optimize code for bwd performance and refine code. (#145)

* optimize code for bwd performance and refine code.

* refine README to add test SW version

README.md

@@ -210,11 +210,12 @@ python inference.py target.fasta data/pdb_mmcif/mmcif_files/ \
 
 ### Inference or Training on Intel Habana
 
-To run AlphaFold inference or training on Intel Habana, you can follow the instructions in the [Installation Guide](https://docs.habana.ai/en/latest/Installation_Guide/) to set up your environment on Amazon EC2 DL1 instances or on-premise environments.
+To run AlphaFold inference or training on Intel Habana, you can follow the instructions in the [Installation Guide](https://docs.habana.ai/en/latest/Installation_Guide/) to set up your environment on Amazon EC2 DL1 instances or on-premise environments, and please use SynapseAI R1.7.1 to test as it was verified internally.
 
 Once you have prepared your dataset and installed fastfold, you can use the following scripts:
 
 ```shell
+cd fastfold/habana/fastnn/custom_op/; python setup.py build (this is for Gaudi, for Gaudi2 please use setup2.py) ; cd -
 bash habana/inference.sh
 bash habana/train.sh
 ```

fastfold/habana/distributed/__init__.py

 from .comm import (All_to_All, _gather, _reduce, _split, col_to_row, copy,
                    gather, reduce, row_to_col, scatter)
-from .core import init_dist
+from .core import init_dist, get_data_parallel_world_size
 
 __all__ = [
-    'init_dist', '_reduce', '_split', '_gather', 'copy', 'scatter', 'reduce', 'gather',
+    'init_dist', 'get_data_parallel_world_size', '_reduce', '_split', '_gather', 'copy', 'scatter', 'reduce', 'gather',
     'col_to_row', 'row_to_col', 'All_to_All'
 ]

fastfold/utils/rigid_utils.py

@@ -18,7 +18,7 @@ from typing import Tuple, Any, Sequence, Callable, Optional
 
 import numpy as np
 import torch
-
+import fastfold.habana as habana
 
 def rot_matmul(
     a: torch.Tensor, 
@@ -34,6 +34,19 @@ def rot_matmul(
         Returns:
             The product ab
     """
+    if habana.is_habana():
+        if len(a.shape) == 4 and a.shape[1] == 1:
+            aa = a.permute(0, 1, 3, 2)
+            bb = b.permute(0, 1, 3, 2)
+            cc = bb @ aa
+            cc = cc.permute(0, 1, 3, 2)
+            return cc
+        elif len(a.shape) == 4 and a.shape[1] != 1:
+            pass
+        else:
+            cc = a @ b
+            return cc
+
     row_1 = torch.stack(
         [
             a[..., 0, 0] * b[..., 0, 0]
@@ -94,6 +107,20 @@ def rot_vec_mul(
         Returns:
             [*, 3] rotated coordinates
     """
+    if habana.is_habana():
+        cont = True
+        if len(t.shape) == 4 and t.shape[1] == 1:
+            cont = False
+        elif len(t.shape) == 3 and t.shape[0] != r.shape[0] and t.shape[0] == 1:
+            cont = False
+
+        if cont:
+            tt = t.unsqueeze(-2)
+            rr = r.transpose(-2, -1)
+            cc = tt @ rr
+            cc = cc.squeeze(-2)
+            return cc
+
     x = t[..., 0]
     y = t[..., 1]
     z = t[..., 2]

habana/inference.sh

+export GC_KERNEL_PATH=./fastfold/habana/fastnn/custom_op/libcustom_tpc_perf_lib.so:$GC_KERNEL_PATH
+export PYTHONPATH=./:$PYTHONPATH
+
 # add '--gpus [N]' to use N gpus for inference
 # add '--enable_workflow' to use parallel workflow for data processing
 # add '--use_precomputed_alignments [path_to_alignments]' to use precomputed msa

habana/train.py

@@ -10,7 +10,7 @@ from tqdm import tqdm
 import fastfold.habana as habana
 from fastfold.config import model_config
 from fastfold.data.data_modules import SetupTrainDataset, TrainDataLoader
-from fastfold.habana.distributed import init_dist
+from fastfold.habana.distributed import init_dist, get_data_parallel_world_size
 from fastfold.habana.inject_habana import inject_habana
 from fastfold.model.hub import AlphaFold, AlphaFoldLoss, AlphaFoldLRScheduler
 from fastfold.utils.tensor_utils import tensor_tree_map
@@ -156,7 +156,8 @@ def main():
     model = inject_habana(model)
 
     model = model.to(device="hpu")
-    model = DDP(model)
+    if get_data_parallel_world_size() > 1:
+        model = DDP(model, gradient_as_bucket_view=True, bucket_cap_mb=400)
 
     train_dataset, test_dataset = SetupTrainDataset(
         config=config.data,
@@ -201,27 +202,32 @@ def main():
                     isVerbose=args.hmp_verbose)
         print("========= HMP ENABLED!!")
 
+    idx = 0
     for epoch in range(200):
         model.train()
         train_dataloader = tqdm(train_dataloader)
         for batch in train_dataloader:
             perf = hpu_perf("train step")
-            batch = {k: torch.as_tensor(v).to(device="hpu") for k, v in batch.items()}
+            batch = {k: torch.as_tensor(v).to(device="hpu", non_blocking=True) for k, v in batch.items()}
             optimizer.zero_grad()
+            perf.checknow("prepare input and zero grad")
             output = model(batch)
             perf.checknow("forward")
             
             batch = tensor_tree_map(lambda t: t[..., -1], batch)
+            perf.checknow("prepare loss input")
             loss, loss_breakdown = criterion(output, batch, _return_breakdown=True)
             perf.checknow("loss")
 
             loss.backward()
-            train_dataloader.set_postfix(loss=float(loss))
+            if idx % 10 == 0:
+                train_dataloader.set_postfix(loss=float(loss))
             perf.checknow("backward")
 
             with hmp.disable_casts():
                 optimizer.step()
             perf.checknow("optimizer")
+            idx += 1
 
         lr_scheduler.step()
 

habana/train.sh

-DATA_DIR=/mnt/usb/training-demo
+export GC_KERNEL_PATH=./fastfold/habana/fastnn/custom_op/libcustom_tpc_perf_lib.so:$GC_KERNEL_PATH
+export PYTHONPATH=./:$PYTHONPATH
+
+DATA_DIR=../FastFold-dataset/train
 
 hpus_per_node=1