Merge pull request #1090 from paulromano/more-valgrind-fixes

More valgrind fixes

include/openmc/hdf5_interface.h

@@ -1,9 +1,11 @@
 #ifndef OPENMC_HDF5_INTERFACE_H
 #define OPENMC_HDF5_INTERFACE_H
 
+#include <algorithm> // for min
 #include <array>
 #include <complex>
 #include <cstddef>
+#include <cstring> // for strlen
 #include <string>
 #include <sstream>
 #include <vector>
@@ -193,13 +195,13 @@ read_attribute(hid_t obj_id, const char* name, std::vector<std::string>& vec)
 
   // Allocate a C char array to get strings
   auto n = attribute_typesize(obj_id, name);
-  char buffer[m][n+1];
+  char buffer[m][n];
 
   // Read char data in attribute
   read_attr_string(obj_id, name, n, buffer[0]);
 
   for (int i = 0; i < m; ++i) {
-    vec.emplace_back(&buffer[i][0]);
+    vec.emplace_back(&buffer[i][0], std::min(strlen(buffer[i]), n));
   }
 }
 

src/hdf5_interface.F90

@@ -1131,6 +1131,7 @@ contains
     do i = 0, dims(1) - 1
       n = len_trim(buffer(i+1)) + 1
       buffer_(i*m+1 : i*m+n) = to_c_string(buffer(i+1))
+      if (n < m) buffer_(i*m+n : i*m+m) = C_NULL_CHAR
     end do
 
     call write_string_c(group_id, 1, dims, m, to_c_string(name), &
@@ -1361,7 +1362,7 @@ contains
     ! Allocate a C char array to get strings
     n = attribute_typesize(obj_id, to_c_string(name))
     m = size(buffer)
-    allocate(buffer_((n+1)*m))
+    allocate(buffer_(n*m))
 
     ! Read attribute
     call read_attr_string_c(obj_id, to_c_string(name), n, buffer_)
@@ -1370,7 +1371,7 @@ contains
     do i = 1, m
       buffer(i) = ''
       do j = 1, n
-        k = (i-1)*(n+1) + j
+        k = (i-1)*n + j
         if (buffer_(k) == C_NULL_CHAR) exit
         buffer(i)(j:j) = buffer_(k)
       end do

src/hdf5_interface.cpp

@@ -392,7 +392,7 @@ object_name(hid_t obj_id)
 
   // Read and return name
   H5Iget_name(obj_id, buffer, size);
-  return {buffer, size};
+  return buffer;
 }
 
 
@@ -439,7 +439,9 @@ read_attr_string(hid_t obj_id, const char* name, size_t slen, char* buffer)
 {
   // Create datatype for a string
   hid_t datatype = H5Tcopy(H5T_C_S1);
-  H5Tset_size(datatype, slen + 1);
+  H5Tset_size(datatype, slen);
+  // numpy uses null-padding when writing fixed-length strings
+  H5Tset_strpad(datatype, H5T_STR_NULLPAD);
 
   // Read data into buffer
   read_attr(obj_id, name, datatype, buffer);
@@ -503,7 +505,9 @@ read_string(hid_t obj_id, const char* name, size_t slen, char* buffer, bool inde
 {
   // Create datatype for a string
   hid_t datatype = H5Tcopy(H5T_C_S1);
-  H5Tset_size(datatype, slen + 1);
+  H5Tset_size(datatype, slen);
+  // numpy uses null-padding when writing fixed-length strings
+  H5Tset_strpad(datatype, H5T_STR_NULLPAD);
 
   // Read data into buffer
   read_dataset(obj_id, name, datatype, buffer, indep);

src/initialize.cpp

@@ -115,10 +115,9 @@ parse_command_line(int argc, char* argv[])
 
         // Check what type of file this is
         hid_t file_id = file_open(argv[i], 'r', true);
-        size_t len = attribute_typesize(file_id, "filetype");
-        read_attr_string(file_id, "filetype", len, buffer);
+        std::string filetype;
+        read_attribute(file_id, "filetype", filetype);
         file_close(file_id);
-        std::string filetype {buffer};
 
         // Set path and flag for type of run
         if (filetype == "statepoint") {
@@ -141,8 +140,7 @@ parse_command_line(int argc, char* argv[])
 
             // Check file type is a source file
             file_id = file_open(argv[i+1], 'r', true);
-            len = attribute_typesize(file_id, "filetype");
-            read_attr_string(file_id, "filetype", len, buffer);
+            read_attribute(file_id, "filetype", filetype);
             file_close(file_id);
             if (filetype != "source") {
               std::string msg {"Second file after restart flag must be a source file"};

src/mgxs_interface.cpp

@@ -208,7 +208,7 @@ void
 get_name_c(int index, int name_len, char* name)
 {
   // First blank out our input string
-  std::string str(name_len, ' ');
+  std::string str(name_len - 1, ' ');
   std::strcpy(name, str.c_str());
 
   // Now get the data and copy to the C-string