Slow training time of the same model in two repositories

I have cloned a GitHub repository onto my local computer in two different locations. In one of these locations, I have added new modules and expanded the repository, but the original setups and experiments are still preserved. The other location contains the original repository, untouched.

When attempting to run one of the original experiments in both repositories, I have noticed that the modified version runs significantly slower. Specifically, one epoch takes 200 seconds in the modified repository, while it only takes 17 seconds in the original repository.

After carefully examining the dataset location, data loaders, model, loss function, optimizer, and configurations, I proceeded to train a Resnet18 on CIFAR10 in a continual setting. Each task consists of two classes, with a batch size of 16 and the number of workers set to 4. The experiments are being run on two GPUs of the same type, both located on the same machine.

However, upon monitoring the behavior of the GPUs, I noticed that one of the experiments was significantly slower than the other. Surprisingly, the slow experiment was only utilizing the GPU up to 14%, with the lowest usage being at 3%, while the faster experiment was using the GPU up to 70% and dropping down to 0%.

I am confused by this behavior, as the settings for both experiments appear to be identical. Is there anything else that I should investigate to identify the source of this issue?

I would try to verify that exactly the same data is used from the same location etc. as well as the same model.
If you’ve already done it, you should profile the code using e.g. Nsight Systems and check the timeline of a few iterations to see which part of the model training slows down.
Based on your observation regarding the GPU utilization I would guess the data loading and processing code is slower in one setup which then lets the GPU starve.

I used the following code in both repos to measure the running time of each component of the model (ResNet18).

def measure_time(self, model, input):
            # Record the start time

            # Forward pass
            output = model(input)

            # Record the end time

            # Wait for the events to complete

            # Compute the elapsed time
            elapsed_time = self.start_event.elapsed_time(self.end_event)

            return elapsed_time, output

and then:

def _train(
        self, train_loader, memory_loader, optimizer, criterion
        total_loss, correct, num_data = 0.0, 0.0, 0.0

        if memory_loader is not None and train_loader is not None:
            data_iterator = zip(train_loader, cycle(memory_loader))
        elif memory_loader is not None:
            data_iterator = memory_loader
        elif train_loader is not None:
            data_iterator = train_loader
            raise NotImplementedError("None of dataloder is valid")
        for i, data in enumerate(data_iterator):
            if len(data) == 2:
                stream_data, mem_data = data
                x =[stream_data["image"], mem_data["image"]])
                y =[stream_data["label"], mem_data["label"]])
                x = data["image"]
                y = data["label"]

            x =
            y =
            # measure each operation time of the forward pass for one batch
            # ---------------------------------------------------
            if i==0:
                # Conv1
                conv1_time, output = self.measure_time(self.model.conv1, x)
                print('conv1_time', conv1_time)
                # BatchNorm1
                bn1_time, output = self.measure_time(self.model.bn1, output)
                print('bn1_time', bn1_time)
                # ReLU
                relu_time, output = self.measure_time(self.model.relu, output)
                print('relu_time', relu_time)
                # MaxPool
                maxpool_time, output = self.measure_time(self.model.maxpool, output)
                print('maxpool_time', maxpool_time)
                # Layer1
                layer1_time, output = self.measure_time(self.model.layer1, output)
                print('layer1_time', layer1_time)
                # Layer2
                layer2_time, output = self.measure_time(self.model.layer2 , output)
                print('layer2_time', layer2_time)
                # Layer3
                layer3_time, output = self.measure_time(self.model.layer3, output)
                print('layer3_time', layer3_time)
                # Layer4
                layer4_time, output = self.measure_time(self.model.layer4, output)
                print('layer4_time', layer4_time)
                # AvgPool
                avgpool_time, output = self.measure_time(self.model.avgpool, output )
                print('avgpool_time ', avgpool_time)
                output = torch.flatten(output, 1)
                # Fc
                fc_time, _ = self.measure_time(self.model.fc, output)
                print('fc-time ', fc_time)
            # ------------------------------------------------------
            # this is equivalent to the step code in the test repo
            l, c, d = self.update_model(x, y, criterion, optimizer)
            # Compute the moving averages - equivalent to MovingAverage in the test repo
            total_loss += l
            correct += c
            num_data += d

I get the following values:
in the fast repo I have:

conv1_time 919.8919677734375
bn1_time 65.71724700927734
relu_time 0.2734079957008362
maxpool_time 0.3357119858264923
layer1_time 1.3231040239334106
layer2_time 1.3721599578857422
layer3_time 1.2472319602966309
layer4_time 1.7541120052337646
avgpool_time 0.18943999707698822
fc-time 0.4814079999923706

and in the slow one:

conv1_time 974.81005859375
bn1_time 112.70028686523438
relu_time 17.454816818237305
maxpool_time 16.718528747558594
layer1_time 266.0933532714844
layer2_time 317.3957824707031
layer3_time 310.3487854003906
layer4_time 317.3232727050781
avgpool_time  9.390975952148438
fc-time  30.7589111328125

The difference is huge. These measurements belong to the first iteration of the first epoch. The values continue to be like this. I checked the dtype of the model parameters and both cases, they are float32.
Is there any reason than can cause this? can I still rule out dataloader performance? I am running my code on the same environment and the same GPU model.

I would still recommend profiling the code properly using Nsight Systems to see what exactly and where slows down. Nsight will allow you to also hover over kernels, check the stacktrace (if enabled), see the bandwidth for copies etc.