97 lines
3.2 KiB
ReStructuredText
97 lines
3.2 KiB
ReStructuredText
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.. _outputs:
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Outputs
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#######
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hmc_perfomance.txt
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==================
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This text file is appended with a new line every time the HMC is used.
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Each column has the following meaning:
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- epsilon used in the integrator
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- number of timesteps
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- variation of energy between first and last step (:math:`\Delta H = H_{final} - H_{initial}`). Please note
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that you actually want this one to be negative or order 1 as the acceptance is determined by the probability
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:math:`exp(-\Delta H)`.
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- wall seconds taken to do the entire HMC run
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- scheme used to integrate
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- value of the final hamiltonian
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.. _log_files:
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log files
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=========
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The log files are formatted by libLSS/tools/console.hpp. If you have not
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explicitly disabled the debug level, then all the messages emitted by
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the code are saved in those files. Otherwise, it is limited to verbose
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level. Each line starts with square brackets, with the level of the
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message indicated "[LEVEL]". Each new indentation corresponds to a new
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subcontext. If timing information were requested at compile time, each
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termination of context gives also the time taken in the context itself,
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including everything called inside this same context.
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.. _restart_files:
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restart files
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=============
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This file gives you access to the relevant infromation required to
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restart an MCMC run, such as the initial configuration. The ares
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framework creates one restart file per MPI task. Each file is suffixed
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by "_X" where X is the MPI task id. Most of the variables are just the
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same from one file to the other. The exception are the arrays explicitly
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sliced by the MPI parallelization which are only present by slab.
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The file contains the following groups:
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- galaxy_catalog_0
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- galaxy_kecorrection_0
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- random_generator
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- scalars
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The python script "scripts/merge_mpi_restart.py" can merge all these
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restart files into a single restart.h5 file. Be aware that it may
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consume quite a lot of memory. However it is a required step to allow
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the user to change the number of MPI task for an exisiting ARES run. The
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MPI run may be resumed with the option "SPECIAL_RESUME" instead of
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"RESUME" and it will read restart.h5 to recreate the set of
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"restart.h5_XX" files with the new number of MPI tasks.
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.. _mcmc_files:
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MCMC files
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==========
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Depending on length of run, a series of mcmc files will be produced with
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file names 'mcmc_chainNumber.h5'. All attributes of the file are
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contained within the group 'scalars', for example the following for the
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basic run in "examples":
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- catalog_foreground_coefficient_0
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- galaxy_bias_0
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- galaxy_nmean_0
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- powerspectrum
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- s_field
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- spectrum_c_eval_counter
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For reference, these groups and attributes can be easily searched
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through a few lines of python:
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.. code:: python
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import h5py as h5
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# access mcmc file
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hf = h5.File("mcmc_0.h5")
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# list groups within file
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list(hf.keys())
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# list attributes within 'scalars' group
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list(hf['scalars'].keys())
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A tutorial to read and plot basic ARES outputs with python is available :ref:`here <tutorial_ares_basic_outputs>`.
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If one wishes to access the MCMC files in C++, functions are available
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in CosmoTool and LibLSS: see :ref:`this code tutorial <reading_in_meta_parameters_and_arrays>`.
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