The example is garbled but offers a few clues. Where are you closing the pnt_ch->filespace_id handle that you acquire in H5Dget_space? If you keep re-assigning that w/o previously closing the existing one, that’s a memory leak right there. Generally, the most common source of the kind of leakage you are seeing is a lack of handle discipline. “You acquire a handle, you own it (and the resources that go with it).” (Colin Powell) Make sure that there is a matching H5*close with each hid_t handle you acquire. Use H5Fget_obj_count (https://portal.hdfgroup.org/display/HDF5/H5F_GET_OBJ_COUNT) to check for open handles. Use H5F_OBJ_ALL for types. Check that before shutting down your application! If the count returned is greater than one (you have at least one open file handle), that typically signals trouble. G.