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README

=====================================================================================
                      MRS3D - MultiResolution in Spherical 3D            
                                Library and tools                          
                                  v1.0b  09/2013                           
=====================================================================================


MRS3D is a C++ package providing a library and a set of tools allowing the manipulation
of Spherical Fourier-Bessel Coefficients and the implementation of MultiResolution
algorithms adapted to 3D data in spherical coordinates.
In particular, MRS3D implements a Spherical 3D Isotropic Wavelet Decomposition. 

As a part of MRS3D, this package also contains the FastDSBT C++ library wich implements
a Discrete Spherical Bessel Transform based on a matrix formalism.

MRS3D is distributed under the CeCILL License (see LICENSE.CeCILL) in the hope that it 
will be usefull but without any warranty. 

The following softwares are used in MRS3D:
    - HEALPix (http://healpix.jpl.nasa.gov/) distributed under the GNU GPL
    - 3DEX (https://github.com/ixkael/3DEX) developed by Boris Leistedt and released
under the CeCiLL License. See the ArXiV paper http://arxiv.org/abs/1111.3591.

Author: François Lanusse (francois.lanusse@gmail.com)

Copyright CEA 2013

===================
   Requirements
===================

In order to be able to compile the MRS3D package, the following softwares are required:

    - cmake 	     (http://cmake.org/cmake/resources/software.html)
    - HEALPix 	     (http://sourceforge.net/projects/healpix/files/)
    - cfitsio        (http://heasarc.gsfc.nasa.gov/fitsio/)
    - OpenMPI or other MPI implementation
    - gfortran and gcc
    

The following softwares are optional:
    - Doxygen
    - IDL     

===================
     Building
===================

Before building the MRS3D package, it is necessary to build and install the HEALPix 
package (Fortran AND CXX versions).

First, unpack the tar.gz archive:
  
    $ tar -xvzf MRS3D.tar.gz
    $ cd MRS3D
    
Set the CFITSIO_DIR environment variable to the directory containing libcfitsio.a:

    $ export CFITSIO_DIR=/usr/lib

If IDL is installed on your system, you can build the MRS3D IDL interface by setting
the environment variable IDL_DIR to the IDL root directory:

    $ export IDL_DIR=/Applications/itt/idl

By default, the binary tools, headers and libraries will be installed in the MRS3D 
directory. To install them elsewhere on your sytem (e.g. /usr/local), you can set 
the INSTALL_DIR environment variable:

    $ export INSTALL_DIR=/usr/local        [ Optional ]

Compile the package:

    $ mkdir build
    $ cd build
    $ cmake ..
    $ make all
    $ make install  

To build the documentation:
    
    $ make doc

The html documentation will be available at doc/html/index.html.

If LaTeX is installed on your system, you can also build the pdf documentation by
going to the doc/latex subdirectory and typing make.


===================
 Running the code
===================

The transformations implemented in MRS3D require the values of zeros of Bessel functions.
Instead of behing calculated each time, these values are tabulated inside a binary FITS
file. This file, referred to as qlnTable, must be provided as first argument of all MRS3D
commands.
A precomputed qlnTable is provided with MRS3D and contains the first 3000 zeros of Bessel
functions up to the order 2000. This file should be sufficient for most applications.
To compute a larger qlnTable, the gen_qln tool is provided. The following command will
generate a table containing the first 2000 zeros of Bessel functions up to order 4000.

    $ gen_qln qlnTable.fits 4000 2000


MRS3D provides two main binary tools almn2wavelet and waveletThresholding:

  > almn2wavelet : Computes an Isotropic Undecimated Spherical 3D Wavelet decomposition 
from an almn .fits file.

  > waveletThresholding : Applies wavelet hard thresholding to the input almn .fits file.


These tools work on Spherical Fourier-Bessel coefficients stored in "almn" FITS files.
In order to compute almn coefficients to test these functions, two additional tools are
provided field2almn and almn2field:
  
  > field2almn : Computes the Discrete Spherical Fourier-Bessel Transform from a 3D 
cartesian field .fits file.

  > almn2field : Reconstructs a cartesian 3D field from an almn .fits file.


As an example, to decompose a field into wavelet scales from the MRS3D root directory run:

    $ bin/field2almn test/qlnTable.fits test/VirgoField256.fits test/VirgoAlmn.fits 512 250.0 256 256 256
Will store in "VirgoAlmn.fits" coefficients computed from the field "VirgoField256.fits" 
using a HEALPix resolution of nside=512, a boundary condition rmax=250.0 Mpc/h, up to 
the orders lmax=256, mmax=256 and nmax=256.

    $ bin/almn2wavelet test/qlnTable.fits test/VirgoAlmn.fits wavelet 512 4 3.5
This command will produce 5 FITS files (wavelet_0.fits wavelet_1.fits...), one for each
wavelet scale, plus one for the smoothed density. The cutoff frequency of the low pass 
filter is set to 3.5

    $ bin/almn2field test/qlnTable.fits test/wavelet_0.fits test/waveletField_0.fits 256 479.0 512
Reconstructs the density field of the first wavelet scale inside a cube of size
256x256x256 and physical size 479.0 Mpc/h using a Healpix resolution of nside=512.


Now, to visualize the density fields, the IDL interface can be used, see the next section.


===================
  IDL Interface
===================

To work on spherical Fourier-Bessel coefficients and 3D fields from IDL, MRS3D comes with
an IDL interface. The IDL procedures are in src/IDL. In order to work these procedures
load libMRS3DIDL and by default expect the library to be in the same directory.
To setup the IDL procedures, go to src/IDL and create a symlink to the libMRS3DIDL library:

    $ ln -s ../../lib/libmrs3d_IDL.dylib ./libmrs3d_IDL.dylib

To setup the FastDSBT IDL interface use as well:

    $ ln -s ../../lib/libfastDSBT_IDL.dylib ./libfastDSBT_IDL.dylib

(under linux, the libraries in /lib will be .so and not .dylib but keep the name in .dylib
for the symlinks)

In the /src/IDL directory, launch IDL.

Available features: 
    - Compute power spectrum from almn
    - Save/Load power spectrum to/from FITS files
    - Save/Load almn to/from FITS files
    - Save/Load cartesian density fiels to/from FITS files
    - Convert almn to field and field to almn (The use of the binary tools is prefered)

Example of how to visualize the wavelet scale computed at the previous section:

    IDL> fieldWavelet = mrs3d_load_field('/path-to-MRS3D/test/waveletField_0.fits')
    IDL> ivolume, fieldWavelet

To get help on the mrs3d_* commands, set the help keyword (e.g. mrs3d_save_field,/help)


===================
 Parallel execution
===================

MRS3D is designed to take full advantage of OpenMP and MPI. 

All the tools provided with MRS3D are parallelized using OpenMP and will by default run using a thread by processor core.
To manually set the number of threads used by the command set the environment variable OMP_NUM_THREADS:
    export OMP_NUM_THREADS=4   (bash)
or  setenv OMP_NUM_THREADS 4   (tcsh)


To launch a command using several MPI processes:
  mpirun -np 4 [command followed by arguments]

!!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!
When using MPI, be sure to use powers of 2 for the number
of l,m and n coefficients.
Since l goes from 0 to lmax, you must set l=2^i -1 !!!!
The same goes for m.
Since n varies from 1 to nmax you can directly set nmax= 2^l

A valid set of (lmax,mmax,nmax) is : 1023 1023 512
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 

An example of a PBS script to run a command on a computer cluster is provided below:

-----------------------------------waveletThresholding.job----------------------------------
#!/bin/sh
#PBS -l pmem=15G
#PBS -l pvmem=16G
#PBS -l mem=120G
#PBS -l vmem=128G
#PBS -l nodes=8:ppn=1
#PBS -W x=NACCESSPOLICY:SINGLEJOB
#PBS -l walltime=100:00:00

#PBS -M [your email address]
#PBS -m abe

export OMP_NUM_THREADS=8
cd [path to working directory]
cat $PBS_NODEFILE | sort | uniq > machinefile.txt

echo "----Begining job----" > log
date >> log
echo "--------------------" >> log

mpiexec -machinefile machinefile.txt -np 8 ./waveletThresholding qlnTable_2000_3000.fits Almn.fits ThresholdedAlmn.fits 2048 250.0 5 5 9.0 0.75 >> log

echo "----Job done--------" >> log
date >> log

----------------------------------------------------------------------------------------------

To launch the job : qsub waveletThresholding.job

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