Merge pull request #2858 from pnorbert/fortran-F90-strings

Remove F2008 string allocation from Fortran binding. sadios2_availabl…

bindings/Fortran/f2c/adios2_f2c_io.cpp

@@ -236,7 +236,6 @@ void FC_GLOBAL(adios2_available_variables_f2c,
     cnamelist *info = new (cnamelist);
     info->names = adios2_available_variables(*io, &info->count);
     *vars_count = static_cast<int>(info->count);
-
     size_t maxlen = 0;
     for (size_t i = 0; i < info->count; ++i)
     {
@@ -247,47 +246,10 @@ void FC_GLOBAL(adios2_available_variables_f2c,
         }
     }
     *max_var_name_len = static_cast<int>(maxlen);
-
     *namestruct = static_cast<int64_t>(reinterpret_cast<std::uintptr_t>(info));
     *ierr = 0;
 }
 
-void FC_GLOBAL(adios2_retrieve_variable_names_f2c,
-               ADIOS2_RETRIEVE_VARIABLE_NAMES_F2C)(int64_t *namestruct,
-                                                   int *count,
-                                                   int *max_name_len,
-                                                   void *vnamelist, int *ierr,
-                                                   int vnamelist_len)
-{
-    cnamelist *info = reinterpret_cast<cnamelist *>(*namestruct);
-    int cnt = info->count;
-    if (cnt > *count)
-    {
-        cnt = *count;
-    }
-    if (info != NULL && static_cast<size_t>(*count) == info->count)
-    {
-        for (int i = 0; i < *count; i++)
-        {
-            char *fs = (char *)vnamelist + i * vnamelist_len;
-            size_t len = strlen(info->names[i]);
-            if (len > static_cast<size_t>(vnamelist_len))
-            {
-                len = static_cast<size_t>(vnamelist_len);
-            }
-            // copy C string without '\0'
-            strncpy(fs, info->names[i], len);
-            // pad with spaces
-            memset(fs + len, ' ', vnamelist_len - len);
-        }
-        *ierr = 0;
-    }
-    else
-    {
-        *ierr = 1;
-    }
-}
-
 void FC_GLOBAL(adios2_available_attributes_f2c,
                ADIOS2_AVAILABLE_ATTRIBUTES_F2C)(adios2_io **io,
                                                 int64_t *namestruct,
@@ -314,35 +276,30 @@ void FC_GLOBAL(adios2_available_attributes_f2c,
     *ierr = 0;
 }
 
-void FC_GLOBAL(adios2_retrieve_attribute_names_f2c,
-               ADIOS2_RETRIEVE_ATTRIBUTE_NAMES_F2C)(int64_t *namestruct,
-                                                    int *count,
-                                                    int *max_name_len,
-                                                    void *anamelist, int *ierr,
-                                                    int anamelist_len)
+void FC_GLOBAL(adios2_retrieve_namelist_f2c,
+               ADIOS2_RETRIEVE_NAMELIST_F2C)(int64_t *namestruct,
+                                             void *namelist, int *ierr,
+                                             int namelist_len)
 {
     cnamelist *info = reinterpret_cast<cnamelist *>(*namestruct);
-    int cnt = info->count;
-    if (cnt > *count)
-    {
-        cnt = *count;
-    }
-    if (info != NULL && static_cast<size_t>(*count) == info->count)
+    if (info != NULL)
     {
-        for (int i = 0; i < *count; i++)
+        for (size_t i = 0; i < info->count; i++)
         {
-            char *fs = (char *)anamelist + i * anamelist_len;
+            char *fs = (char *)namelist + i * namelist_len;
             size_t len = strlen(info->names[i]);
-            if (len > static_cast<size_t>(anamelist_len))
+            if (len > static_cast<size_t>(namelist_len))
             {
-                len = static_cast<size_t>(anamelist_len);
+                len = static_cast<size_t>(namelist_len);
             }
             // copy C string without '\0'
             strncpy(fs, info->names[i], len);
             // pad with spaces
-            memset(fs + len, ' ', anamelist_len - len);
+            memset(fs + len, ' ', namelist_len - len);
         }
         *ierr = 0;
+        delete (info);
+        *namestruct = 0;
     }
     else
     {

bindings/Fortran/modules/adios2_io_mod.f90

@@ -24,6 +24,9 @@ module adios2_io_mod
     external adios2_get_parameter_f2c
     external adios2_get_parameter_length_f2c
     external adios2_in_config_file_f2c
+    external adios2_available_variables_f2c
+    external adios2_available_attributes_f2c
+    external adios2_retrieve_namelist_f2c
     external adios2_inquire_attribute_f2c
     external adios2_inquire_variable_f2c
     external adios2_io_engine_type_f2c
@@ -158,26 +161,53 @@ subroutine adios2_set_transport_parameter(io, transport_index, key, value, &
     end subroutine
 
 
-    subroutine adios2_available_variables(io, nvars, varnamelist, ierr)
+    subroutine adios2_available_variables(io, namestruct, ierr)
         type(adios2_io), intent(in) :: io
-        integer, intent(out) :: nvars
-        character(len=:), dimension(:), allocatable, intent(out) :: varnamelist
+        type(adios2_namestruct), intent(out) :: namestruct
         integer, intent(out) :: ierr
 
-        integer(kind=8):: namestruct
-        integer :: count, max_name_len
-
-        call adios2_available_variables_f2c(io%f2c, namestruct, count, &
-                        max_name_len, ierr)
+        call adios2_available_variables_f2c(io%f2c, namestruct%f2c, &
+                   namestruct%count,  namestruct%max_name_len, ierr)
         if (ierr == 0) then
-            allocate(character(len=max_name_len) :: varnamelist(count))
+            namestruct%valid = .true.
         endif
+    end subroutine
+
+    subroutine adios2_retrieve_names(namestruct, namelist, ierr)
+        type(adios2_namestruct), intent(inout) :: namestruct
+        character(*), dimension(*), intent(inout) :: namelist
+        integer, intent(out) :: ierr
 
-        call adios2_retrieve_variable_names_f2c(namestruct, count, &
-                        max_name_len, varnamelist, ierr)
-        nvars = count
+        if (namestruct%valid .and. namestruct%f2c > 0_8) then
+            call adios2_retrieve_namelist_f2c(namestruct%f2c, namelist, ierr)
+        else
+            write(*,*) "ADIOS2 Fortran ERROR: invalid namestruct when calling adios2_retrieve_names()"
+        endif
+        namestruct%valid = .false.
     end subroutine
 
+    !
+    ! F2008 implementation that allows for allocating a character array inside
+    !
+    ! subroutine adios2_available_variables(io, nvars, varnamelist, ierr)
+    !     type(adios2_io), intent(in) :: io
+    !     integer, intent(out) :: nvars
+    !     character(len=:), dimension(:), allocatable, intent(out) :: varnamelist
+    !     integer, intent(out) :: ierr
+
+    !     integer(kind=8):: namestruct
+    !     integer :: count, max_name_len
+
+    !     call adios2_available_variables_f2c(io%f2c, namestruct, count, &
+    !                     max_name_len, ierr)
+    !     if (ierr == 0) then
+    !         allocate(character(len=max_name_len) :: varnamelist(count))
+    !     endif
+
+    !     call adios2_retrieve_variable_names_f2c(namestruct, varnamelist, ierr)
+    !     nvars = count
+    ! end subroutine
+
 
     subroutine adios2_inquire_variable(variable, io, name, ierr)
         type(adios2_variable), intent(out) :: variable
@@ -233,26 +263,38 @@ subroutine adios2_remove_all_variables(io, ierr)
 
     end subroutine
 
-    subroutine adios2_available_attributes(io, nattrs, attrnamelist, ierr)
+    subroutine adios2_available_attributes(io, namestruct, ierr)
         type(adios2_io), intent(in) :: io
-        integer, intent(out) :: nattrs
-        character(len=:), dimension(:), allocatable, intent(out) :: attrnamelist
+        type(adios2_namestruct), intent(out) :: namestruct
         integer, intent(out) :: ierr
 
-        integer(kind=8):: namestruct
-        integer :: count, max_name_len
-
-        call adios2_available_attributes_f2c(io%f2c, namestruct, count, &
-                        max_name_len, ierr)
+        call adios2_available_attributes_f2c(io%f2c, namestruct%f2c, &
+                   namestruct%count,  namestruct%max_name_len, ierr)
         if (ierr == 0) then
-            allocate(character(len=max_name_len) :: attrnamelist(count))
+            namestruct%valid = .true.
         endif
-
-        call adios2_retrieve_attribute_names_f2c(namestruct, count, &
-                        max_name_len, attrnamelist, ierr)
-        nattrs = count
     end subroutine
 
+    ! subroutine adios2_available_attributes(io, nattrs, attrnamelist, ierr)
+    !     type(adios2_io), intent(in) :: io
+    !     integer, intent(out) :: nattrs
+    !     character(len=:), dimension(:), allocatable, intent(out) :: attrnamelist
+    !     integer, intent(out) :: ierr
+
+    !     integer(kind=8):: namestruct
+    !     integer :: count, max_name_len
+
+    !     call adios2_available_attributes_f2c(io%f2c, namestruct, count, &
+    !                     max_name_len, ierr)
+    !     if (ierr == 0) then
+    !         allocate(character(len=max_name_len) :: attrnamelist(count))
+    !     endif
+
+    !     call adios2_retrieve_attribute_names_f2c(namestruct, count, &
+    !                     max_name_len, attrnamelist, ierr)
+    !     nattrs = count
+    ! end subroutine
+
     subroutine adios2_inquire_attribute(attribute, io, name, ierr)
         type(adios2_attribute), intent(out) :: attribute
         type(adios2_io), intent(in) :: io

bindings/Fortran/modules/adios2_parameters_mod.f90

@@ -127,4 +127,11 @@ module adios2_parameters_mod
         character(len=64):: type = ''
     end type
 
+    type adios2_namestruct
+        integer(kind=8):: f2c = 0_8
+        logical :: valid = .false.
+        integer :: count
+        integer :: max_name_len
+    end type
+
 end module

docs/environment.yml

@@ -9,6 +9,7 @@ dependencies:
   - adios2-openmpi
   - sphinx
   - breathe=4.18.1
+  - funcparserlib>=0.3.6
   - pip
   - pip:
     - blockdiag>=1.5.4

testing/adios2/bindings/fortran/TestBPWriteReadAttributes.F90

@@ -27,8 +27,9 @@ program TestBPWriteAttributes
     real, dimension(3) :: r32_array
     real(kind=8), dimension(3):: r64_array
 
-    character(len=:), dimension(:), allocatable :: attrnamelist
-    integer :: nattrs
+    type(adios2_namestruct) :: namestruct
+    character(len=4096), dimension(:), allocatable :: attrnamelist
+
 
     ! Launch MPI
     call MPI_Init(ierr)
@@ -109,15 +110,27 @@ program TestBPWriteAttributes
 
     call adios2_open(bpReader, ioRead, 'fattr_types.bp', adios2_mode_read, ierr)
 
-    call adios2_available_attributes(ioRead, nattrs, attrnamelist, ierr)
-    if (ierr /= 0) stop 'adios2_available_variables returned with error'
-    write(*,*) 'Number of attributes = ', nattrs
-    if (nattrs /= 14) stop 'adios2_available_attributes returned not the expected 14'
-    do i=1,nattrs
-         write(*,'("Var[",i2,"] = ",a20)') i, attrnamelist(i)
+
+   ! Test getting list of attribute names
+    call adios2_available_attributes(ioRead, namestruct, ierr)
+    if (ierr /= 0) stop 'adios2_available_attributes returned with error'
+    if (.not.namestruct%valid) stop 'adios2_available_attributes returned invalid struct'
+    write(*,*) 'Number of attributes = ', namestruct%count
+    write(*,*) 'Max name length = ', namestruct%max_name_len
+    if (namestruct%count /= 14) stop 'adios2_available_attributes returned not the expected 14'
+
+    allocate(attrnamelist(namestruct%count))
+
+    call adios2_retrieve_names(namestruct, attrnamelist, ierr)
+    if (ierr /= 0) stop 'adios2_retrieve_names returned with error'
+    do i=1,namestruct%count
+         write(*,'("Attr[",i2,"] = ",a20)') i, attrnamelist(i)
     end do
     deallocate(attrnamelist)
 
+    if (namestruct%f2c /= 0_8) stop 'namestruct f2c pointer is not null after adios2_retrieve_names()'
+    if (namestruct%valid) stop 'namestruct is not invalidated after adios2_retrieve_names()'
+
 
     call adios2_inquire_attribute(attributes_in(1), ioRead, 'att_String', ierr)
     call adios2_inquire_attribute(attributes_in(2), ioRead, 'att_i8', ierr)

testing/adios2/bindings/fortran/TestBPWriteTypes.F90

@@ -26,8 +26,8 @@ program TestBPWriteTypes
      integer(kind=4) :: ndims
      integer(kind=8), dimension(:), allocatable :: shape_in
 
-     character(len=:), dimension(:), allocatable :: varnamelist
-     integer :: nvars
+     character(len=4096), dimension(:), allocatable :: varnamelist
+     type(adios2_namestruct) :: namestruct
 
 #if ADIOS2_USE_MPI
      ! Launch MPI
@@ -235,15 +235,25 @@ program TestBPWriteTypes
      call adios2_steps(nsteps, bpReader, ierr)
      if(nsteps /= 3) stop 'ftypes.bp must have 3 steps'
 
-     call adios2_available_variables(ioRead, nvars, varnamelist, ierr)
+     call adios2_available_variables(ioRead, namestruct, ierr)
      if (ierr /= 0) stop 'adios2_available_variables returned with error'
-     write(*,*) 'Number of variables = ', nvars
-     if (nvars /= 14) stop 'adios2_available_variables returned not the expected 14'
-     do i=1,nvars
+     if (.not.namestruct%valid) stop 'adios2_available_variables returned invalid struct'
+     write(*,*) 'Number of variables = ', namestruct%count
+     write(*,*) 'Max name length = ', namestruct%max_name_len
+     if (namestruct%count /= 14) stop 'adios2_available_variables returned not the expected 14'
+
+     allocate(varnamelist(namestruct%count))
+
+     call adios2_retrieve_names(namestruct, varnamelist, ierr)
+     if (ierr /= 0) stop 'adios2_retrieve_names returned with error'
+     do i=1,namestruct%count
           write(*,'("Var[",i2,"] = ",a12)') i, varnamelist(i)
      end do
      deallocate(varnamelist)
 
+     if (namestruct%f2c /= 0_8) stop 'namestruct f2c pointer is not null after adios2_retrieve_names()'
+     if (namestruct%valid) stop 'namestruct is not invalidated after adios2_retrieve_names()'
+
 
      call adios2_inquire_variable(variables(1), ioRead, "var_I8", ierr)
      if (variables(1)%name /= 'var_I8') stop 'var_I8 not recognized'