ fprintf(stderr, "*** ERRORS DETECTED ***\n");
+ return 1;
+}
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