update to pybind11 2.6.1

new_python/CMakeLists.txt

@@ -5,7 +5,7 @@ include(FetchContent)
 FetchContent_Declare(
     pybind11
     GIT_REPOSITORY https://github.com/pybind/pybind11.git 
-    GIT_TAG v2.5
+    GIT_TAG v2.6.1
 )
 
 FetchContent_GetProperties(pybind11)

new_python/genericio.cpp

@@ -84,21 +84,21 @@ public:
         );
       if (varp != variables.end()) {
         // extra space
-        size_t readsize = num_elem + requestedExtraSpace()/(*varp).ElementSize;
+        py::ssize_t readsize = num_elem + requestedExtraSpace()/(*varp).ElementSize;
         if((*varp).IsFloat && (*varp).ElementSize == 4) {
-          result[var_name] = py::array_t<float>(size_t(readsize));
+          result[var_name] = py::array_t<float>(readsize);
           addVariable(*varp, result[var_name].mutable_data(), gio::GenericIO::VarHasExtraSpace);
         } else if((*varp).IsFloat && (*varp).ElementSize == 8) {
-          result[var_name] = py::array_t<double>(size_t(readsize));
+          result[var_name] = py::array_t<double>(readsize);
           addVariable(*varp, result[var_name].mutable_data(), gio::GenericIO::VarHasExtraSpace);
         } else if(!(*varp).IsFloat && (*varp).ElementSize == 4) {
-          result[var_name] = py::array_t<int32_t>(size_t(readsize));
+          result[var_name] = py::array_t<int32_t>(readsize);
           addVariable(*varp, result[var_name].mutable_data(), gio::GenericIO::VarHasExtraSpace);
         } else if(!(*varp).IsFloat && (*varp).ElementSize == 8) {
-          result[var_name] = py::array_t<int64_t>(size_t(readsize));
+          result[var_name] = py::array_t<int64_t>(readsize);
           addVariable(*varp, result[var_name].mutable_data(), gio::GenericIO::VarHasExtraSpace);
         } else if(!(*varp).IsFloat && (*varp).ElementSize == 2) {
-          result[var_name] = py::array_t<uint16_t>(size_t(readsize));
+          result[var_name] = py::array_t<uint16_t>(readsize);
           addVariable(*varp, result[var_name].mutable_data(), gio::GenericIO::VarHasExtraSpace);
         }
       }
@@ -197,8 +197,10 @@ PYBIND11_MODULE(pygio, m) {
   m.def("_init_mpi", [](){
     int initialized;
     MPI_Initialized(&initialized);
-    if(!initialized)
-      MPI_Init(nullptr, nullptr); 
+    if(!initialized) {
+      int level_provided;
+      MPI_Init_thread(nullptr, nullptr, MPI_THREAD_SINGLE, &level_provided); 
+    }
   });
 #endif
 
@@ -214,7 +216,6 @@ PYBIND11_MODULE(pygio, m) {
     .value("MismatchDisallowed", PyGenericIO::MismatchBehavior::MismatchDisallowed)
     .value("MismatchRedistribute", PyGenericIO::MismatchBehavior::MismatchRedistribute);
 
-  
   pyGenericIO.def(py::init<std::string, PyGenericIO::FileIO, PyGenericIO::MismatchBehavior>(), py::arg("filename"), py::arg("method")=PyGenericIO::FileIO::FileIOPOSIX, py::arg("redistribute")=PyGenericIO::MismatchBehavior::MismatchRedistribute)
       .def("inspect", &PyGenericIO::inspect, "Print variable infos and size of GenericIO file")
       .def("get_variables", &PyGenericIO::get_variables, "Get a list of VariableInformations defined in the GenericIO file")
@@ -224,8 +225,6 @@ PYBIND11_MODULE(pygio, m) {
       .def("read_phys_scale", &PyGenericIO::read_phys_scale)
       .def("read", &PyGenericIO::read, py::arg("variables")=nullptr);
 
-  
-
   py::class_<gio::GenericIO::VariableInfo>(pyGenericIO, "VariableInfo")
       .def_readonly("name", &gio::GenericIO::VariableInfo::Name)
       .def_readonly("size", &gio::GenericIO::VariableInfo::Size)