note that compact dataset write may not work with MPI collective write

Author: scivision

API.md

@@ -182,7 +182,7 @@ class(*), intent(in) :: value(..)  !< array to write
 integer, intent(in), dimension(rank(value)), optional :: dset_dims
 integer, intent(in), optional, dimension(rank(value)) :: istart, iend, stride !< array slicing for hyperslab
 integer, intent(in), optional :: chunk_size(rank(value))  !< override auto-chunking
-logical, intent(in), optional :: compact  !< faster I/O for sub-64 kB datasets
+logical, intent(in), optional :: compact  !< faster I/O for sub-64 kB datasets--May not work for MPI collective write
 ```
 
 Write dataset attribute (e.g. units or instrument)

src/write.f90

@@ -124,7 +124,7 @@
   call set_deflate(self, mem_dims, dcpl, chunk_size)
 endif
 
-if(present(compact)) call set_compact(dcpl, dset_dims, compact)
+if(present(compact)) call set_compact(dcpl, dset_dims, compact, dname)
 
 !> create dataset dataspace
 if(size(dset_dims) == 0) then
@@ -181,21 +181,28 @@
 end procedure hdf_create
 
 
-subroutine set_compact(dcpl, dset_dims, compact)
+subroutine set_compact(dcpl, dset_dims, compact, dset_name)
 !! compact dataset (for very small datasets to increase I/O speed)
+!! NOTE: this does not work for collective writes, at least for HDF5 1.12.2. The dataset will be all zero.
 
 integer(HID_T), intent(inout) :: dcpl
 integer(HSIZE_T), intent(in) :: dset_dims(:)
 logical, intent(in) :: compact
+character(*), intent(in) :: dset_name
 
 integer :: ierr
+integer(HSIZE_T) :: Nbytes
 
 if(.not. compact) return
 
 if(dcpl /= H5P_DEFAULT_F) return
 !! datasets are EITHER compact or chunked.
 
-if(product(dset_dims) * 8 > 60000) return
+Nbytes = product(dset_dims) * 8
+if(Nbytes > 60000) then
+  write(stderr,'(a,i0,1x,a)') "WARNING:h5fortran:set_compact: dataset is too large to be compact: bytes: ", Nbytes, dset_name
+  return
+endif
 !! 64000 byte limit, here we assumed 8 bytes / element
 
 call h5pcreate_f(H5P_DATASET_CREATE_F, dcpl, ierr)
@@ -204,6 +211,8 @@ subroutine set_compact(dcpl, dset_dims, compact)
 call h5pset_layout_f(dcpl, H5D_COMPACT_F, ierr)
 if (ierr /= 0) error stop "ERROR:h5fortran:hdf_create:h5pset_layout:set_compact"
 
+print *, "TRACE:h5fortran:set_compact: " // dset_name
+
 end subroutine set_compact
 
 

test/CMakeLists.txt

@@ -16,49 +16,62 @@ endif()
 
 # --- h5fortran unit tests
 
-function(setup_test names use_runner)
+function(nompi_test names)
+
+foreach(name IN LISTS names)
+
+add_executable(test_${name} test_${name}.f90)
+target_link_libraries(test_${name} PRIVATE h5mpi::h5mpi)
+
+add_test(NAME ${name} COMMAND test_${name})
+
+endforeach()
+
+endfunction(nompi_test)
+
+
+function(mpi_test names use_runner)
 
 foreach(name IN LISTS names)
 
 add_executable(test_${name} test_${name}.f90)
 target_link_libraries(test_${name} PRIVATE h5mpi::h5mpi)
 
 if(use_runner)
-set(cmd test_runner -exe $<TARGET_FILE:test_${name}> -mpiexec ${MPIEXEC_EXECUTABLE} -lx 1000)
+  set(cmd test_runner -exe $<TARGET_FILE:test_${name}> -mpiexec ${MPIEXEC_EXECUTABLE} -lx 1000)
 else()
-set(cmd ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} $<TARGET_FILE:test_${name}>)
-# these tests could also be -n 2 instead of max_numprocs.
-# Just trying to keep aware of possible problems vs. MPI worker count.
+  set(cmd ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} $<TARGET_FILE:test_${name}>)
+  # these tests could also be -n 2 instead of max_numprocs.
+  # Just trying to keep aware of possible problems vs. MPI worker count.
+endif()
+
 if(${name} STREQUAL "string_read")
   list(APPEND cmd ${string_file})
 endif()
-endif()
-
-
 
 add_test(NAME ${name} COMMAND ${cmd})
 
+set_tests_properties(${name} PROPERTIES
+RESOUCE_LOCK cpu_mpi
+)
+
 endforeach()
 
-endfunction(setup_test)
+endfunction(mpi_test)
 
 cmake_path(SET string_file ${CMAKE_CURRENT_BINARY_DIR}/test_string_py.h5)
 
 # --- write test data
-add_executable(test_write test_write.f90)
-target_link_libraries(test_write PRIVATE h5mpi::h5mpi)
-
-add_test(NAME write COMMAND test_write)
 
-set(test_names array attributes cast destructor exist fill groups layout shape
-string string_read
+set(mpi_tests array_mpi attributes cast destructor exist fill groups layout shape
+string string_read write
 )
 
-setup_test("${test_names}" false)
+mpi_test("${mpi_tests}" false)
 
 set(runner_tests deflate_write deflate_props deflate_read)
 
-setup_test("${runner_tests}" true)
+mpi_test("${runner_tests}" true)
 
 # --- test dependencies
 
@@ -68,7 +81,7 @@ FIXTURES_SETUP test_files
 
 set_tests_properties(layout shape PROPERTIES
 FIXTURES_REQUIRED test_files
-REQUIRED_FILES ${CMAKE_CURRENT_BINARY_DIR}/test_write.h5
+REQUIRED_FILES "${CMAKE_CURRENT_BINARY_DIR}/test_write.h5;${CMAKE_CURRENT_BINARY_DIR}/test_layout.h5"
 )
 
 set_tests_properties(deflate_write PROPERTIES
@@ -87,13 +100,6 @@ EXECUTABLE ${CMAKE_CTEST_COMMAND}
 )
 endif()
 
-# --- Windows shared DLLs
-if(WIN32 AND CMAKE_VERSION VERSION_GREATER_EQUAL 3.22)
-  set_tests_properties(${test_names} PROPERTIES
-  ENVIRONMENT_MODIFICATION "PATH=path_list_append:${ZLIB_INCLUDE_DIRS}/../bin;PATH=path_list_append:${ZLIB_INCLUDE_DIR}/../bin"
-  )
-endif()
-
 # --- Python h5py
 find_package(Python COMPONENTS Interpreter)
 if(NOT DEFINED h5py_ok)
@@ -117,14 +123,22 @@ COMMAND ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/test_string.py ${string
 )
 
 set_tests_properties(PythonString PROPERTIES
-FIXTURES_REQUIRED h5lib
 FIXTURES_SETUP h5str
 DISABLED $<NOT:$<BOOL:${h5py_ok}>>
 )
 
+# --- test properties
+
 get_property(test_names DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY TESTS)
 
 set_tests_properties(${test_names} PROPERTIES
 TIMEOUT 30
 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 )
+
+# --- Windows shared DLLs
+if(WIN32 AND CMAKE_VERSION VERSION_GREATER_EQUAL 3.22)
+  set_tests_properties(${test_names} PROPERTIES
+  ENVIRONMENT_MODIFICATION "PATH=path_list_append:${ZLIB_INCLUDE_DIRS}/../bin;PATH=path_list_append:${ZLIB_INCLUDE_DIR}/../bin"
+  )
+endif()

test/test_array.f90 renamed to test/test_array_mpi.f90

@@ -1,6 +1,6 @@
 program test_layout
 
-use, intrinsic :: iso_fortran_env, only : real32, real64, int32
+use, intrinsic :: iso_fortran_env, only : real32, real64, int32, stderr => error_unit
 
 use h5mpi, only : hdf5_file
 
@@ -48,18 +48,21 @@ subroutine test_layout_read(fn)
 call h%open(fn, action="r", mpi=.true.)
 
 call h%read("/compact_r32", r64)
-if(r64 /= 142) error stop "read real32 => real64"
+if(abs(r64 - 142) > 0.001) then
+  write(stderr,*) r64
+  error stop "ERROR:test_layout_read: read real32 => real64: " // fn
+endif
 call h%read("/compact_r64", r32)
-if(r32 /= 142) error stop "read real64 => real32"
+if(abs(r32 - 142) > 0.001) error stop "ERROR:test_layout_read: read real64 => real32"
 call h%read("/compact_i32", i32)
-if(r32 /= 142) error stop "read int32 => int32"
+if(r32 /= 142) error stop "ERROR:test_layout_read: read int32 => int32"
 
 
 call h%read("/compact7d_32", r7_64)
-if (any(r7_64 /= 42)) error stop "read real32 => real64"
+if (any(r7_64 /= 42)) error stop "ERROR:test_layout: read real32 => real64"
 
 call h%read("/compact7d_64", r7_32)
-if (any(r7_32 /= 42)) error stop "read real64 => real32"
+if (any(r7_32 /= 42)) error stop "ERROR:test_layout: read real64 => real32"
 
 call h%close()
 

test/test_layout.f90

@@ -20,8 +20,10 @@ program test_scalar
 call test_simple_write('test_write.h5')
 if(mpi_id == 0) print *, "OK: test simple write"
 
-call test_layout_write('test_layout.h5')
-if(mpi_id == 0) print *, "OK: test layout write"
+if(mpi_id == 0) then
+  call test_layout_write('test_layout.h5')
+  print *, "OK: test layout write"
+endif
 
 call mpi_finalize(ierr)
 if (ierr /= 0) error stop "mpi_finalize"
@@ -38,6 +40,16 @@ subroutine test_simple_write(fn)
 
 call h5%open(fn, action="w", mpi=.true.)
 
+!> just to have some default value
+d0 = 0
+d1 = 1
+d2 = 2
+d3 = 3
+d4 = 4
+d5 = 5
+d6 = 6
+d7 = 7
+
 call h5%write("/d0", d0)
 call h5%write("/d1", d1)
 call h5%write("/d2", d2)
@@ -53,7 +65,7 @@ end subroutine test_simple_write
 
 
 subroutine test_layout_write(fn)
-
+!! NOTE: compact datsets do not work for collective writes, at least for HDF5 1.12.2. The dataset will be all zero.
 character(*), intent(in) :: fn
 
 type(hdf5_file) :: h
@@ -65,7 +77,7 @@ subroutine test_layout_write(fn)
 d7_64 = 42
 
 
-call h%open(fn, action="w", mpi=.true.)
+call h%open(fn, action="w", mpi=.false.)
 
 call h%write("/compact1d", [1,2,3], compact=.true.)
 call h%write("/contig1d", [1,2,3], compact=.false.)