Profiling

Is the skill and art of finding which part of your code needs the most time, and therefore to find the place where you can (should, need to) optimize (first). The optimization can be different things, like using library functions instead of self-written ones, re-arranging memory access, removing function calls, writing C/Fortran functions for your Python code.

The profiling can be done manually by adding time and print statements to your code or (better) by using tools like Valgrind, TAU, HPCToolkit, Score-P or Python’s Scalene or cProfile.

Tools to profile applications and perform efficiency, scaling and energy analysis are described in this document by the Virtual Institute High Performance Computing: https://www.vi-hps.org/cms/upload/material/general/ToolsGuide.pdf




## Monitoring jobs on the node

It is possible to submit a second (this time) interactive job to the node where the main job is running, check with squeue where your job is running, then submit

srun -w <nodename> --pty htop

Note that there must be free slots on the machine, so if you cannot use -n 80 or --exclusive for your main job (use -n 79).

Alternative method if you have X11, e.g. on Linux computers:

When you login to base/amp, use ssh -X UniID@base.hpc.taltech.ee,

then submit your main job with srun --x11 -n <numtasks> --cpus-per-task=<numthreads> --pty bash and start an xterm -e htop &` in the session.

In sbatch the option --x11=batch can be used, note that the ssh session to vase needs to stay open!




Valgrind


Manual: http://valgrind.org/docs/manual/manual.html

Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools.

The Valgrind distribution currently includes seven production-quality tools: a memory error detector, two thread error detectors, a cache and branch-prediction profiler, a call-graph generating cache and branch-prediction profiler, and two different heap profilers. It also includes an experimental SimPoint basic block vector generator.

Callgrind

Cachegrind




Profiling Python


Python is very slow, the best improvement is achieved by rewriting (parts of) the program in Fortran or C. See also “Python Performance Matters” by Emery Berger (Strange Loop 2022) https://www.youtube.com/watch?v=vVUnCXKuNOg

Python Scalene

Scalene is a CPU, GPU and memory profiler for Python that is very performant (introduces very little overhead).

Installation: load your favourite Python module, e.g.

module load green-spack
module load python/3.8.7-gcc-10.3.0-plhb
py-pip/21.1.2-gcc-10.3.0-python-3.8.7-bj7d

then install using pip:

python -m pip install --user scalene

Homepage and quickstart: https://github.com/plasma-umass/scalene

Python cProfile




perf


https://perf.wiki.kernel.org/index.php/Main_Page

perf is powerful: it can instrument CPU performance counters, tracepoints, kprobes, and uprobes (dynamic tracing). It is capable of lightweight profiling. It is also included in the Linux kernel, under tools/perf, and is frequently updated and enhanced.

perf began as a tool for using the performance counters subsystem in Linux, and has had various enhancements to add tracing capabilities.




TAU, Jumpshot, Paraprof


TAU can be used for profiling and for MPI tracing (not at the same time, though). See e.g. https://wiki.mpich.org/mpich/index.php/TAU_by_example

Load the spack TAU module:

module load green-spack
module load tau/2.30.2-gcc-10.3.0-2wge

Profiling

TAU supports different methods of instrumentation:

- Dynamic: statistical sampling of a binary through preloading of libraries
- Source: parser-aided automatic instrumentation at compile time
- Selective: a subcategory of source, it is automatic, but guided source code instrumentation

The simplest and only for existing binary software is dynamic profiling through tau_exec, just run

srun tau_exec your_program

several profile.* files will be created. This method can unfortunately only profile MPI functions and not user-defined ones. Note, that profile files are only generated if the program exits normally, not if an error occurs or SLURM kills it!

You can generate reports with pprof and visualize with paraprof.

MPI tracing

The tracing can take a lot of space, it is not uncommon that tracefiles are several GB in size for each MPI-task!

export TAU_TRACE=1
srun  -n 2 tau_exec ./pingpong-lg-mpi4
tau_treemerge.pl

TAU does not have a tracing visualizer, but provides tools to convert its traces to other formats, e.g. slog2 for jumpshot, otf(2) or paraver:

tau2slog2 tau.trc tau.edf -o tau.slog2
tau_convert -paraver tau.trc tau.edf trace.prv

The traces can be visualized using jumpshot (in the tau module), just run

jumpshot tau.slog2

jumpshot may open a huge window (larger than screen size), in this case use the “maximize” option of your window manager (fvwm: in the left window corner menu), jumpshot opens 3 windows: “jumpshot-4”, “Legend” and “Timeline” (if you cannof find them, use window manager menu, e.g. fvwm: right mouse button on desktop background).




EZTrace + ViTE


EZTrace 1.1 and ViTE 1.2 are installed on amp and viz.

EZTrace is a tool to analyze event traces, it has several modules:

stdio   Module for stdio functions (read, write, select, poll, etc.)
starpu  module for StarPU framework
pthread Module for PThread synchronization functions (mutex, semaphore, spinlock, etc.)
papi    Module for PAPI Performance counters
openmpi Module for MPI functions
memory  Module for memory functions (malloc, free, etc.)

ViTE is the visualization tool to visualize the generated traces, it can visualize also .otf2 traces obtained from other MPI tracing tools (e.g. converted from TAU)




HPCToolkit


Load modules

module load hpctoolkit

run application with binary instrumentation

srun -n 2 -p green-ib hpcrun <your_application>
hpcstruct `which <your_application>`
hpcprof hpctoolkit-<your_application>-measurements-<PID>

run GUI tool for interpretation

hpcviewer hpctoolkit-<your_application>-database-<PID>

starts hpcviewer and opens the database.




Paraver trace visualizer_


Load the module

module load green

module load Paraver

start paraver

wxparaver

then load the .prv trace file




Extrae





Score-P


Scalable Performance Measurement Infrastructure for Parallel Codes

module load green-spack
module load scorep

The module with hash “mlw5” contains the PDT instrumenter. The module with hash “o4v3” contains the PDT instrumenter and libunwind.

https://scorepci.pages.jsc.fz-juelich.de/scorep-pipelines/docs/scorep-4.1/html/quickstart.html

compilation: prefix the compiler command with “scorep”, e.g. scorep gcc ... or scorep mpicc ..., this can also be used in Makefiles:

MPICC = $(PREP) mpicc

(and analogously for linkers and other compilers). One can then use the same makefile to either build an instrumented version with the

make PREP="scorep"

a simple make will generate an uninstrumented binary.

The environment variables SCOREP_ENABLE_TRACING and SCOREP_ENABLE_PROFILING control whether event trace data or profiles are stored in this directory. By setting either variable to true, the corresponding data will be written to the directory. The default values are true for SCOREP_ENABLE_PROFILING and false for SCOREP_ENABLE_TRACING.




Scalasca


Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks – in particular those concerning communication and synchronization – and offers guidance in exploring their causes.

module load green-spack
module load scalasca



Open|SpeedShop


module load green-spack
module load openspeedshop
module load openspeedshop-utils



DiscoPoP


to be installed

analyses source-code to find areas that can be parallelized

works only with LLVM 11.1 (included in the module)

module load green
module load discopop



PGI / Nvidia HPC SDK


On the GPU servers, the Nvidia HPC SDK is installed, which contains the PGI compilers and profilers.




IgProf


The Ignominous Profiler. IgProf is a simple nice tool for measuring and analysing application memory and performance characteristics. IgProf requires no changes to the application or the build process.

Quick start: https://igprof.org/running.html