[SYSTEMDS-3829] BERT layer forward pass

This patch introduces the forward pass of the BERT layer from the
BERT transformer architecture as a built-in.

Closes #2184

scripts/nn/layers/bert_layer.dml

@@ -0,0 +1,186 @@
+#-------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+#-------------------------------------------------------------
+
+source("nn/layers/affine.dml") as affine
+source("nn/layers/multi_attention.dml") as attention
+source("nn/layers/dropout.dml") as dropout
+source("nn/layers/batch_norm1d.dml") as batch_norm
+source("nn/layers/tanh.dml") as tanh
+source("nn/layers/gelu.dml") as gelu
+
+linear_tensor_forward = function(matrix[double] X, matrix[double] W, matrix[double] b, int B, int C)
+  return (matrix[double] out) {
+  /* 
+   * Helper function for computing linear layer with tensor input, of shape (A, B*C) 
+   */
+  A = nrow(X)
+  C_new = ncol(W)
+  out = affine::forward(matrix(X, rows=A*B, cols=C), W, b)
+  out = matrix(out, rows=A, cols=B*C_new)
+}
+
+layer_norm_forward = function(matrix[double] X, matrix[double] gamma, matrix[double] beta, double epsilon, int B, int C)
+  return (matrix[double] out, matrix[double] cache_mean, matrix[double] cache_var, matrix[double] cache_norm) {
+  /*
+   * Helper function for computing layer norm via 1D batch norm with tensor input, of shpae (A, B*C)
+   */
+  A = nrow(X)
+  batch_norm_input = t(matrix(X, rows=A*B, cols=C))
+  # EMA matrices are unused and thus empty matrices will be provided
+  emas_mat = matrix(0, rows=1, cols=A*B)
+  [batch_norm_out, unused1, unused2, cache_mean, cache_var, cache_norm] = batch_norm::forward(
+    batch_norm_input, t(gamma), t(beta), "train", emas_mat, emas_mat, 0.0, epsilon)
+  out = matrix(t(batch_norm_out), rows=A, cols=B*C)
+}
+
+forward = function(matrix[double] states,
+      int H, int T, int d, int I,
+      matrix[double] W_Q, matrix[double] b_Q, 
+      matrix[double] W_K, matrix[double] b_K, 
+      matrix[double] W_V, matrix[double] b_V,
+      matrix[double] W_context, matrix[double] b_context, 
+      matrix[double] W_intermediate, matrix[double] b_intermediate, 
+      matrix[double] W_out, matrix[double] b_out, 
+      double dropout_p_attention, 
+      double dropout_p_output,
+      double epsilon_ln,
+      matrix[double] gamma_ln1, matrix[double] beta_ln1,
+      matrix[double] gamma_ln2, matrix[double] beta_ln2,
+      string activation)
+    return (matrix[double] out_states, matrix[double] attention,
+      list[unknown] outputs,
+      matrix[double] dropout_mask_attention, 
+      matrix[double] dropout_mask_output_1,
+      matrix[double] dropout_mask_output_2,
+      matrix[double] cache_mean_ln1, matrix[double] cache_var_ln1, matrix[double] cache_norm_ln1,
+      matrix[double] cache_mean_ln2, matrix[double] cache_var_ln2, matrix[double] cache_norm_ln2) {
+  /*
+   * Computes the forward pass for a layer of the BERT transformer architecture.
+   *
+   * Inputs (B: Batch size, T: Sequence length, D: Embedding length, H: Heads):
+   * - states: Hidden states, of shape (B, T*D).
+   * - H: Head count.
+   * - T: Sequence length.
+   * - d: Embedding length of single token per head with d*H = D.
+   * - I: Intemediate embedding length.
+   * - W_Q: Weights for linear query layer, of shape (D, D).
+   * - b_Q: Biases for linear query layer, of shape (1, D).
+   * - W_K: Weights for linear key layer, of shape (D, D).
+   * - b_K: Biases for linear key layer, of shape (1, D).
+   * - W_V: Weights for linear value layer, of shape (D, D).
+   * - b_V: Biases for linear value layer, of shape (1, D).
+   * - W_context: Weights for linear output layer on context, of shape (D, D).
+   * - b_context: Biases for linear output layer on context, of shape (1, D).
+   * - W_intermediate: Weights for intermediate linear layer, of shape (D, I).
+   * - b_intermediate: Biases for intermediate linear layer, of shape (1, I).
+   * - W_out: Weights for last linear output layer, of shape (D, D).
+   * - b_out: Biases for last linear output layer, of shape (1, D).
+   * - dropout_p_attention: Probability for dropout on attention.
+   * - dropout_p_output: Probability for dropout on output.
+   * - epsilon_ln: Epsilon value for layer norm.
+   * - gamma_ln1: Gamma params for layer norm 1, of shape (1, D).
+   * - beta_ln1: Beta params for layer norm 1, of shape (1, D).
+   * - gamma_ln2: Gamma params for layer norm 2, of shape (1, D).
+   * - beta_ln2: Beta params for layer norm 2, of shape (1, D).
+   * - activation: String specifying type of activation to use.
+   *     Can be tanh or gelu.
+   *
+   * Outputs:
+   * - out_states: Token output states, of shape (B, T*D)
+   * - attention: Attention values for keys & querys, of shape (B, H*T*T)
+   * - outputs: List of relevant outputs for backward pass with following
+   *     order/content:
+   *   -> 1: Output of linear query layer, of shape (B, T*D).
+   *   -> 2: Output of linear key layer, of shape (B, T*D).
+   *   -> 3: Output of linear value layer, of shape (B, T*D).
+   *   -> 4: Output context of attention layer, of shape (B, T*D).
+   *   -> 5: Output attention of attention layer, of shape (B, T*D).
+   *   -> 6: Output of residual pass 1, of shape (B, T*D).
+   *   -> 7: Output of layer norm 1, of shape (B, T*D).
+   *   -> 8: Output of intermediate linear layer, of shape (B, T*I).
+   *   -> 9: Output of activation layer, of shape (B, T*I).
+   *   -> 10: Output of residual pass 2, of shape (B, T*D).
+   * - dropout_mask_attention: Dropout mask used on attention, of shape (B, H*T*T)
+   * - dropout_mask_output_1: Dropout mask used on attention output, of shape (B, T*D)
+   * - dropout_mask_output_2: Dropout mask used on attention output, of shape (B, T*D)
+   * - cache_mean_ln1: Cached mean from layer norm 1, of shape (1, B*T)
+   * - cache_var_ln1: Cached mean from layer norm 1, of shape (1, B*T)
+   * - cache_norm_ln1: Cached mean from layer norm 1, of shape (1, B*T)
+   * - cache_mean_ln2: Cached mean from layer norm 2, of shape (1, B*T)
+   * - cache_var_ln2: Cached mean from layer norm 2, of shape (1, B*T)
+   * - cache_norm_ln2: Cached mean from layer norm 2, of shape (1, B*T)
+   */
+  # Embedding dim
+  D = d * H
+
+  # Linear layers for Q, K, V
+  Q = linear_tensor_forward(states, W_Q, b_Q, T, D)  # Shape (B, T*D)
+  K = linear_tensor_forward(states, W_K, b_K, T, D)  # Shape (B, T*D)
+  V = linear_tensor_forward(states, W_V, b_V, T, D)  # Shape (B, T*D)
+
+  # Multi-head self attention
+  [context, attention, dropout_mask_attention] = attention::forward(Q, K, V, H, T, d, dropout_p_attention)
+  # Shapes (B, T*D), (B, H*T*T), (B, H*T*T)
+  outputs = list(Q, K, V, context, attention)
+
+  # Linear layer on attention output (output layer)
+  out_states = linear_tensor_forward(context, W_context, b_context, T, D)  # Shape (B, T*D)
+  # Dropout on output 1
+  dropout_mask_output_1 = matrix(0, 1, 1)
+  if (dropout_p_output > 0.0) {
+    [out_states, dropout_mask_output_1] = dropout::forward(out_states, dropout_p_output, -1)
+  }
+
+  # Residual pass 1
+  out_states = out_states + states  # Shapes (B, T*D).
+  outputs = append(outputs, out_states)
+  # Layer norm 1 for each token
+  [out_states, cache_mean_ln1, cache_var_ln1, cache_norm_ln1] = layer_norm_forward(
+    out_states, gamma_ln1, beta_ln1, epsilon_ln, T, D)
+  outputs = append(outputs, out_states)
+
+  # Save out_states for residual pass
+  out_states_identity = out_states
+  # Linear layer of intermediate part
+  out_states = linear_tensor_forward(out_states, W_intermediate, b_intermediate, T, D)  # Shape (B, T*I)
+  outputs = append(outputs, out_states)
+  # Activation
+  if (activation == "gelu") {
+    out_states = gelu::forward(out_states)
+  } else if (activation == "tanh") {
+    out_states = tanh::forward(out_states)
+  }
+  outputs = append(outputs, out_states)
+
+  # Final linear output layer
+  out_states = linear_tensor_forward(out_states, W_out, b_out, T, I)  # Shape (B, T*D)
+  # Dropout on output 2
+  dropout_mask_output_2 = matrix(0, 1, 1)
+  if (dropout_p_output > 0.0) {
+    [out_states, dropout_mask_output_2] = dropout::forward(out_states, dropout_p_output, -1)
+  }
+  # Residual pass 2
+  out_states = out_states + out_states_identity
+  outputs = append(outputs, out_states)
+  # Layer norm 2 for each token
+  [out_states, cache_mean_ln2, cache_var_ln2, cache_norm_ln2] = layer_norm_forward(
+    out_states, gamma_ln2, beta_ln2, epsilon_ln, T, D)
+}

src/test/java/org/apache/sysds/test/applications/nn/transformers/BertLayerTest.java

@@ -0,0 +1,117 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+package org.apache.sysds.test.applications.nn.transformers;
+
+import org.apache.sysds.common.Types;
+import org.apache.sysds.test.AutomatedTestBase;
+import org.apache.sysds.test.TestConfiguration;
+import org.apache.sysds.test.TestUtils;
+import org.junit.Test;
+
+public class BertLayerTest extends AutomatedTestBase{
+	private static final String TEST_NAME_FORWARD = "bert_layer_forward";
+	private static final String TEST_DIR = "applications/nn/component/";
+	private static final String RESOURCE_DIR = "src/test/resources/component/transformers/bert_layer/";
+
+	@Override
+	public void setUp() {
+		TestUtils.clearAssertionInformation();
+		addTestConfiguration(TEST_NAME_FORWARD, new TestConfiguration(TEST_DIR, TEST_NAME_FORWARD));
+	}
+
+	@Test
+	public void testBertLayerForwardNormalTanh() {
+		runBertLayerTest("test1", 5, 4, 6, 2, 3, 7, "tanh", 0, TEST_NAME_FORWARD, 
+            1e-5, true);
+	}
+
+	@Test
+	public void testBertLayerForwardNormalGelu() {
+		runBertLayerTest("test2", 4, 4, 8, 2, 4, 7, "gelu", 0, TEST_NAME_FORWARD, 
+            1e-5, true);
+	}
+
+	private void runBertLayerTest(String testSuffix, int batchSize, int seqLength, int embeddingDim, int numHeads,
+            int perHeadEmbeddingDim, int intermediateEmbeddingDim, String activation, int debug, String testname, double precision, 
+            boolean isForward) {
+		// Set execution platform
+		Types.ExecMode platformOld = setExecMode(Types.ExecMode.SINGLE_NODE);
+
+		try {
+			// Load test configuration
+			getAndLoadTestConfiguration(testname);
+			fullDMLScriptName = getScript();
+
+			// Program arguments
+			if (isForward) {
+				programArgs = new String[] { 
+					"-stats", "-args",
+					String.valueOf(debug), String.valueOf(batchSize), 
+                    String.valueOf(seqLength), String.valueOf(embeddingDim),
+					String.valueOf(numHeads), String.valueOf(perHeadEmbeddingDim),
+                    String.valueOf(intermediateEmbeddingDim), activation,
+					RESOURCE_DIR + "input_states_" + testSuffix + ".csv",
+					RESOURCE_DIR + "input_W_Q_" + testSuffix + ".csv",
+					RESOURCE_DIR + "input_b_Q_" + testSuffix + ".csv",
+                    RESOURCE_DIR + "input_W_K_" + testSuffix + ".csv",
+					RESOURCE_DIR + "input_b_K_" + testSuffix + ".csv",
+                    RESOURCE_DIR + "input_W_V_" + testSuffix + ".csv",
+					RESOURCE_DIR + "input_b_V_" + testSuffix + ".csv",
+                    RESOURCE_DIR + "input_W_context_" + testSuffix + ".csv",
+					RESOURCE_DIR + "input_b_context_" + testSuffix + ".csv",
+                    RESOURCE_DIR + "input_W_intermediate_" + testSuffix + ".csv",
+					RESOURCE_DIR + "input_b_intermediate_" + testSuffix + ".csv",
+                    RESOURCE_DIR + "input_W_out_" + testSuffix + ".csv",
+					RESOURCE_DIR + "input_b_out_" + testSuffix + ".csv",
+                    RESOURCE_DIR + "input_gamma_ln1_" + testSuffix + ".csv",
+					RESOURCE_DIR + "input_beta_ln1_" + testSuffix + ".csv",
+                    RESOURCE_DIR + "input_gamma_ln2_" + testSuffix + ".csv",
+					RESOURCE_DIR + "input_beta_ln2_" + testSuffix + ".csv",
+					RESOURCE_DIR + "output_states_" + testSuffix + ".csv",
+					RESOURCE_DIR + "output_attention_" + testSuffix + ".csv",
+					output("states_error"),
+					output("attention_error"), 
+				};
+			}
+
+			// Run the test
+			runTest(true, EXCEPTION_NOT_EXPECTED, null, -1);
+
+			// Compare results
+			if (isForward) {
+				double statesMaxError = (Double) readDMLScalarFromOutputDir("states_error").values().toArray()[0];
+				assert statesMaxError < precision;
+				double attentionMaxError = (Double) readDMLScalarFromOutputDir("attention_error").values().toArray()[0];
+				assert attentionMaxError < precision;
+			} else {
+				double dqueryMaxError = (Double) readDMLScalarFromOutputDir("dquery_error").values().toArray()[0];
+				assert dqueryMaxError < precision;
+				double dkeyMaxError = (Double) readDMLScalarFromOutputDir("dkey_error").values().toArray()[0];
+				assert dkeyMaxError < precision;
+				double dvalueMaxError = (Double) readDMLScalarFromOutputDir("dvalue_error").values().toArray()[0];
+				assert dvalueMaxError < precision;
+			}
+		} catch (Throwable ex) {
+			ex.printStackTrace(System.out); // Log or debug all exceptions or errors
+			throw new RuntimeException(ex);
+		} finally {
+			resetExecMode(platformOld);
+		}
+	}
+}

src/test/java/org/apache/sysds/test/applications/nn/transformers/MultiAttentionLayerTest.java

@@ -119,7 +119,7 @@ private void runMultiAttentionTest(String testSuffix, int batchSize, int seqLeng
 			if (isForward) {
 				double contextMaxError = (Double) readDMLScalarFromOutputDir("context_error").values().toArray()[0];
 				assert contextMaxError < precision;
-				double attentionMaxError = (Double) readDMLScalarFromOutputDir("context_error").values().toArray()[0];
+				double attentionMaxError = (Double) readDMLScalarFromOutputDir("attention_error").values().toArray()[0];
 				assert attentionMaxError < precision;
 			} else {
 				double dqueryMaxError = (Double) readDMLScalarFromOutputDir("dquery_error").values().toArray()[0];

src/test/resources/component/transformers/bert_layer/input_W_K_test1.csv

@@ -0,0 +1,6 @@
+-0.366342,-0.367447,-0.368428,0.043807,-0.098173,-0.287969
+-0.352497,-0.027552,0.258298,-0.085474,-0.085857,0.018208
+-0.063882,0.359021,-0.047110,0.291535,-0.336430,-0.287788
+0.005280,-0.166521,-0.182245,0.113960,0.221207,-0.224734
+-0.185457,0.368649,0.326457,0.196166,0.324140,-0.237889
+0.153787,0.147849,-0.329904,0.144177,0.279334,0.139517

src/test/resources/component/transformers/bert_layer/input_W_K_test2.csv

@@ -0,0 +1,8 @@
+0.014873,0.127848,-0.276551,-0.306393,0.044137,0.116741,0.004873,-0.350424
+0.227909,0.044769,-0.185308,0.175143,0.316675,0.265246,-0.060110,0.159592
+-0.267258,-0.002632,0.285492,-0.251829,0.216273,-0.113814,-0.186207,-0.169799
+-0.242719,-0.069891,-0.286925,-0.100361,-0.223521,0.000566,0.046730,-0.235940
+-0.205295,0.044359,-0.025387,-0.118623,0.158570,0.182018,0.292360,-0.203683
+0.247464,-0.080732,0.349749,-0.052357,-0.249925,-0.341919,-0.103351,0.203278
+-0.127090,-0.002484,0.127717,0.003867,-0.149845,0.255612,-0.209903,0.187233
+0.298218,0.045111,0.010010,0.291613,0.103988,-0.292361,-0.130758,0.271360

src/test/resources/component/transformers/bert_layer/input_W_Q_test1.csv

@@ -0,0 +1,6 @@
+0.160208,-0.102197,-0.265960,0.082622,-0.366738,-0.382060
+0.024454,-0.198863,-0.020951,0.259580,-0.193541,-0.344565
+-0.199196,-0.142819,0.292245,0.386712,0.277978,-0.082808
+0.193179,-0.334609,-0.041968,0.259260,-0.002646,0.223886
+-0.391612,-0.086841,0.011346,0.387596,-0.202918,0.220716
+-0.241971,0.087266,-0.035219,-0.029525,-0.312845,-0.393728

src/test/resources/component/transformers/bert_layer/input_W_Q_test2.csv

@@ -0,0 +1,8 @@
+-0.123685,0.009826,-0.317605,-0.071714,-0.068100,-0.318219,-0.040798,0.169884
+-0.289780,-0.030501,-0.167612,0.193891,-0.069418,-0.023860,-0.157829,0.124861
+-0.075206,0.071553,0.240736,0.191146,-0.317261,0.310922,0.282720,-0.085021
+0.075574,0.224803,-0.002292,-0.340978,-0.305271,-0.144212,-0.285705,-0.074354
+-0.230328,0.334902,-0.175732,0.220540,-0.055324,0.319260,0.037938,-0.291357
+-0.018144,0.224526,-0.270932,-0.276659,0.004572,0.128041,-0.074023,0.191571
+0.253091,0.335668,-0.330874,-0.074745,-0.160610,-0.319068,0.252477,0.280714
+-0.036345,-0.025570,-0.298402,-0.143356,0.133183,0.223692,0.098693,0.241910

src/test/resources/component/transformers/bert_layer/input_W_V_test1.csv

@@ -0,0 +1,6 @@
+-0.237054,-0.003039,-0.319334,0.147474,-0.136974,0.249731
+0.285747,-0.080703,-0.213976,0.011559,-0.060456,-0.258100
+-0.146751,0.051221,0.329658,-0.353792,0.004466,0.183101
+0.344353,-0.093221,-0.331313,0.202237,0.336726,-0.288589
+0.147626,-0.002869,-0.029315,-0.290787,0.050965,-0.173026
+0.051695,0.052090,0.403855,-0.115887,0.365665,0.120075

src/test/resources/component/transformers/bert_layer/input_W_V_test2.csv

@@ -0,0 +1,8 @@
+-0.334274,0.011264,-0.080849,0.244498,0.069431,0.122792,0.029533,0.165114
+0.076385,-0.237900,-0.015723,-0.263194,-0.262510,-0.129004,0.044147,-0.171997
+-0.198408,-0.285785,-0.215330,0.144839,0.058866,0.134202,-0.277945,-0.292986
+-0.315220,0.281811,0.119572,-0.118884,0.150589,0.235453,0.027785,-0.304028
+0.310023,0.057572,0.111782,-0.170578,0.139947,-0.184608,0.244825,0.352708
+-0.229602,0.293317,-0.007293,0.063514,-0.044505,0.003487,0.318592,0.224432
+-0.040221,-0.118525,-0.079515,-0.183656,-0.289839,0.146194,0.207801,-0.244388
+0.101291,0.104141,-0.217941,0.081460,-0.054502,0.027711,0.047377,0.138325

src/test/resources/component/transformers/bert_layer/input_W_context_test1.csv

@@ -0,0 +1,6 @@
+0.295156,0.337588,-0.196067,0.148081,-0.193161,0.357983
+-0.337590,-0.119339,-0.272441,-0.136338,-0.191908,-0.265121
+0.005627,-0.242375,-0.235192,-0.114084,-0.385986,-0.046443
+-0.069409,-0.150986,0.234725,0.120609,0.088201,0.116961
+-0.215013,-0.404635,0.216198,0.335594,-0.229102,0.013006
+0.053959,0.184281,0.313339,0.111000,-0.363984,-0.274703

src/test/resources/component/transformers/bert_layer/input_W_context_test2.csv

@@ -0,0 +1,8 @@
+-0.212761,-0.063619,-0.239211,-0.241276,0.290790,0.116962,-0.199302,0.226094
+0.317851,0.137643,-0.348794,-0.057128,0.289475,0.353439,-0.198385,0.026281
+0.170822,0.062799,-0.283923,-0.229609,0.253087,0.183375,-0.272053,-0.166925
+0.192735,0.150426,0.279120,0.245506,0.272988,0.219786,0.237351,0.324932
+-0.221599,-0.120147,0.191285,-0.267289,0.314375,-0.123741,0.251352,0.144582
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src/test/resources/component/transformers/bert_layer/input_W_intermediate_test1.csv

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src/test/resources/component/transformers/bert_layer/input_W_intermediate_test2.csv

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