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INSTALLATION
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INSTALLATION
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*****************************************************************
* PINOCCHIO V4.1 *
* (PINpointing Orbit-Crossing Collapsed HIerarchical Objects) *
*****************************************************************
This code was written by
Pierluigi Monaco
Dipartimento di Fisica, Universita` di Trieste
Copyright (C) 2016
web page: http://adlibitum.oats.inaf.it/monaco/pinocchio.html
The original code was developed with:
Tom Theuns Institute for Computational Cosmology, University of Durham
Giuliano Taffoni INAF - Osservatorio Astronomico di Trieste
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
********************************************************************
This file contains information on how to compile PINOCCHIO 4.1
********************************************************************
Pinocchio is a C, fully parallel (MPI) code, and should work on most
unix machines.
REQUIREMENTS
Pinocchio-4.1 requires:
Message Passing Interface (MPI) libraries;
fftw3 libraries with MPI support (http://www.fftw.org/);
the GNU Scientific Libraries (http://www.gnu.org/software/gsl/).
SETUP
We assume that all the libraries listed above are properly installed in
the system.
1. Extract pinocchio from the .tar.gz file
prompt> tar xvzf pinocchio-4.1.tar.gz
or (if you don't have gnu tar)
prompt> gunzip pinocchio-4.1.tar.gz ; tar xvf pinocchio-4.1.tar
2. Change directory to Pinocchio-4.1/src/
prompt> cd Pinocchio-4.1/src/
3. Edit the Makefile and set the values of compilation flags and
variables to those suitable for your system. You find an example
valid for a generic linux machine, using the gnu C compiler.
4. Make the executable by typing
prompt> make
If the code does not compile, check carefully the Makefile and ask
support to your local system manager. If everything fails, email
all the details to monaco@oats.inaf.it.
5. A utility, called memorytest, has been written to help design a run.
Compile it with:
prompt> make memorytest
Instruction on how to use it are given in the DOCUMENTATION file.
The codes read_pinocchio_binary.c and read_pinocchio_binary.f90 can be
easily compiled as indicated in the file headers.
RUN THE CODE
The executable is found in the src/ directory after compilation, and
is pinocchio.x (file name specified by the EXEC variable in the
Makefile). In the example/ directory you find a small working example
of a 500 Mpc/h box sampled with 200^3 particles, run with 4 MPI tasks.
It requires ~2Gb of RAM. The code has been compiled with TWO_LPT,
THREE_LPT and PLC options, as in the provided Makefile.
Open a new directory my.example/ and copy there the three files
parameter_file, outputs and PlotExample.py that can be found in the
example/ directory. The parameter file contains all needed parameters
with a quick comment, read the DOCUMENTATION for more details. The
file outputs contains a list of redshifts at which output is required.
chdir to my.directory and run the code:
> mpirun -np 4 ../src/pinocchio.x parameter_file > log
The code will generate four catalogs and four mass function files, a
past-light cone file and a cosmology file that contains basic
cosmological quantities. These files, including the log file, should
be nearly identical to the ones provided in the example/ directory. A
quick check can be performed with the PlotExample.py python script
contained in the example/ directory.
prompt> ipython
[...]
In [1]: %run PlotExample.py
The script will produce three plots, mf.png with the mass function at
z=0, lss.png with a slice of the box and plc.png, with a 3D
visualization of the past-light cone in comoving coordinates; rotation
can be adjusted in the panel produced by python.