Practical Tips

Start MUSIC using mpirun

There is an alternative way to start a MUSIC simulation without the music binary. The logic for parsing the configuration file is built into the library itself. So we can start each binary explicitly using mpirun. We give the config file name and the corresponding app label as command line options:

mpirun -np 2 <binary> --music_config <config file> --app-label <label> : ...

So to start a simulation with the and recv programs, we can do:

mpirun -np 2 ./ --music-config --app-label from :/
   -np 2 ./recv --music-config --app-label to

This looks long and cumbersome, of course, but it can be useful. Since it’s parsed by the shell you are not limited to what the music launcher can parse, but the binary can be anything the shell can handle, including an explicit interpreter invocation or a shell script.

As a note, the config file no longer needs to contain the right binary names. But it does need to have a non-empty binary=<something> line for each process. The parser expects it and will complain (or crash) otherwise. Also, if you try to process comand line options in your Pynest script, it is very likely you will confuse MUSIC.

Disable Messages

NEST can be quite chatty as it connects things, especially with large networks. If we don’t want all that output, we can tell it to display only error messages:

nest.sli_run("M_ERROR setverbosity")

There is unfortunately no straightforward way to suppress the initial welcome message. That is somewhat unfortunate, as they add up quickly in the output of a simulation when you use more than a few hundred cores.

Comma as decimal point

Sorting output spikes may fail if you, like the authors, come from a country that uses a comma as decimal separator and runs your computer in your native language. The problem is that sort respects the language settings and expects the decimal separator to be a comma. When it sees the decimal point in the input it assumes the numeral has ended and sorts only on the integer part.

The way to fix this is to set LC\_ALL=C before running the sort command. In a script or in the terminal you can do:

export LC_ALL=C
cat output-*|sort -k 2 -n >output.spikes

Or, if you want to do this temporarily for only one command:

cat output-*|LC_ALL=C sort -k 2 -n >output.spikes

Build Autotool-enable project

To build an Autotool-enabled C/C++ project, you don’t actually need to be in the main directory. You can create a subdirectory and build everything from there. For instance, with the simple C++ MUSIC project in section C++ build, we can do this:

mkdir build
cd build

Why do that? Because all files you generate when building the project ends up under the build subdirectory, keeping the source directories completely clean and untouched. You can have multiple builds debug, noMPI and so on with different build options enabled, and you can completely clean out a build simply by deleting the directory.

This is surely completely obvious to many of you, but this author is almost ashamed to admit just how many years it took before I realized you could do this. I sometimes actually kept two copies of projects checked out just so I could build a separate debug version.