Run It

Operation System

lmt is available for Linux operation systems only.

How to start

lmt is always started from the Linux command line interface.

@<mode> and parameter file mode

lmt can run on various task. Some tasks may be readily described via a bunch of command line arguments, other task are so complex that describing them via command line arguments may yield an unreadable convoluted command line, hence a parameter file is needed. Whether a parameter file is required or not is determined by the optional @<mode> command line argument. If available lmt will run in the specified mode without requiring a parameter file. For instance the command line argument @ped turns lmt into a pedigree analysis program which fully runs on command line arguments. If lmt cannot find @<mode> it will assume that it runs in parameter file mode. lmt will look in the run time directory for a file named para.xml which is the parameter file. However, the default parameter file name can be overwritten by providing the command line argument -f <my_parameterfile_name>.

Note that this manual describes the only the parameter file interface.

Available command line arguments for any @<mode> and their meaning can be inferred by the --help command line argument provided together with the @<mode> argument (e.g. lmt @ped - -help).

Currently supported @<mode> modes are

@ped

Turns lmt into a pedigree analysis program. For a list of commandline arguments type @ped --help.

Run time environment

lmt is developed for Linux operation systems on computers with an Intel architecture. Thus using lmt on AMD architecture will result in increased run time. For executables running on Windows or Mac please contact the author.

lmt requires that some environment variables are set to specific values. lmt will check those settings at start and will stop if the settings are wrong.

• stack size must be set to unlimited via ulimit -s unlimited
• OMP_DYNAMIC=FALSE
• OMP_STACKSIZE='a reasonable value (i.e. 2000M)'
• OMP_NESTED=TRUE

lmt is highly threaded and will try to use all available computing resources. Will this is desirable for very large models it can hamper performance when crunching medium to small data sets resulting in an increased run time. What "medium to small" means de- pends on the actual computer and must therefore be determined by the user. The user can set the lmt threading behaviour via the two environment variables OMP_NUM_THREADS and MKL_NUM_THREADS.

The performance of multi-threaded programs can also be heavily affected by thread affinity settings where the optimal settings must be found via trial and error. However, as a starting point, it is advisable to set the environment variable KMP_AFFINITY=granularity=core,scatter.

If you run several instances of lmt at the same time on the same computer you may experience a severe drop in performance of each of the runs. This is usually caused by competition for resources and therefore parallel runs of several lmt instances should be avoided. However, using the numactl environment may provide an option to avoid performance drops. Please check out numactl --help for further reading.