.....

src/hdf5.cpp

@@ -696,6 +696,13 @@ void writeReturnDataDiagnosis(
         );
 }
 
+// work-around for macos segfaults, use struct without std::string
+struct LogItemCStr {
+    int severity;
+    const char* identifier;
+    const char* message;
+};
+
 void writeLogItemsToHDF5(
     H5::H5File const& file, std::vector<amici::LogItem> const& logItems,
     std::string const& hdf5Location
@@ -707,26 +714,52 @@ void writeLogItemsToHDF5(
         hsize_t dims[1] = {logItems.size()};
         H5::DataSpace dataspace(1, dims);
 
+        /*
         // Create a compound datatype for the LogItem struct.
         H5::CompType logItemType(sizeof(amici::LogItem));
         logItemType.insertMember(
             "severity", HOFFSET(amici::LogItem, severity),
             H5::PredType::NATIVE_INT
         );
-        // crashes on macos?
-        /*
+        auto vlstr_type = H5::StrType(H5::PredType::C_S1, H5T_VARIABLE);
         logItemType.insertMember(
-            "identifier", HOFFSET(amici::LogItem, identifier),
-            H5::StrType(H5::PredType::C_S1, H5T_VARIABLE)
+            "identifier", HOFFSET(amici::LogItem, identifier), vlstr_type
         );
         logItemType.insertMember(
-            "message", HOFFSET(amici::LogItem, message),
-            H5::StrType(H5::PredType::C_S1, H5T_VARIABLE)
+            "message", HOFFSET(amici::LogItem, message), vlstr_type
         );
-        */
         H5::DataSet dataset
             = file.createDataSet(hdf5Location, logItemType, dataspace);
+
+        // works on Ubuntu, but segfaultson macos
         dataset.write(logItems.data(), logItemType);
+        */
+
+        H5::CompType logItemType(sizeof(LogItemCStr));
+        logItemType.insertMember(
+            "severity", HOFFSET(LogItemCStr, severity),
+            H5::PredType::NATIVE_INT
+        );
+        auto vlstr_type = H5::StrType(H5::PredType::C_S1, H5T_VARIABLE);
+        logItemType.insertMember(
+            "identifier", HOFFSET(LogItemCStr, identifier), vlstr_type
+        );
+        logItemType.insertMember(
+            "message", HOFFSET(LogItemCStr, message), vlstr_type
+        );
+        H5::DataSet dataset
+            = file.createDataSet(hdf5Location, logItemType, dataspace);
+
+        // Convert std::vector<LogItem> to std::vector<LogItemCStr>
+        std::vector<LogItemCStr> buffer(logItems.size());
+        for (size_t i = 0; i < logItems.size(); ++i) {
+            buffer[i].severity = static_cast<int>(logItems[i].severity);
+            buffer[i].identifier = logItems[i].identifier.c_str();
+            buffer[i].message = logItems[i].message.c_str();
+        }
+
+        // Write the data to the dataset.
+        dataset.write(buffer.data(), logItemType);
     } catch (H5::Exception& e) {
         throw AmiException(e.getCDetailMsg());
     }