Merge branch 'TREX-CoE:master' into master

python/install_pytrexio.sh

@@ -16,7 +16,43 @@ done
 # check that both variables are set
 if [[ -z ${H5_LDFLAGS_LOCAL} ]] || [[ -z ${H5_CFLAGS_LOCAL} ]]; then
     if [[ -z ${H5_LDFLAGS} ]] || [[ -z ${H5_CFLAGS} ]]; then
+        which h5cc &> /dev/null
+        if [[ $? -eq 0 ]] ; then
+              HDF5_tmp_flags=$(h5cc -showconfig \
+                  | grep  'FLAGS\|Extra libraries:' \
+                  | awk  -F: '{printf("%s "), $2}' )
+              echo $HDF5_tmp_flags
+
+              # Find the installation directory and append include/
+              HDF5_tmp_inst=$(h5cc -showconfig \
+                  | grep  'Installation point:' \
+                  | awk  '{print $NF}' )
+              echo $HDF5_tmp_inst
+
+              # Add this to the CPPFLAGS
+              HDF5_CPPFLAGS="-I${HDF5_tmp_inst}/include"
+
+              HDF5_SHOW=$(h5cc -show)
+
+              # Now sort the flags out based upon their prefixes
+              for arg in $HDF5_SHOW $HDF5_tmp_flags ; do
+                case "$arg" in
+                  -I*) echo $HDF5_CPPFLAGS | grep -e "$arg" 2>&1 >/dev/null \
+                        || HDF5_CPPFLAGS="$HDF5_CPPFLAGS $arg"
+                    ;;
+                  -L*) echo $HDF5_LDFLAGS | grep -e "$arg" 2>&1 >/dev/null \
+                        || HDF5_LDFLAGS="$HDF5_LDFLAGS $arg"
+                    ;;
+                  -l*) echo $HDF5_LIBS | grep -e "$arg" 2>&1 >/dev/null \
+                        || HDF5_LIBS="$HDF5_LIBS $arg"
+                    ;;
+                esac
+              done
+              export H5_LDFLAGS="$HDF5_LDFLAGS"
+              export H5_CFLAGS="$HDF5_CPPFLAGS"
+        else
             echo "Paths to the HDF5 installation are not provided. pkgconfig will try to detect them."
+        fi
     else
         echo "Using exported H5_LDFLAGS and H5_CFLAGS environment variables."
     fi

src/templates_text/templator_text.org

@@ -166,7 +166,11 @@ On non-POSIX file systems, the function ~mkdtemp~ might is not defined.
 In that case, we define an alternate one, which is not as safe as the original one.
 
     #+begin_src c :tangle basic_text.c
-#if defined _POSIX_C_SOURCE && (_POSIX_C_SOURCE - 0) >= 200809L
+#if /* Since glibc 2.19: */ _DEFAULT_SOURCE \
+           || /* Glibc 2.19 and earlier: */ _BSD_SOURCE \
+           || /* Since glibc 2.10: */ _POSIX_C_SOURCE >= 200809L
+
+/* mkdtemp is defined */
 #else
 
 char* mkdtemp(char* template) {

tests/io_dset_sparse.c

@@ -46,7 +46,7 @@ static int test_write_dset_sparse (const char* file_name, const back_end_t backe
   uint64_t chunk_size = (uint64_t) size/N_CHUNKS;
   chunk_size = chunk_size > 0 ? chunk_size : (uint64_t) size;
   int n_chunks = size/chunk_size;
-  printf("chunk_size = %ld\n", chunk_size);
+  printf("chunk_size = %lld\n", chunk_size);
   printf("n_chunks   = %d\n", n_chunks);
 
   uint64_t offset_f = 0UL + offset;
@@ -55,7 +55,7 @@ static int test_write_dset_sparse (const char* file_name, const back_end_t backe
   // write n_chunks times using write_sparse
   while(offset_d < size) {
     if (offset_d+chunk_size > size) chunk_size = size-offset_d;
-  printf("chunk_size = %ld\n", chunk_size);
+  printf("chunk_size = %lld\n", chunk_size);
     if (chunk_size == 0L) break;
     rc = trexio_write_mo_2e_int_eri(file, offset_f, chunk_size, &index[4*offset_d], &value[offset_d]);
     printf("%5d: %s\n", __LINE__, trexio_string_of_error(rc));
@@ -163,7 +163,7 @@ static int test_read_dset_sparse (const char* file_name, const back_end_t backen
   printf("%5d: %s\n", __LINE__, trexio_string_of_error(rc));
 /*
   for (int i=0 ; i<chunk_read ; ++i) {
-    printf("%d %d | %ld %ld %ld\n", i, index_read[i], offset, offset_file_read, chunk_read);
+    printf("%d %d | %lld %lld %lld\n", i, index_read[i], offset, offset_file_read, chunk_read);
   }
 */
   //assert(rc == TREXIO_SUCCESS);
@@ -184,7 +184,7 @@ static int test_read_dset_sparse (const char* file_name, const back_end_t backen
   printf("%5d: %s\n", __LINE__, trexio_string_of_error(rc));
   assert(rc == TREXIO_END);
   printf("%d %d  x\n", (int32_t) index_read[0], (int32_t) (4L*offset_file_read));
-  printf("%ld  %ld\n", chunk_read, eof_read_size_check);
+  printf("%lld  %lld\n", chunk_read, eof_read_size_check);
   assert(chunk_read == eof_read_size_check);
   printf("%d %d\n", index_read[0] , (int32_t) (offset_file_read - offset));
   assert(index_read[0] == (int32_t) offset_file_read - offset);
@@ -222,7 +222,7 @@ static int test_read_dset_sparse_size (const char* file_name, const back_end_t b
   // read one chunk using the aforementioned parameters
   rc = trexio_read_mo_2e_int_eri_size(file, &size_written);
   assert(rc == TREXIO_SUCCESS);
-  printf("%5d: %ld %ld\n", __LINE__, size_written, size_check);
+  printf("%5d: %lld %lld\n", __LINE__, size_written, size_check);
   assert(size_written == size_check);
 
   // close current session

tests/test_f.f90

@@ -69,8 +69,8 @@ subroutine test_write(file_name, back_end)
   double precision :: charge(12)
   double precision :: coord(3,12)
 
-  character(len=:), allocatable :: sym_str
+  character(len=32), allocatable :: sym_str
-  character(len=:), allocatable :: label(:)
+  character(len=8), allocatable :: label(:)
   double precision, allocatable :: energy(:)
   integer         , allocatable :: spin(:)
 
@@ -131,7 +131,7 @@ subroutine test_write(file_name, back_end)
   basis_shell_num = 24
   basis_nucleus_index = (/ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 /)
 
-  allocate(character(len=8) :: label(12))
+  allocate(label(12))
   label(1) = 'C'
   label(2) = 'Na'
   label(3) = 'C'

tools/generator_tools.py

@@ -611,13 +611,13 @@ def get_detailed_num_dict (configuration: dict) -> dict:
                     tmp_dict.update(get_dtype_dict(v2[0], 'num'))
                     if v2[0] in ['int', 'dim', 'dim readonly']:
                         tmp_dict['trex_json_int_type'] = v2[0]
-                        tmp_dict['is_index'] = 'false'
+                        tmp_dict['is_index'] = '(false)'
                     elif v2[0] in ['index']:
                         tmp_dict['trex_json_int_type'] = v2[0]
                         tmp_dict['is_index'] = 'file->one_based'
                     else:
                         tmp_dict['trex_json_int_type'] = ''
-                        tmp_dict['is_index'] = 'false'
+                        tmp_dict['is_index'] = '(false)'
 
                     num_dict[tmp_num] = tmp_dict
 
@@ -721,7 +721,7 @@ def split_dset_dict_detailed (datasets: dict) -> tuple:
         if 'index' in datatype:
             tmp_dict['is_index'] = 'file->one_based'
         else:
-            tmp_dict['is_index'] = 'false'
+            tmp_dict['is_index'] = '(false)'
 
         # add the list of dimensions
         tmp_dict['dims'] = [dim.replace('.','_') for dim in v[1]]