Use of multiple processors by pynbody

A large amount of the code in pynbody is designed to run on multiple processors on a single shared-memory machine. There are three distinct ways in which parallelization works in pynbody.

  1. Native threading, using the python module threading, or in C code, the POSIX standard pthread library. On any modern Mac and Linux machine, this “just works”. This is mainly used in the SPH module where we have gone to some lengths to create algorithms that scale well to moderately large numbers of cores (16 certainly, often 32) that you’d fine on a typical analysis workstation.
  2. OpenMP threading. This is used by a large number of parts of the library, for example some of the halo analysis code, where simple, inexpensive parallelization is possible. If you have an OpenMP compiler this will also “just work”. However, you might not do - see below.
  3. Process threading. This is currently used only by the ramses loader to get around problems with the python GIL. It requires shared memory support, for which you need the the appropriate python module.

In cases (2) and (3), you may have to do some work to get everything working. For (1), it should just work out the box.

Limiting the number of CPUs used by pynbody

In most cases, one just wants the code to be as responsive as possible and so by default pynbody uses all CPUs on your machine. However, sometimes this is not so desirable - perhaps you need to leave resources for other users, or for other processes you are running.

Therefore you can limit the number of processors used by pynbody, either during a session or permanently. During a python session, you can type

pynbody.config['number_of_threads']=2

which, as an example, limits the number of CPUs in use to 2. To make the change permanent, create a .pynbodyrc file in your home directory with the following section:

[general]
number-of-threads: 2

More information on the pynbody configuration system is available here.

Checking and fixing OpenMP support

If pynbody is installed on a machine without OpenMP support, it’ll normally throw up some complaint during the installation procedure. The installation will succeed, but many parallel procedures will run only on one core.

To check if this has happened to you, try the following commands

In [1]: import pynbody

In [2]: pynbody.config['number_of_threads']
Out[2]: 8

So far, we can see that the main pynbody configuration has seen more than one core on the machine. But let’s see how many cores OpenMP can see:

In [3]: pynbody.openmp.get_cpus()
Out[3]: 1

If this number is larger than one, OpenMP support is enabled and you don’t need to do anything more. If it’s 1, however, OpenMP support is disabled and you’re losing out.

This happens when, during setup, pynbody could not find the OpenMP library. The most common scenario where this happens is on a Mac - Apple’s default compilers do not support OpenMP. A fast solution is to download the latest GNU compilers http://hpc.sourceforge.net, install them, and point the setup procedure to gcc. At your shell, something like this would do it -

$ export CC='/usr/local/bin/gcc'
$ cd pynbody
$ rm -rf build/
$ python setup.py build
$ python setup.py install

Now, with luck, you’ll see that OpenMP is enabled.

In [1]: import pynbody

In [2]: pynbody.openmp.get_cpus()
Out[2]: 8

If you’re still having trouble, you can try asking us for further help.

Parallel ramses reader support

The ramses reader speeds up load times by using multiple concurrent processes to read files. There are two differences between this and the standard threading techniques used above.

First, the correct number of processes to use may not be the number of CPUs on your machine - it’s tied more to IO performance than to raw computing power. Second, for technical reasons related to the Python GIL you need an extra module to make this work. The module is known as posix_ipc, and it normally compiles very straight-forwardly on Linux or Mac OS. At your standard command prompt just type:

$ easy_install posix_ipc

and you should be done. There’s not even any need to reinstall pynbody.

As explained above, you may well want to change the number of processes used for the reading process. This can be done using pynbody’s standard configuration system; for instance, create a .pynbodyrc file in your home directory with the following section:

[ramses]
parallel-read: 4

This specifies 4 processes. You can experiment with this number to see what works best on your system, which depends on a combination of CPU and IO performance.

Note

Many systems limit the amount of shared memory available, which can cause problems once you enable parallel-reading. See our separate note on this issue.