TAU by example

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ParaProf with QMCPACK

TAU (Tuning and Analysis Utilities) is a toolkit for profiling and tracing parallel programs written in C, C++, Fortran and others. It supports dynamic (library-based), compiler and source-level instrumentation. Unlike MPE, TAU is not limited to profiling MPI code, being geared towards parallel programming in general, including CUDA, OpenMP and regular pthreads.

As TAU is already extensively documented, this page will only provide a short introduction to some common features, along with some basic example code.

Contents

Installation

Desktop linux (ubuntu 12.04.1)

After downloading both TAU and PDT from here, unpack them wherever convenient and run the following command to configure, compile and install TAU. If MPICH2/PDT were installed on another prefix, the part within brackets must be appropriately setup: set $MPI_PATH to the directory where MPICH2 was installed, and adjust $PDT_DIR accordingly. Otherwise, it can be left out.

(If MPICH2 was configured with --enable-shared, it is not necessary to pass the -mpilibrary argument below.)

   % ./configure -mpilibrary='-lmpich -lmpl -lopa' [-mpilib=$MPI_PATH/lib -mpiinc=$MPI_PATH/include -pdt=$PDT_DIR]
   % make -j clean install

For more information, please refer to its installation manual.

Wave2D

Description

Solution to the wave equation

The wave equation is a partial differential equation used to describe the behavior of waves as they occur in physics:

{ \partial^2 u \over \partial t^2 } = c^2 \nabla^2 u

Here, the variable u represents a physical measure such as pressure or water depth. This equation can be discretized over a 2D grid using a finite differencing scheme, leading to the following update rule:

u_{x,y}^{t+1} = c^2 \left(u_{x+1,y}^{t}+u_{x-1,y}^{t}+u_{x,y+1}^{t}+u_{x,y-1}^{t}-4u_{x,y}^{t}\right)- u_{x,y}^{t-1} +2 u_{x,y}^{t}

where u is defined over a rectangular 2D grid in dimensions x, y, and time step t. The constant c defines the wave's propagation speed.

We hence obtain the iterative five-point stencil code wave2d.

Profiling

A list of the different instrumentation methods used for e.g. profiling (and which features they support) can be found here. We will cover three different methods:

  1. Dynamic: statistical sampling;[1]
  2. Source: parser-aided automatic code categorization;
  3. Selective: uses a separate file to "manually control which parts of the application are profiled and how they are profiled"; this is technically part of the source instrumentation above (and hence also requires PDT).

Dynamic instrumentation

The most straightforward way of getting started with TAU is through tau_exec, which does dynamic instrumentation. This method makes use of statistical sampling to estimate which percentage of the execution time is taken by each function (as well as the absolute time spent). We first compile as usual:

   % mpicxx wave2d.cpp -o wave2d

The difference occurs when executing the program, which is done as follows:[2]

   % mpirun -np 12 tau_exec ./wave2d 500 500 3 4 5

Unfortunately, this method does not support profiling user-defined routines, only those from MPI. For this reason, we do not recommend this method for real-world applications (which very likely spend less time on MPI calls than on computation itself, which would be unaccounted for).

Source instrumentation

If PDT is installed, it is possible to use the compiler wrapper scripts tau_cc.sh/tau_cxx.sh to automatically instrument our code. In this case, the difference is that one call to TAU_PROFILE is inserted in every user-defined function, with this modified function's header.[3]

First, we select which features we want TAU to use (e.g. MPI support, tracing, CUDA hardware counters, etc), which is done by setting an environment variable called TAU_MAKEFILE to point to one of the (informatively-named) default Makefiles that are located in <TAU_HOME>/lib/. For now, we only want to profile MPI code, so we write:

   % export TAU_MAKEFILE=$TAU_HOME/lib/Makefile.tau-mpi-pdt

Next, to build the instrumented wave2d program, we replace the regular mpicc or mpicxx commands by tau_cc.sh or tau_cxx.sh.

   % tau_cxx.sh wave2d.cpp -o wave2d

If all goes right, we can then execute the code as usual:

   % mpirun -np 12 ./wave2d 500 500 3 4 5

Compiler-based instrumentation

Additionally, TAU has a compiler instrumentation method, which sits in between dynamic and source. Unlike dynamic, it requires compilation, but also inherits some features from source such as being able to profile user-defined functions. However, it cannot provide information about finer constructs such as loops and so on. To use this method, the argument -tau_options=-optCompInst should be added to tau_cc.sh/tau_cxx.sh when compiling (or, equivalently, to the TAU_OPTIONS environment variable); visualization and program execution remain exactly the same.

In practice, we recommend installing PDT and using the source mode.

Selective instrumentation

A large program might have dozens of auxiliary functions that do not constitute a significant chunk of the execution time, and hence visually pollute the profile. Also, it may happen that a function will have two or more time-consuming loops, which will not be individually represented in the profile.

For this and other reasons we may want to selectively exclude functions, annotate (outer) loops, etc, using TAU's support for selectively profiling applications.

Consider the following example, which we will name select.tau:

   BEGIN_EXCLUDE_LIST
   
   void foo(int *, double)
   void barToo_#(int *)
   
   END_EXCLUDE_LIST
   
   BEGIN_INSTRUMENT_SECTION
   
   loops file="random.cpp" routine="int FooClass::fooToo(double, double)"
   
   END_INSTRUMENT_SECTION

Here, the symbol # in the function names acts as a wildcard.

To make use of this file, we define the TAU_OPTIONS environment variable:

   % export TAU_OPTIONS="-optTauSelectFile=select.tau"

Warning: This does not as expected with regular C code. After every function in the exclude list, a C should be added. Otherwise, a # should be added after every function name.This is a consequence of the design used by TAU, and is effectively arbitrary.

For some more information, check the official manual.

Visualization

Regardless of the instrumentation method, we will then obtain a number of profile.r.* files (r being a rank). These can now be visualized in a number of manners.

pprof

Text-based; can be invoked by a simple pprof:

   % pprof
   Reading Profile files in profile.*
   
   NODE 0;CONTEXT 0;THREAD 0:
   ---------------------------------------------------------------------------------------
   %Time    Exclusive    Inclusive       #Call      #Subrs  Inclusive Name
                 msec   total msec                          usec/call 
   ---------------------------------------------------------------------------------------
   100.0        0.097        3,839           1           8    3839163 int main(int, char **) 
    98.5        0.172        3,783           1         200    3783485 void Grid::doIterations(int) 
    61.6        2,365        2,365         100           0      23653 void Grid::doOneIteration() 
    36.9            4        1,418         100         900      14181 void Grid::exchangeEdges() 
    36.8        1,412        1,412         100           0      14125 MPI_Waitall() 
     0.8            4           29           1           2      29727 void Grid::Grid(int, int, int, int, int) 
     0.6           24           24           1           0      24824 void Grid::initGrid(int) 
     0.5           18           18           1           0      18584 MPI_Finalize() 
     0.2            6            6           1           0       6387 MPI_Init() 
     0.0        0.931        0.931         400           0          2 MPI_Send() 
     0.0         0.84         0.84           1           0        840 void Grid::~Grid() 
     0.0        0.557        0.557         400           0          1 MPI_Irecv() 
     0.0        0.042        0.042           1           0         42 MPI_Bcast() 
     0.0        0.004        0.004           2           0          2 MPI_Comm_rank() 
     0.0        0.001        0.001           1           0          1 MPI_Comm_size() 
   ---------------------------------------------------------------------------------------
   
   USER EVENTS Profile :NODE 0, CONTEXT 0, THREAD 0
   ---------------------------------------------------------------------------------------
   NumSamples   MaxValue   MinValue  MeanValue  Std. Dev.  Event Name
   ---------------------------------------------------------------------------------------
            1          4          4          4          0  Message size for broadcast
   ---------------------------------------------------------------------------------------
   
   
   ... the same table for every rank ...
   
   
   FUNCTION SUMMARY (total):
   ---------------------------------------------------------------------------------------
   %Time    Exclusive    Inclusive       #Call      #Subrs  Inclusive Name
                 msec   total msec                          usec/call 
   ---------------------------------------------------------------------------------------
   100.0            1       46,076          12          96    3839746 int main(int, char **) 
    98.3            2       45,278          12        2400    3773202 void Grid::doIterations(int) 
    63.2       29,121       29,121        1200           0      24268 void Grid::doOneIteration() 
    35.1           49       16,154        1200       10800      13462 void Grid::exchangeEdges() 
    34.9       16,075       16,075        1200           0      13396 MPI_Waitall() 
     1.2           52          540          12          24      45051 void Grid::Grid(int, int, int, int, int) 
     1.1          487          487          12           0      40646 void Grid::initGrid(int) 
     0.2          106          106          12           0       8895 MPI_Finalize() 
     0.2           93           93          12           0       7759 MPI_Init() 
     0.1           48           48          12           0       4049 MPI_Bcast() 
     0.1           23           23        4800           0          5 MPI_Send() 
     0.0            8            8          12           0        686 void Grid::~Grid() 
     0.0            6            6        4800           0          1 MPI_Irecv() 
     0.0        0.035        0.035          24           0          1 MPI_Comm_rank() 
     0.0        0.008        0.008          12           0          1 MPI_Comm_size() 
   
   
   ... the same table, but now with mean values ...

More information about how to sort the data differently can be found by doing pprof -h.

ParaProf

A much richer, graphical interface for visualization and analysis, ParaProf can also be initialized simply by paraprof.

ParaProf with inclusive metric

The vast majority of the functionality can be found by navigating the menus. For instance, a graph of functions ordered by time taken on average can be obtained by right-clicking Mean and selecting Show Mean Bar Chart.

Inclusive execution time per routine on one rank

Analogously, it is possible to see the execution time for a given function on all ranks. A way of doing it is right clicking on the corresponding function bar, and going to Show Function Bar Chart. Alternatively, the menu Windows->Function->Bar Chart displays a list of all profiled functions.

Tracing

Jumpshot main window

In addition to profiling, TAU can automatically instrument the code to do tracing without user intervention (unlike MPE, which requires manual insertion of tracing code). This depends on PDT (in particular, on its C/C++ parser), which is why we used a makefile ending with pdt in the previous section. However, tracing is disabled by default, so we enable it first:

   % export TAU_TRACE=1

(Note that this disables profiling, i.e. no profile.* files will be generated.)

Jumpshot legend window

Now the program can be executed normally (with mpirun in this case), which will generate many .edf and .trc files. These must then be merged as follows:

   % tau_treemerge.pl
   % tau2slog2 tau.trc tau.edf -o tau.slog2

All that is left is to visualizer the tracing data (tau.slog2) with Jumpshot (or another such tool), as TAU does not have a tracing visualizer. Notice on the legend window that all functions have been automatically instrumented.

Ring

ParaProf plot for time spent per function/per rank

This toy example implements a ring whose elements (ranks) asynchronously send their successor a buffer whose size is dependent on their rank (as well as the amount of work needed to prepare it). The image to the left, which is a three-dimensional variation of the original 2D profiler plotter (on the top of the page). It can be accessed by navigating to Window->3D Visualization. The menu on the right has a few more plot configurations; of note is the scatter plot option.

This buffer size dependence on the originating rank can also be seen in the communication matrix, which may be enabled (before run-time) by setting the environment variable TAU_COMM_MATRIX:

3D Communication matrix

   % export TAU_COMM_MATRIX=1

From this graph it should be clear that the amount of communication between a node and its successor is increasing approximately in proportion to the square of the originating rank (the actual power is 2.3).

NWChem

Here we focus on the scatter plot option on ParaProf. The idea of this viewer is to help developers identify groups of functions whose running time are tightly related. In the case of NWChem, this can be used to help develop a time model for the (new) static load balancing mechanism.

The horizontal axis of this 3D scatter plot shows the exclusive execution time of the two dominant kernels in NWChem coupled cluster simulations (DGEMM and TCE_SORT). The vertical axis shows the time spent on dynamic load balancing.

Clustering view for NWChem

We see that smaller tasks which take less time in the kernels take more time dynamic load balancing. Also, we see that the reason this occurs is possibly because of the size of the input data for the kernels - the red colored points correspond to large operations that take more time in the GA_Accumulate() operation compared to the green points.[4]

Hardware counters

Like HPCToolkit, TAU can be built with PAPI support, which adds support for profiling branching and cache access patterns, time stalled waiting for resources (such as in memory reads), etc. The only change required in the configuration phase above is the addition of the argument -papi=, followed by the folder where PAPI was installed (say, /), e.g.:

   % ./configure -mpilibrary='-lmpich -lmpl -lopa' -papi=/opt/papi

(The same comment above about MPICH2 and --enable-shared applies here.)

This will produce a new TAU makefile, Makefile.tau-papi-mpi-pdt, which should be used in the export TAU_MAKEFILE= commands above.

Up to 25 counters/events can then be recorded by exporting the environment variables COUNTER1 through COUNTER25, as follows:

   % export COUNTER1=PAPI_TOT_CYC
   % export COUNTER2=PAPI_FML_INS
   % export COUNTER3=PAPI_FMA_INS

Compilation and execution then proceeds exactly as usual. Instead of producing a set of profile.* files, TAU will generate one folder for each counter:

   % ls
   MULTI__PAPI_TOT_CYC  MULTI__PAPI_FML_INS  MULTI__PAPI_FMA_INS ...

Counter statistics for HPCToolkit's matrix multiply example

Paraprof can then be used to visualize the recorded metrics, as on the left, under the Windows/Thread submenu. For a simple use case, see the corresponding section on HPCToolkit.

Notes

^  Referred to as "binary rewriting" in TAU's manual.

^  The first two numbers are the dimensions for every rank's rectangle; the next two are the number of rectangles in the x and y dimensions (their product should be the number of ranks); the last is the number of initial perturbations in the wave (i.e. the circles in the image above).

^  To see the modifications made by the TAU script, you can add -optKeepFiles to the TAU_OPTIONS environment variable. The instrumented code will be written to PROGNAME.inst.c if PROGNAME is the executable's name, and similarly for C++.

^  Result from David Ozog, a PhD student from MCS/UOregon.

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