Using GenX from the command line (with mpi)¶

Introduction¶

Using GenX from the command line lets you in the simplest case start up the gui. As of version 2.3 you can also run fits without starting up the gui at all. This opens possibilities to make batch script of multiple GenX runs and in addition you can run GenX on machines without a desktop environment. As GenX also since 2.3 supports mpi for fitting in parallel opens up the possibility to use it on clusters. The mpi implementation was contributed by Canrong Qiu. Note that currently the command line is only fully implemented in the source version.

Dependencies¶

If you only intend to run GenX from the command line you do not need an installation of wxPython, appdirs or matplotlib. Thus the packages you need are:

• Numpy version > 1.0
• Scipy version > 0.5
• h5py version > ?
• If using mpi you will need mpi4py as well as an mpi installation.

Command line arguments¶

The arguments to GenX can be viewed by executing the program with the --help option.

$python genx.py --help usage: genx.py [-h] [-r | --mpi] [--pr PR] [--cs CS] [--mgen MGEN] [--pops POPS] [--asi ASI] [--km KM] [--kr KR] [-s] [-e] [infile] [outfile] GenX 2.3.5, fits data to a model. positional arguments: infile The .gx or .hgx file to load outfile The .gx or hgx file to save into optional arguments: -h, --help show this help message and exit -r, --run run GenX fit (no gui) --mpi run GenX fit with mpi (no gui) optimization arguments: --pr PR Number of processes used in parallel fitting. --cs CS Chunk size used for parallel processing. --mgen MGEN Maximum number of generations that is used in a fit --pops POPS Population size - number of individuals. --asi ASI Auto save interval (generations). --km KM Mutation constant (float 0 < km < 1) --kr KR Cross over constant (float 0 < kr < 1) -s, --esave Force save evals to gx file. -e, --error Calculate error bars before saving to file. For support, manuals and bug reporting see http://genx.sf.net  To run a fit using the multiprocessing module (forking different processes) which is the same code as in the gui the following command can be executed. $ python genx.py --run --mgen=10 ./examples/X-ray_Reflectivity.gx test.gx
Simulating model...
Setting up the optimizer...
DE initilized
Setting up a pool of workers ...
Starting a pool with 2 workers ...
Saving the initial model to /Users/GenX/Desktop/v2.3.5/test.gx
Fitting starting...
Calculating start FOM ...
Going into optimization ...
FOM: 0.277 Generation: 1 Speed: 541.6
FOM: 0.277 Generation: 2 Speed: 550.4
FOM: 0.268 Generation: 3 Speed: 528.7
FOM: 0.268 Generation: 4 Speed: 544.2
FOM: 0.243 Generation: 5 Speed: 546.8
FOM: 0.243 Generation: 6 Speed: 544.7
FOM: 0.243 Generation: 7 Speed: 549.8
FOM: 0.243 Generation: 8 Speed: 544.1
FOM: 0.218 Generation: 9 Speed: 546.9
FOM: 0.215 Generation: 10 Speed: 550.1
Stopped at Generation: 10 after 500 fom evaluations...
Fitting finished!
Time to fit:  0.0183591683706  min
Updating the parameters
Saving the fit to /Users/GenX/Desktop/v2.3.5/test.gx
Fitting successfully completed


As can be seen this loads the file ./examples/X-ray_Reflectivity.gx sets the maximum number of generation to run to 10 and then runs the fit. The result is saved to test.gx. Note that to be able to analyse the fits (calculate error bars for example) the option --esave should be used. If the fits take a long time to run it is advisable to save them every now and then with the --asi command that specifies how often the current result should be written to file. It can also be good idea to directly calculate the errorbars before saving to file with the -e command. Another point to see is that there is a significant speed-up when only using the command line. This is probably due to that the GUI does not have to be updated.

Using MPI¶

If MPI and mpi4py is installed on the system the --mpi switch will be activated. Note that the description for --mpi in the help will not appear until the mpi4py can loaded correctly. In order to use mpi the command mpirun or mpiexec has to be used. The argument -np defines how many processes to use. An example can be seen below.

\$ mpirun -np 2 python genx.py --mpi --mgen=10 ./examples/X-ray_Reflectivity.gx test.gx
Simulating model...
Setting up the optimizer...
DE initilized
Inits mpi with 2 processes ...
Saving the initial model to /Users/GenX/Desktop/v2.3.5/test.gx
Fitting starting...
Calculating start FOM ...
Going into optimization ...
FOM: 0.288 Generation: 1 Speed: 549.5
FOM: 0.288 Generation: 2 Speed: 550.3
FOM: 0.288 Generation: 3 Speed: 561.3
FOM: 0.240 Generation: 4 Speed: 563.7
FOM: 0.240 Generation: 5 Speed: 566.1
FOM: 0.240 Generation: 6 Speed: 560.2
FOM: 0.209 Generation: 7 Speed: 563.9
FOM: 0.209 Generation: 8 Speed: 559.6
FOM: 0.209 Generation: 9 Speed: 564.2
FOM: 0.190 Generation: 10 Speed: 559.5
Stopped at Generation: 10 after 500 fom evaluations...
Fitting finished!
Time to fit:  0.0177068511645  min
Updating the parameters
Saving the fit to /Users/GenX/Desktop/v2.3.5/test.gx
Fitting successfully completed


As MPI defines its process externally and the code calculates the chunk size automatically the arguments -pr and --cr will not be used in this case. This should be the only changes compared to using it from the command line as usual.