add script for benchmarking & benchmark results

benchmark/perf_others.py

@@ -0,0 +1,179 @@
+# modified from https://github.com/hpcaitech/FastFold/blob/main/benchmark/perf.py
+import argparse
+import os
+
+import torch
+import torch.nn as nn
+
+from fastfold.distributed import init_dap
+from fastfold.model.fastnn import Evoformer
+
+
+def main():
+
+    parser = argparse.ArgumentParser(description='Evoformer Standalone Perf Benchmark')
+    parser.add_argument("--dap-size", default=1, type=int, help='batch size')
+    parser.add_argument('--batch-size', default=1, type=int, help='batch size')
+    parser.add_argument('--msa-length', default=128, type=int, help='Sequence Length of MSA')
+    parser.add_argument('--res-length',
+                        default=256,
+                        type=int,
+                        help='Sequence Length of Residues')
+    parser.add_argument('--trials', default=50, type=int, help='Number of Trials to Execute')
+    parser.add_argument('--warmup-trials', default=5, type=int, help='Warmup Trials to discard')
+    parser.add_argument('--layers',
+                        default=4,
+                        type=int,
+                        help='Evoformer Layers to Execute')
+    parser.add_argument('--cm', default=256, type=int, help='MSA hidden dimension')
+    parser.add_argument('--cz', default=128, type=int, help='Pair hidden dimension')
+    parser.add_argument('--heads', default=8, type=int, help='Number of Multihead Attention heads')
+    parser.add_argument('--openfold',
+                        action='store_true',
+                        help='Benchmark with Evoformer Implementation from OpenFold.')
+    parser.add_argument('--openfold-lma',
+                        action='store_true',
+                        help='set use_lma to True in openfold.')
+    parser.add_argument('--fwd', action='store_true', help='Only execute Fwd Pass.')
+
+    args = parser.parse_args()
+
+    init_dap(args.dap_size)
+
+    precision = torch.bfloat16
+    if args.dap_size > 1:
+        # (PyTorch issue) Currently All2All communication does not support the Bfloat16 datatype in PyTorch
+        precision = torch.float16
+
+    if not torch.cuda.is_available():
+        raise NotImplementedError('Running on CPU is not supported')
+
+    torch.manual_seed(42)
+    if torch.cuda.is_available():
+        torch.cuda.manual_seed_all(42)
+
+    if args.openfold:
+        from openfold.model.evoformer import EvoformerBlock
+
+        class OpenFoldEvoformer(nn.Module):
+
+            def __init__(self, d_node, d_pair):
+                super(OpenFoldEvoformer, self).__init__()
+                self.d_node = d_node
+                self.d_pair = d_pair
+
+                self.c_hidden_msa_att = int(d_node / 8)
+                self.c_hidden_pair_att = int(d_pair / 4)
+
+                self.EvoformerBlock = EvoformerBlock(c_m=d_node,
+                                                     c_z=d_pair,
+                                                     c_hidden_msa_att=self.c_hidden_msa_att,
+                                                     c_hidden_opm=self.c_hidden_msa_att,
+                                                     c_hidden_mul=self.d_pair,
+                                                     c_hidden_pair_att=self.c_hidden_pair_att,
+                                                     no_heads_msa=8,
+                                                     no_heads_pair=4,
+                                                     transition_n=4,
+                                                     msa_dropout=0.15,
+                                                     pair_dropout=0.25,
+                                                     inf=1e9,
+                                                     eps=1e-10)
+
+            def forward(self, node, pair, node_mask, pair_mask):
+                node, pair = self.EvoformerBlock(node, pair, node_mask, pair_mask, use_lma=args.openfold_lma)
+                return node, pair
+
+    attn_layers = []
+    for idx in range(0, args.layers):
+        if args.openfold:
+            attn_layers.append(OpenFoldEvoformer(d_node=args.cm, d_pair=args.cz))
+        else:
+            attn_layers.append(Evoformer(d_node=args.cm, d_pair=args.cz))
+        attn_layers[idx].cuda()
+        attn_layers[idx].to(dtype=precision)
+
+    start_evt_fwd = []
+    start_evt_bwd = []
+    stop_evt_bwd = []
+    for recorded_trial in range(0, args.trials):
+        start_evt_fwd.append(torch.cuda.Event(enable_timing=True))
+        start_evt_bwd.append(torch.cuda.Event(enable_timing=True))
+        stop_evt_bwd.append(torch.cuda.Event(enable_timing=True))
+
+    inputs_node = torch.randn(args.batch_size,
+                              args.msa_length // args.dap_size,
+                              args.res_length,
+                              args.cm,
+                              dtype=precision,
+                              device=torch.device("cuda")).requires_grad_(True)
+    inputs_pair = torch.randn(args.batch_size,
+                              args.res_length // args.dap_size,
+                              args.res_length,
+                              args.cz,
+                              dtype=precision,
+                              device=torch.device("cuda")).requires_grad_(True)
+    node_mask = torch.ones((args.batch_size, args.msa_length, args.res_length),
+                           dtype=precision,
+                           device=torch.device("cuda")).requires_grad_(False)
+    pair_mask = torch.ones((args.batch_size, args.res_length, args.res_length),
+                           dtype=precision,
+                           device=torch.device("cuda")).requires_grad_(False)
+
+
+    total_used_mem_gb = 0
+    for trial in range(0, args.trials + args.warmup_trials):
+        layer_inputs = inputs_node, inputs_pair
+        evt_idx = trial - args.warmup_trials
+
+        torch.distributed.barrier()
+        torch.cuda.synchronize()
+        torch.cuda.reset_peak_memory_stats()
+        if evt_idx >= 0:
+            start_evt_fwd[evt_idx].record()
+        with torch.set_grad_enabled(not args.fwd):
+            for lyr_idx in range(0, args.layers):
+                layer_inputs = attn_layers[lyr_idx].forward(
+                    *layer_inputs,
+                    node_mask,
+                    pair_mask,
+                )
+
+        torch.cuda.synchronize()
+
+        if evt_idx >= 0:
+            start_evt_bwd[evt_idx].record()
+
+        if not args.fwd:
+            s = layer_inputs[0].mean() + layer_inputs[1].mean()
+            s.backward()
+
+        torch.cuda.synchronize()
+        cur_cost_mem = torch.cuda.max_memory_allocated() / 1024 / 1024 / 1024
+        total_used_mem_gb += cur_cost_mem
+        if evt_idx >= 0:
+            stop_evt_bwd[evt_idx].record()
+
+
+    torch.cuda.synchronize()
+    elapsed_time_fwd = 0.0
+    elapsed_time_bwd = 0.0
+    for evt_idx in range(0, args.trials):
+        elapsed_time_fwd += start_evt_fwd[evt_idx].elapsed_time(start_evt_bwd[evt_idx])
+        elapsed_time_bwd += start_evt_bwd[evt_idx].elapsed_time(stop_evt_bwd[evt_idx])
+
+    print(
+        "Input: {:4d}, {:4d}, {:4d}, ({:4d} {:4d}), Fwd Time / Layer: {:.3f} ms, Bwd Time / Layer: {:.3f} ms, Memory cost {:.3f} GB".format(
+            args.batch_size,
+            args.msa_length,
+            args.res_length,
+            args.cm,
+            args.cz,
+            elapsed_time_fwd  / (args.trials * args.layers),
+            elapsed_time_bwd  / (args.trials * args.layers),
+            total_used_mem_gb / (args.trials),
+        )
+    )
+
+
+if __name__ == '__main__':
+    main()