The new protocol in the GUI

A model-free analysis can be performed within the GUI (see Figure 1.8 on page ). This analysis is that of the fully automated d'Auvergne protocol which can be chosen via the analysis selection wizard (Figure 1.4 on page ). Please see Section 7.7 on page  for a description of this new model-free protocol. As mentioned previously, please note that this protocol requires multiple field relaxation data.

The GUI is designed to be robust - you should be able to set up all the input data and parameters in any order with relax returning you warnings if something is missing. The analysis will only execute once everything is correctly set up. If this is not the case, clicking on the “Execute relax” button will display a warning window explaining what the issue is rather than initialising the analysis. Despite the self-explanatory nature of the GUI a tutorial on how to use the GUI, with screenshots, will be presented below.

If the “Protocol mode” field is left to the “Fully automated” setting then, after clicking on “Execute relax”, the calculation can be left to complete. It is highly recommended to check the log messages in the relax controller window, at least at the start of the analysis, to make sure that all the data is being read correctly and everything is set up as desired. All warnings should be carefully checked as these can indicate a fatal problem. If you would like to log all the messages into a file, relax can be run with:

$ relax -g -log log

Note that the size of this log file could end up being in the gigabyte range for a model-free analysis.

For the full analysis to complete, for a protein system this may take about a week. Depending on the nature of the problem and the speed of the computer, the calculation time may be significantly shorter or longer. To speed up the calculations, if you have access to multiple cores and/or hyper-threading, the GUI can be run using Gary Thompson's multi-processor framework (see section 1.3 on page ). For example on a dual-core, dual-CPU system, four calculations can be run simultaneously. In this case, the GUI can be launched with:

$ mpirun -np 5 /usr/local/bin/relax -multi=`mpi4py' -gui -log log

This assumes that OpenMPI and the Python mpi4py module have been installed on your system, and relax is installed into the /usr/local/bin/ directory. If this is successful, you should only see a single relax GUI window (and not five windows) and in the relax controller, you should see text similar to:

Processor fabric: MPI 2.1 running via mpi4py with 4 slave processors & 1 master. Using Open MPI 1.4.3.

If you are using a different MPI implementation, please see the documentation of that implementation to see how to launch a program in MPI mode. Finally as the calculation takes so long, we will run the calculations at a lower priority so that the computer is not slowed down too much and remains responsive. Therefore this model-free GUI analysis tutorial will be launched with the full command:

$ nice -n 15 mpirun -np 5 /usr/local/bin/relax -multi=`mpi4py' -gui -log log