Avoiding problems in Theano computation graphs

17 minute read

Notes on writing, testing, and debugging Theano computation graphs

NumPy as a reference

Theano interface is made as similar to NumPy as possible. Theano code often closely resembles NumPy code, but the interface is limited and some differences are necessary because of how Theano works. If you’re not confident that the matrix operations do what you intended, you can esily test them by running the same operations in an interactive Python session using NumPy.

While Theano documentation is not perfect, it often helps to look at the corresponding NumPy documentation. If you’re new to both Theano and NumPy, you should at least familiarize yourself with broadcasting, and slicing and indexing, which are explained more thoroughly in NumPy documentation.

A couple notable deviations from NumPy are worth mentioning, though. Theano uses integers to represent booleans. Thus you cannot index a matrix with a boolean matrix. You’ll have to convert the boolean matrix to a matrix of indices with nonzero(). And since Theano never modifies a tensor, for creating a tensor where a subset of the matrix elements have been updated, you need to call set_subtensor(). The following example sets the data elements to zero where the mask is nonzero:

import numpy
from theano import tensor, function
data = tensor.matrix('data')
mask = tensor.matrix('mask', dtype='int8')
indices = mask.nonzero()
output = tensor.set_subtensor(data[indices], 0)
f = function([data, mask], output)
toy_data = numpy.arange(9).reshape(3, 3)
toy_mask = numpy.zeros((3, 3), dtype='int8')
numpy.fill_diagonal(toy_mask, 1)
print(f(toy_data, toy_mask))

The example produces a matrix whose main diagonal has been zeroed out:

[[ 0.  1.  2.]
 [ 3.  0.  5.]
 [ 6.  7.  0.]]

In NumPy you could simply modify the array in place, using data[mask == 1] = 0.

Test values

The biggest difference when writing writing a function with Theano versus NumPy is obviously that when expressing a mathematical operation using Theano, the Python code doesn’t process the actual data, but symbolic variables that will be used to construct the computation graph. The concept is easy to understand, but also easy to forget when you’re writing a Theano function, and makes debugging somewhat harder.

The fact that the actual data is not known when building the computation graph makes it difficult for Theano to produce understandable error messages. A solution to this is to always set a test value, when creating a shared variable. This allows Theano to produce an error message at the exact location where you are adding an invalid operation to the graph.

The test value is a NumPy matrix. Usually random numbers work. The important thing is that the shape and data type (and maybe the range of values) correspond to the data used in the actual application. Typical errors are caused by a mismatch in the dimensionality or shape of the arguments of an operation. The error messages can still be quite difficult to interpret. The nice thing is that you can also print the computed test values (and their dtype, shape, etc. attributes).

Evaluation of the expressions using test values is enabled by setting the compute_test_value configuration attribute. Naturally executing the graph using the test values introduces computational overhead, so you probably don’t want to keep this enabled except when you need to debug an error in the graph. The example below prints probably 9, which has been computed using the test value provided for the input data, while the actual data is not available yet:

import numpy
from theano import tensor, config
config.compute_test_value = 'warn'
data = tensor.matrix('data', dtype='int64')
data.tag.test_value = numpy.random.randint(0, 10, size=(100, 100))
maximum = data.max()
print(maximum.tag.test_value)

Printing

Printing the actual value of a tensor during computation is possible using a theano.printing.Print operation. The constructor takes an optional message argument. The data that is given to the created operation object as an argument will be printed during execution of the graph, and also passed on as the output of the operation. In order to print something, the computation graph has to use the value returned by the print operation. Printing e.g. the shape of a matrix would be difficult, but luckily the Print constructor takes another parameter attrs for the purpose of printing certain attributes instead of the value of a tensor.

If you encounter an error while compiling the function, this doesn’t help. In that case you can print the test value only. But the print operation can be used to print values computed from the actual inputs, if necessary. This example prints identity shape = (3, 3) during the execution of the graph:

import numpy
from theano import tensor, printing, function
data = tensor.matrix('data', dtype='int64')
identity = tensor.identity_like(data)
print_op = printing.Print("identity", attrs=['shape'])
identity = print_op(identity)
f = function([data], identity.sum())
toy_data = numpy.arange(9).reshape(3, 3)
f(toy_data)

Assertions

Often one would like to make sure for example that the result of an operation is of the correct shape. There is an assertion operation that works in the same way as the print operation. A theano.tensor.opt.Assert object is added somewhere in the graph. The constructor takes an optional message argument. The first argument is the data that will be passed on as the output of the operation, and the second argument is the assertion. Note that the assertion has to be a tensor, so for comparison you’ll have to use theano.tensor.eq(), theano.tensor.neq(), etc. The example below verifies that the number of output and input dimensions are equal:

import numpy
from theano import tensor, function
data = tensor.matrix('data', dtype='int64')
identity = tensor.identity_like(data)
assert_op = tensor.opt.Assert("Shape mismatch!")
output = assert_op(identity, tensor.eq(identity.ndim, data.ndim))
f = function([data], output)
toy_data = numpy.arange(9).reshape(3, 3)
f(toy_data)

Assertions are not very convenient to use either, and in case an assertion fails, the printed message usually gives you less information than if you simply let the computation continue until the next error.

Unit tests

Testing the correctness of some higher level functions that use neural networks is difficult because of the nondeterministic nature of neural networks. I have separated the network structure from the classes that create and use the actual Theano functions. If I want to write a unit test for a function that performs some operation on neural network output, I replace the neural network with a simple dummy network.

So let’s say I have a class Processor that uses neural network output to perform some task. The function process_file() reads input from one file and writes output to another file.

from theano import tensor, function
class NeuralNetwork:
    def __init__(self):
        self.input = tensor.scalar()
        self.output = complex_theano_operation(self.input)
class Processor:
    def __init__(self, network):
        self.compute_output = function([network.input],
                                       network.output)
    def process_file(self, input_file, output_file):
        for line in input_file:
            output_file.write(str(self.compute_output(float(line))
                              + "\n")

When writing unit tests for Processor, I would create a dummy neural network that produces simple deterministic output, then pass that dummy network to Processor before testing its functions. The trivial example below tries to illustrate this approach:

class DummyNetwork:
    def __init__(self):
        self.input = tensor.scalar()
        self.output = self.input + 1
class ProcessorTest(unittest.TestCase):
    def test_process(self):
        network = DummyNetwork()
        processor = Processor(network)
        with open('input.txt', 'r') as input_file,
             open('output.txt', 'w') as output_file:
            processor.process(input_file, output_file)
        # Assert that each line in the output file equals to the
        # corresponding line in the input file plus one.

Performance issues in computation graph

Performance problems can be very challenging to track down. Looking at the computation graph is necessary to know what Theano is actually doing under the hood. Analyzing the graph is easier if you first try to simplify the computation, as long as the performance issue won’t disappear.

Print the computation graph using theano.printing.debugprint(). You can print the graph at any point when you’re constructing it, but only the final graph compiled using theano.function() shows the actual operations and memory transfers that will take place. You can display the compiled graph of function f using theano.printing.debugprint(f). If you have Graphviz and pydot installed, you can even print a pretty image using theano.printing.pydotprint(f, outfile="graph.png").

One thing that can be immediately noted on the graph is the HostFromGpu and GpuFromHost operations. These are the expensive memory transfers between the host computer and the GPU memory. You can also notice from the names of the operations of the compiled graph, whether they run on GPU or not—GPU operations have the Gpu prefix. Ideally your shared variables are stored on the GPU and you have only one HostFromGpu operation in the end, as in the graph below:

HostFromGpu [id A] ''   136
 |GpuElemwise{Composite{((-i0) / i1)}}[(0, 0)] [id B] ''   133
   |GpuCAReduce{add}{1,1} [id C] ''   128
   | |GpuElemwise{Composite{((log((i0 + (i1 / i2))) + i3) * i4)}}
   |   |CudaNdarrayConstant{[[  9.99999997e-07]]} [id E]
   |   |GpuElemwise{true_div,no_inplace} [id F] ''   119
   |   | |GpuElemwise{Exp}[(0, 0)] [id G] ''   118
   |   | | |GpuReshape{2} [id H] ''   116
   |   | |   |GpuElemwise{Add}[(0, 1)] [id I] ''   114
   |   | |   | |GpuReshape{3} [id J] ''   112
   |   | |   | | |GpuCAReduce{add}{0,1} [id K] ''   110
   |   | |   | | | |GpuReshape{2} [id L] ''   108
   |   | |   | | |   |GpuElemwise{mul,no_inplace} [id M] ''   66
   |   | |   | | |   | |GpuDimShuffle{0,1,x,2} [id N] ''   58
   |   | |   | | |   | | |GpuReshape{3} [id O] ''   55
   |   | |   | | |   | |   |GpuAdvancedSubtensor1 [id P] ''   35
   |   | |   | | |   | |   | |layers/projection_layer/W [id Q]

Some operations force memory to be transferred back and forth. If you’re still using the old GPU backend (device=gpu), chances are that the reason is that the GPU operations are implemented for float32 only. Make sure that you set the flags floatX=float32 and that your shared variables are float32. All the floating point constants should be cast to numpy.float32 as well. Another example is multinomial sampling—uniform sampling is performed on GPU, but MultinomialFromUniform forces a transfer to host memory:

MultinomialFromUniform{int64} [id CH] ''
 |HostFromGpu [id CI] ''
 | |GpuReshape{2} [id CJ] ''
 | ...
 |HostFromGpu [id CT] ''
 | |GPU_mrg_uniform{CudaNdarrayType(float32, vector),inplace}.1
 |   |<CudaNdarrayType(float32, vector)> [id CV]
 |   |MakeVector{dtype='int64'} [id CW] ''

Profiling performance

Profiling is important after making changes to a Theano function, to make sure that the compiled code won’t run inefficiently. Profiling can be enabled by setting the flag profile=True, or for certain functions individually by passing the argument profile=True to theano.function().

When profiling is enabled, the function runs very slowly, so if your program calls it repeatedly, you probably want to exit after a few iterations. When the program exits, theano prints several tables. I have found the Apply table to be the most useful. It displays the time spent in each node of the computation graph, in descending order:

Apply
------
<% time> <sum %> <apply time> <time per call> <#call> <id>
  89.2%    89.2%     383.470s       2.52e-01s   1523   116
    input 0: dtype=float32, shape=(10001,), strides=(1,)
    input 1: dtype=float32, shape=(18000,), strides=(1,)
    input 2: dtype=int64, shape=(18000,), strides=c
    output 0: dtype=float32, shape=(10001,), strides=(1,)
   3.6%    92.8%      15.575s       1.02e-02s   1523   111
    input 0: dtype=float32, shape=(10001,), strides=(1,)
    input 1: dtype=float32, shape=(720,), strides=(1,)
    input 2: dtype=int64, shape=(720,), strides=c
    output 0: dtype=float32, shape=(10001,), strides=(1,)

In the above example, the most expensive operation is node 116, which consumes 89 % of the total processing time, so there’s clearly something wrong with this operation. The ID 116 can be used to locate this node in the computation graph:

GpuAdvancedIncSubtensor1{inplace,inc} [id CY] ''   116
 |GpuAdvancedIncSubtensor1{inplace,inc} [id CZ] ''   111
 | |GpuAlloc{memset_0=True} [id DA] ''   22
 | | |CudaNdarrayConstant{[ 0.]} [id DB]
 | | |Shape_i{0} [id DC] ''   13
 | |   |bias [id BU]

It is essential to name all the shared variables by providing the name argument to the their constructors. This makes it easier to understand which function calls generated a specific part of the graph. In this case, the graph shows that the bottleneck GpuAdvancedIncSubtensor1 operates on the bias variable and we can find the code that produced this operation. It looks like this:

value = numpy.zeros(size).astype(theano.config.floatX)
bias = theano.shared(value, name='bias')
...
bias = bias[targets]
bias = bias.reshape([minibatch_size, -1])

GpuAdvancedIncSubtensor1 is responsible for updating the specific elements of the bias vector (the elements indexed by targets), when the bias parameter is updated. So how can the performance be improved? It can be difficult to know what’s wrong, especially while Theano is still under quite heavy development and some things may be broken. If you have a working version without the performance problem, the best bet might be to make small changes to the code to see what causes the problem to appear.

In this particular case, turned out that a faster variant of the op, GpuAdvancedIncSubtensor1_dev20 was implemented only for two-dimensional input, and the performance was radically improved by first converting the bias to 2D:

bias = bias[:, None]
bias = bias[targets, 0]

Memory usage

The memory usage of a neural network application can be crucial, current GPU boards usually containing no more than 12 GB of memory. When Theano runs out of memory, it throws an exception (GpuArrayException in the new backend) with the message out of memory. It means that some of the variables, either the tensor variables used as the input of a function, shared variables, or the intermediate variables created during the execution of the graph, do not fit in the GPU memory.

The size of the shared variables, such as neural network weights, can be easily observed, and it is clear how the layer sizes affect the sizes of the weight matrices. Weight matrix dimensions are defined by the number of inputs and the number of outputs, so the weight matrices get large when two large layers follow each other (or the number of inputs/outputs and the first/last layer are large).

The shared variables and inputs constitute just part of the memory usage, however. Theano also needs to save the intermediate results of the graph nodes, e.g. outputs of each layer. The size of these outputs depend on the batch size, as well as the layer size. When Theano fails to save an intermediate result, it prints a lot of useful information, including the opration that produced the data, the node in the computation graph, and all the variables in the memory:

Apply node that caused the error:
  GpuDot22(GpuReshape{2}.0, layer_1/W)
Toposort index: 62
Inputs types: [GpuArrayType<None>(float32),
               GpuArrayType<None>(float32)]
Inputs shapes: [(482112, 200), (200, 4000)]
Inputs strides: [(800, 4), (16000, 4)]
Inputs values: ['not shown', 'not shown']
Inputs type_num: [11, 11]
Outputs clients: [[GpuReshape{3}(GpuDot22.0,
                   MakeVector{dtype='int64'}.0)]]

Debugprint of the apply node:
GpuDot22 [id A] <GpuArrayType<None>(float32)> ''
 |GpuReshape{2} [id B] <GpuArrayType<None>(float32)> ''
 | |GpuAdvancedSubtensor1 [id C] <GpuArrayType<None>(float32)> ''
 | | |projection_layer/W [id D] <GpuArrayType<None>(float32)>
 | ...
 |layer_1/W [id BA] <GpuArrayType<None>(float32)>

Storage map footprint:
 - GpuReshape{2}.0, Shape: (482112, 200),
   ElemSize: 4 Byte(s), TotalSize: 385689600 Byte(s)
 - layer_1/W, Shared Input, Shape: (200, 4000),
   ElemSize: 4 Byte(s), TotalSize: 3200000 Byte(s)

The above message (slightly edited for clarity) shows that the product of two matrices, layer 1 weight and the output of the projection layer would not fit in the GPU memory. The output of the projection layer is 482112✕200, which takes 482112✕200✕4 = 386 MB of memory. The weight matrix is 200✕4000, so the result would require 482112✕4000✕4 = 7714 MB of memory. Either the batch size or the layer size needs to be reduced.

If you have multiple GPUs, the new gpuarray backend allows defining the context of shared variables, instructing Theano to place the variable in a specific GPU. This way you can split a large model over multiple GPUs. This also causes the computation to be performed and the intermediate results to be saved in the corresponding GPU, when possible.

If your program is working but you want to observe the memory usage, you can enable memory profiling by setting the flags profile=True,profile_memory=True. Theano will print the peak memory usage of each function, and a list of the largest variables.

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