Merge pull request #356 from AntonioMirarchi/hdf5

Fix HDF5 dataset consistency

Author: stefdoerr

tests/test_datasets.py

@@ -10,6 +10,7 @@
 import psutil
 from torchmdnet.datasets import Custom, HDF5, Ace
 from torchmdnet.utils import write_as_hdf5
+from torch_geometric.loader import DataLoader
 import h5py
 import glob
 
@@ -297,3 +298,36 @@ def test_ace(tmpdir):
     assert len(dataset_v2) == 8
     f2.flush()
     f2.close()
+
+
+@mark.parametrize("num_files", [1, 3])
+@mark.parametrize("tile_embed", [True, False])
+@mark.parametrize("batch_size", [1, 5])
+def test_hdf5_with_and_without_caching(num_files, tile_embed, batch_size, tmpdir):
+    """This test ensures that the output from the get of the HDF5 dataset is the same
+    when the dataset is loaded with and without caching."""
+
+    # set up necessary files
+    _ = write_sample_npy_files(True, True, tmpdir, num_files)
+    files = {}
+    files["pos"] = sorted(glob.glob(join(tmpdir, "coords*")))
+    files["z"] = sorted(glob.glob(join(tmpdir, "embed*")))
+    files["y"] = sorted(glob.glob(join(tmpdir, "energy*")))
+    files["neg_dy"] = sorted(glob.glob(join(tmpdir, "forces*")))
+
+    write_as_hdf5(files, join(tmpdir, "test.hdf5"), tile_embed)
+    # Assert file is present in the disk
+    assert os.path.isfile(join(tmpdir, "test.hdf5")), "HDF5 file was not created"
+
+    data = HDF5(join(tmpdir, "test.hdf5"), dataset_preload_limit=0)  # no caching
+    data_cached = HDF5(join(tmpdir, "test.hdf5"), dataset_preload_limit=256)  # caching
+    assert len(data) == len(data_cached), "Number of samples does not match"
+
+    dl = DataLoader(data, batch_size)
+    dl_cached = DataLoader(data_cached, batch_size)
+
+    for sample_cached, sample in zip(dl_cached, dl):
+        assert np.allclose(sample_cached.pos, sample.pos), "Sample has incorrect coords"
+        assert np.allclose(sample_cached.z, sample.z), "Sample has incorrect atom numbers"
+        assert np.allclose(sample_cached.y, sample.y), "Sample has incorrect energy"
+        assert np.allclose(sample_cached.neg_dy, sample.neg_dy), "Sample has incorrect forces"

torchmdnet/datasets/hdf.py

@@ -125,8 +125,13 @@ def get(self, idx):
             if self.index is None:
                 self._setup_index()
             *fields_data, i = self.index[idx]
+            # Assuming the first element of fields_data is 'pos' based on the definition of self.fields
+            size = len(fields_data[0])
             for (name, _, dtype), d in zip(self.fields, fields_data):
-                tensor_input = [[d[i]]] if d.ndim == 1 else d[i]
+                if d.ndim == 1:
+                    tensor_input = [d[i]] if len(d) == size else d[:]
+                else:
+                    tensor_input = d[i]
                 data[name] = torch.tensor(tensor_input, dtype=dtype)
         return data
 

torchmdnet/utils.py

@@ -346,12 +346,13 @@ class MissingEnergyException(Exception):
     pass
 
 
-def write_as_hdf5(files, hdf5_dataset):
+def write_as_hdf5(files, hdf5_dataset, tile_embed=True):
     """Transform the input numpy files to hdf5 format compatible with the HDF5 Dataset class.
     The input files to this function are the same as the ones required by the Custom dataset.
     Args:
         files (dict): Dictionary of numpy input files. Must contain "pos", "z" and at least one of "y" or "neg_dy".
         hdf5_dataset (string): Path to the output HDF5 dataset.
+        tile_embed (bool): Whether to tile the embeddings to match the number of samples. Default: True
     Example:
         >>> files = {}
         >>> files["pos"] = sorted(glob.glob(join(tmpdir, "coords*")))
@@ -370,7 +371,10 @@ def write_as_hdf5(files, hdf5_dataset):
             group = f.create_group(str(i))
             num_samples = coord_data.shape[0]
             group.create_dataset("pos", data=coord_data)
-            group.create_dataset("types", data=np.tile(embed_data, (num_samples, 1)))
+            if tile_embed:
+                group.create_dataset("types", data=np.tile(embed_data, (num_samples, 1)))
+            else:
+                group.create_dataset("types", data=embed_data)
             if "y" in files:
                 energy_data = np.load(files["y"][i], mmap_mode="r")
                 group.create_dataset("energy", data=energy_data)