Hatchet is a Python tool that simplifies the process of analyzing hierarchical performance data such as calling context trees. Hatchet uses pandas dataframes to store the data on each node of the hierarchy and keeps the graph relationships between the nodes in a different data structure that is kept consistent with the dataframe.
Data structures in hatchet¶
Hatchet’s primary data structure is a
GraphFrame, which combines a
structured index in the form of a graph with a pandas dataframe. The images
on the right show the two objects in a
GraphFrame – a
Graph object (the
index), and a
DataFrame object storing the metrics associated with each
Graphframe stores the performance data that is read in from an HPCToolkit database, Caliper Json or Cali file, or gprof/callgrind DOT file. Typically, the raw input data is in the form of a tree. However, since subsequent operations on the tree can lead to new edges being created which can turn the tree into a graph, we store the input data as a directed graph. The graphframe consists of a graph object that stores the edge relationships between nodes and a dataframe that stores different metrics (numerical data) and categorical data associated with each node.
Graph: The graph can be connected or disconnected (multiple roots) and each node in the graph can have one or more parents and children. The node stores its frame, which can be defined by the reader. The callpath is derived by appending the frames from the root to a given node.
Dataframe: The dataframe holds all the numerical and categorical data associated with each node. Since typically the call tree data is per process, a multiindex composed of the node and MPI rank is used to index into the dataframe.
Reading in a dataset¶
One can use one of several static methods defined in the GraphFrame class to
read in an input dataset using hatchet. For example, if a user has an
HPCToolkit database directory that they want to analyze, they can use the
import hatchet as ht if __name__ == "__main__": dirname = "hatchet/tests/data/hpctoolkit-cpi-database" gf = ht.GraphFrame.from_hpctoolkit(dirname)
Similarly if the input file is a split-JSON output by Caliper, they can use
import hatchet as ht if __name__ == "__main__": filename = ("hatchet/tests/data/caliper-lulesh-json/lulesh-sample-annotation-profile.json") gf = ht.GraphFrame.from_caliper_json(filename)
Examples of reading in other file formats can be found in Simple Examples.
Visualizing the data¶
When the graph represented by the input dataset is small, the user may be interested in visualizing it in entirety or a portion of it. Hatchet provides several mechanisms to visualize the graph in hatchet. One can use the
tree() function to convert the graph into a string that can be printed on standard output:
One can also use the
to_dot() function to output the tree as a string in the Graphviz’ DOT format. This can be written to a file and then used to display a tree using the
with open("test.dot", "w") as dot_file: dot_file.write(gf.to_dot())
$ dot -Tpdf test.dot > test.pdf
One can also use the
to_flamegraph function to output the tree as a string
in the folded stack format required by flamegraph. This file can then be used to
create a flamegraph using
with open("test.txt", "w") as folded_stack: folded_stack.write(gf.to_flamegraph())
$ ./flamegraph.pl test.txt > test.svg
One can also print the contents of the dataframe to standard output:
pd.set_option("display.width", 1200) pd.set_option("display.max_colwidth", 20) pd.set_option("display.max_rows", None) print(gf.dataframe)
If there are many processes or threads in the dataframe, one can also print a cross section of the dataframe, say the values for rank 0, like this:
filter takes a user-supplied function and applies that to all
rows in the DataFrame. The resulting Series or DataFrame is used to filter the
DataFrame to only return rows that are true. The returned GraphFrame preserves
the original graph provided as input to the filter operation. The images on the
right show a DataFrame before and after a filter operation.
filtered_gf = gf.filter(lambda x: x['time'] > 10.0)
Filter is one of the operations that leads to the graph object and DataFrame object becoming inconsistent. After a filter operation, there are nodes in the graph that do not return any rows when used to index into the DataFrame. Typically, the user will perform a squash on the GraphFrame after a filter operation to make the graph and DataFrame objects consistent again.
drop_index_levels: When there is per-MPI process or per-thread
data in the DataFrame, a user might be interested in aggregating the data in
some fashion to analyze the graph at a coarser granularity. This function
allows the user to drop the additional index columns in the hierarchical index
by specifying an aggregation function. Essentially, this performs a
aggregate operation on the DataFrame. The user-supplied
function is used to perform the aggregation over all MPI processes or threads
at the per-node granularity.
update_inclusive_columns: When a graph is rewired (i.e., the parent-child connections are modified), all the columns in the DataFrame that store inclusive values of a metric become inaccurate. This function performs a post-order traversal of the graph to update all columns that store inclusive metrics in the DataFrame for each node.
traverse: A generator function that performs a pre-order traversal of the graph and generates a sequence of all nodes in the graph in that order.
squash operation is typically performed by the user after a
filter operation on the DataFrame. The squash operation removes nodes from
the graph that were previously removed from the DataFrame due to a filter
operation. When one or more nodes on a path are removed from the graph, the
nearest remaining ancestor is connected by an edge to the nearest remaining
child on the path. All call paths in the graph are re-wired in this manner.
A squash operation creates a new DataFrame in addition to the new graph. The
new DataFrame contains all rows from the original DataFrame, but its index
points to nodes in the new graph. Additionally, a squash operation will make
the values in all columns containing inclusive metrics inaccurate, since the
parent-child relationships have changed. Hence, the squash operation also calls
update_inclusive_columns to make all inclusive columns in the DataFrame
filtered_gf = gf.filter(lambda x: x['time'] > 10.0) squashed_gf = filtered_gf.squash()
== operation checks whether two graphs have the same nodes
and edge connectivity when traversing from their roots. If they are
equivalent, it returns true, otherwise it returns false.
union function takes two graphs and creates a unified graph,
preserving all edges structure of the original graphs, and merging nodes with
identical context. When Hatchet performs binary operations on two GraphFrames
with unequal graphs, a union is performed beforehand to ensure that the graphs
are structurally equivalent. This ensures that operands to element-wise
operations like add and subtract, can be aligned by their respective nodes.
copy operation returns a shallow copy of a GraphFrame. It
creates a new GraphFrame with a copy of the original GraphFrame’s DataFrame,
but the same graph. As mentioned earlier, graphs in Hatchet use immutable
semantics, and they are copied only when they need to be restructured. This
property allows us to reuse graphs from GraphFrame to GraphFrame if the
operations performed on the GraphFrame do not mutate the graph.
deepcopy operation returns a deep copy of a GraphFrame.
It is similar to
copy, but returns a new GraphFrame with a copy of the
original GraphFrame’s DataFrame and a copy of the original GraphFrame’s graph.
unify operates on GraphFrames, and calls union on the two
graphs, and then reindexes the DataFrames in both GraphFrames to be indexed by
the nodes in the unified graph. Binary operations on GraphFrames call unify
which in turn calls union on the respective graphs.
add: Assuming the graphs in two GraphFrames are equal, the
operation computes the element-wise sum of two DataFrames. In the case where
the two graphs are not identical,
unify (described above) is applied first
to create a unified graph before performing the sum. The DataFrames are copied
and reindexed by the combined graph, and the add operation returns new
GraphFrame with the result of adding these DataFrames. Hatchet also provides an
in-place version of the add operator:
subtract: The subtract operation is similar to the add operation in that
it requires the two graphs to be identical. It applies
union and reindexes
DataFrames if necessary. Once the graphs are unified, the subtract operation
computes the element-wise difference between the two DataFrames. The subtract
operation returns a new GraphFrame, or it modifies one of the GraphFrames in
place in the case of the in-place subtraction (
gf1 = ht.GraphFrame.from_literal( ... ) gf2 = ht.GraphFrame.from_literal( ... ) gf2 -= gf1
tree operation returns the graphframe’s graph structure as a
string that can be printed to the console. By default, the tree uses the
name of each node and the associated
time metric as the string
representation. This operation uses automatic color by default, but True or
False can be used to force override.