Table of contents:

Compilers supported at UPPMAX

UPPMAX supports two kind of compilers:

  • GNU project compilers
  • Intel compilers

This tutorial will show how to use the tools provided with the compilers and some other profiling tools. Since all these tools is strongly connected to the compiler they come with, it is recommended to only have that compiler module loaded.

To make sure that you don't have any other compiler loaded, learn from this example:

$ module list
Currently Loaded Modulefiles:
1)  uppmax    2) intel/19.5
$ module unload intel

Debugging tools

There are debugging tools provided with each of the three compilers.

For C, C++, and Fortran programs the ordinary gnu debugger (gdb) works fine, but for Fortran90/95 programs using gdb doesn't work well. 

The GNU debugger

The GNU debugger, gdb is provided with the GNU compilers. It works fine for C, C++ and Fortran. With older versions there were problems with fortran90/95.

Read more at the GNU debugger homepage.

In order to use gdb do the following.
load a recent gcc module and a gdb module (system gdb is from 2013!). 

$ module load gcc/10.3.0 gdb/11.2

compile your program with flags for debugging added, e.g. -ggdb

$ gcc -ggdb your-program.c -o your-program

run the gdb program:

$ gdb your-program

Then you can use the gdb commands, like run, break, step, help, ...

Exit with <Ctrl-D>.

The intel debugger

The intel debugger, idb was provided with the intel compiler. Now it is depracated and you are advised to use gdb (see above) here as well. 

In order to use gdb with intel do the following.
load the icc module

$ module load intel/20.4

compile your program with flags for debugging added, e.g. -g

$ icc -g your-program.c -o your-program

run the gdb program:

$ gdb your-program

Then you can use the gdb commands, like run, break, step, help, ...

Exit with <Ctrl-D>.

Profiling tools

There are some profiling tools that are available at UPPMAX. Note: some profiling works best without optimization, i.e using the -O0 flag.

Intel VTune Profiler and Advisor

Intel's performance analysis suite can probably answer any question you have about the performance of your code, including MPI and OpenMP code.

VTune is focused choosing optimising techniques that will yield good results, whereas Amplifier is more broadly aimed at performance analysis.

Read more at the Vtune documentation and Advisor documentation.

In order to use VTune do the following:

$ module load intel intel-oneapi vtune

Making sure you have a graphical connection through X or ThinLinc, run VTune graphically:

$ vtune-gui

In order to use Advisor, do the following:

$ module load intel intel-oneapi advisor

Making sure you have a graphical connection through X or ThinLinc, run Advisor graphically:

$ advixe-gui

The GNU profiler

The GNU profiler, gprof is provided with the GNU compiler package.

Read more in the GNU gprof documentation.

In order to use gprof do the following.
Load a recent gcc module and a recent binutils module:

$ module load gcc
$ module load binutils

Compile your program with the -pg -g flags added

$ gcc -O0 -pg -g your-program.c -o your-program

run it:

$ ./your-program

then do:

$ gprof your-program gmon.out > output-file

For more options you run gprof like this:

gprof options [executable-file [profile-data-files…]] [> outfile]

Valgrind

Valgrind is a suite of simulation-based debugging and profiling tools for programs.
Valgrind contains several tools:

  • memcheck, for detecting memory-management problems in your program
  • cachegrind, for cache profiling
  • helgrind, finds data races in multithreded programs
  • callgrind, a call graph profiler
  • drd, a thread error detector
  • massif, a heap profiler
  • ptrcheck, a pointer checking tool
  • lackey, a simple profiler and memory tracer

You can find full documentation on valgrind in the Valgrind user manual. 

Valgrind works best with the gcc- and intel compilers. There is a system valgrid-3.15.0 (2020)

First load compiler:

$ module load gcc

or

$ module load intel

then you can use valgind by:

$ valgrind [options] ./your-program [your programs options]

How to use valgrind with mpi programs


Load your complier, openmpi and the valgrind module as before:
 

$ module load gcc/10.3.0 openmpi/3.1.6

or 

$ module load intel/20.4 openmpi/3.1.6

As of now, Valgrind seems not compatible with openmpi/4.X.X.

Then run:

$ LD_PRELOAD=$VALGRIND_MPI_WRAPPER
$ mpirun -np 2 valgrind ./your-program

Last modified: 2022-12-09
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