HEALPix Facility Installation Guidelines

This document describes the installation for the HEALPix facilities.

Eric Hivon, Anthony J. Banday, Matthias Bartelmann, Benjamin D. Wandelt, Frode K. Hansen and Krzysztof M. Górski


Revision: Version 3.31; January 6, 2017

http://healpix.sf.net


TABLE OF CONTENTS

Introduction

In this document the installation procedure for the HEALPix distribution is outlined. HEALPix comprises a suite of Fortran 90, C++, IDL, Java and Python routines providing both stand-alone facilities and callable subroutines as an alternative for those users who wish to build their own tools. A set of C subroutines and functions is also provided.

The distribution can be downloaded as a gzipped tarred file, or as a zipped file, which can respectively be unpacked by executing the commands1
% gunzip Healpix_3.31.tar.gz
% tar -xpf Healpix_3.31.tar
or
% tar -xzpf Healpix_3.31.tar.gz
or
% unzip Healpix_3.31.zip
creating a directory named Healpix_3.31 whose structure is shown in Figure 1.

Figure 1: The directory structure for the HEALPix distribution.
Image dir_tree

As with most freely available software, the distribution comes with caveats, the major one being that although we have attempted to automate the installation as much as possible, not all eventualities can ever be foreseen. We have tested the installation on the following platforms:
AIX, IRIX, IRIX64, Linux, SunOS, ALPHA and Darwin (MacOS)

There may be problems in the facility build due to the local system configuration which is beyond our control.


Installation Requirements


Table 1: Documentation on the installation and usage of the different packages
Healpix Package Information on installation Information on routines
     
Fortran 90 This document ''Fortran Facilities'' and ''Fortran Subroutines'' documents
     
IDL/GDL This document ''IDL Facilities''
     
C++ This document, or src/cxx/README.compilation ''C++ Facilities and Subroutines'' (HTML only)
     
C This document, or src/C/README ''C Subroutines Overview''
     
Java src/java/README ''Java Overview'' (HTML only)
     
Python This document, or src/healpy/INSTALL ''Healpy Documentation'' (HTML only)
     
   


The major part of the HEALPix distribution is written in both Fortran 90 and C++ and so the appropriate compiler(s) must be present (Linux and Darwin users should look at Section 7.1 about free F90 compilers. Microsoft Windows users should look at Section 7.2). Many visualisation tools and map manipulation routines are provided in IDL (please note that at least version 6.4 is required), Java and Python. Some of the HEALPix routines are also available in C.
Starting with version 3.0, the healpy (HEALPix in Python) library has been integrated into HEALPix releases. Since it is, to a large extent, a wrapper to the C++ routines, installing it also requires a C++ compiler (on top of python and a few supporting Python libraries) but it will perform its own compilation of the current HEALPix C++ library.

This section and the next focus on the compilation and installation of the C, C++, Fortran 90, IDL and Python routines. For more information on the Java routines see table 1

The configure script is written in the Bourne shell. The script attempts to generate a Makefile which is tailored to one of the above Operating Systems (OS's) and using Makefile.in as a template for non system-specific statements. Only the basic UNIX make facility is required to build the software, although we do still recommend the GNU make facility (ftp://ftp.gnu.org/gnu/make/). In addition, several environment configuration files and an IDL/GDL startup file are generated. These automatically establish various environment variables and aliases to make the use of the HEALPix package simpler.

The HEALPix Fortran 90, C++, C and Python distributions also require the publicly available CFITSIO library. Note that the Fortran 90 routines require version 3.20 or more (post August 2009) of CFITSIO

Software Package Source
   
CFITSIO V 3.20 or more http://heasarc.gsfc.nasa.gov/fitsio/
   
 




The IDL visualization software is commercially available at

Software Package Source
   
IDL V 6.4 or more http://www.exelisvis.com/
   
 




while the GNU Data Language GDL, a free clone of IDL 6.0, can also be used (with some caveats, see §7.9) and can be downloaded for free from

Software Package Source
   
GDL 0.9.6 or more http://sourceforge.net/projects/gnudatalanguage
   
 




As it was already the case in version 1.20, users no longer need to acquire the IDL Astronomy User's Library (http://idlastro.gsfc.nasa.gov/homepage.html) or the COBE (IDL) Analysis Software (http://lambda.gsfc.nasa.gov/product/cobe/cgis.cfm), although we do recommend these packages to the user. The 100-odd routines required for version 3.31 are contained in the subdirectory Healpix_3.31/src/idl/zzz_external. These procedures are included in the HEALPix package unchanged and solely for the purpose of making it self contained. In this way, we remove the burden of installation of additional libraries from the end user.

The Python healpy package requires

Software Package Source
   
Python 2.6, 2.7, or 3.2-3.5 http://www.python.org
Numpy 1.0.1 or more http://numpy.scipy.org
Matplotlib 0.91.2 or more http://matplotlib.sourceforge.net
PyFITS http://www.stsci.edu/institute/software_hardware/pyfits
   
 




While not required, the IPython (http://ipython.org) and Cython (http://cython.org) softwares can also be useful.

A parallel implementation (based on OpenMP, for shared memory architectures) of the Spherical Harmonics Transforms involved in F90 synfast, anafast, smoothing, plmgen, alteralm and C++ synalm_cxx, alm2map_cxx, anafast_cxx, smoothing_cxx, rotalm_cxx ... is now available by default and can be readily compiled and used with the standard installation script.

A set of routines with MPI parallelization (for distributed memory architectures) is also available for Spherical Harmonics Transform, thanks to the work of H.K. Eriksen (UIO) and Snorre Boasson (ITEA, NTNU). See the F90 subroutines documentation for more information on how to use those routines in your code.

We found that it was remarkably difficult to find random number generators in the public domain which are simple yet powerful and easy to use. We are providing one (both in C++ and F90) which is an adaptation of an xorshift generator described in Marsaglia (Journal of Statistical Software 2003, vol 8). It has a theoretical period of $2^{128}-1 \approx 3.4\ 10^{38}$.

healpix_doc: an easy access to HEALPix documentation

The shell script healpix_doc now is available to provide easy access to the HTML and/or PDF documentation of all Healpix packages. It will automatically open a web browser or PDF viewer (among those found on the system) on the documentation available locally (at $HEALPIX/doc) or on remote web sites. To use it, simply type
     $HEALPIX/healpix_doc     
or
     $HEALPIX/healpix_doc -p     
to access respectively the HTML and PDF documentation. The default browser and viewer used by healpix_doc can optionally be set with the environment variables $HEALPIX_HTML_BROWSER and $HEALPIX_PDF_VIEWER.

The Installation Procedure

If the user has one of the supported OS's, then installation proceeds utilizing the following commands. If your OS is not supported, the configuration step should be omitted, Makefile.in should be copied as Makefile and explicitly tailored to the user environment.

% ./configure [-L] uses Makefile.in as a template to build the correct Makefile (from user inputs as required), it will also configure the IDL/GDL routines
% make builds all the facilities
% make test tests all the facility previously compiled
% make clean removes object (*.o) files
% make tidy removes object files, module files (*.mod), executables and libraries
% make distclean same as above and restores the directories to the state of the original distribution
These different steps are detailed below.

./configure [-L]

The ./configure script manages the configuration of the C, C++, Fortran90, IDL and Python suites of routines and facilities.

Since v2.11, it accepts the -L option to write the HEALPix specific configuration files into the HEALPix directory itself rather than in installer's home directory (see § 4.1.1). Using the -L option is recommended when doing a project or system wide installation of HEALPix to be accessed by several different users.

An online help is available with ./configure -h, while ./configure -v will return the HEALPix release number (currently 3.31) and exit.


Configuration profile

A feature introduced in previous releases and enhanced since v2.10, is that the configure script creates a shell configuration file
(located in ${HOME}/.healpix/3_31 _$\langle$OS_TYPE$\rangle$/config or in
${HEALPIX}/confdir/3_31 _$\langle$OS_TYPE$\rangle$/config if ./configure -L was used) according to shell type in which various environment variables and aliases are defined for your convenience. If you agree upon prompting, it will also change your default system profile during installation to automatically source this profile. If you do not agree to this change, you will need to explicitly source the configuration file above for any session in which you intend to run HEALPix facilities. In particular, you will have to make sure that the HEALPIX system variable is correctly defined (as the full path to the HEALPix directory) before running the package.

C configuration

The ./configure script will ask for the C compiler and options to be used, and for the full path of an installed cfitsio library to link to. By default, only a static library is created, but the user can also ask for a shared (Unix/Linux systems) or dynamic (Darwin) library.
After compilation (see make section) and linking, all libraries will be in ${HEALPIX}/lib/chealpix.* .


C++ configuration

Two options are available:
* The interactive ./configure script will ask for the full path to an installed cfitsio library to link to, and then provide a choice of predefined targets corresponding to different combinations of C++ compilers and options. Each of those targets is defined in a configuration file located in Healpix_3.31/src/cxx/config/config.target. The user can therefore add new targets or edit existing ones, and the ./configure script will update its menu accordingly. If a fairly recent version (4.2 or higher) of gcc and g++ is installed on the system, the target "generic_gcc" should always work, except under MacOSX, where ``osx'' target is required.
The environment variables EXTERNAL_CFITSIO, CFITSIO_EXT_LIB, CFITSIO_EXT_INC and HEALPIX_TARGET will be set according to the choices made above.
If the HEALPIX configuration file is sourced as described in § 4.1.1, the full path to the C++ executables will be added to the environment PATH variable.

* Starting with HEALPix 3.0, an automated (autoconf generated) configure script is available in Healpix_3.31/src/cxx/configure. To use it (and also make the compilation, and test it) do
     cd src/cxx     
     ./configure     
     make     
     make test     
which will put the compilation products in Healpix_3.31/src/cxx/auto.

Fortran 90 configuration

When you run ./configure on a supported system you will be prompted to enter compiler optimisation flags. We have not attempted to provide the best optimisation flags for all operating systems. The configure script will have a guess at optimisation options for some systems, but it is up to the user to figure out an optimal set2. From our experience, we have not found significant accumulation of numerical error even when using the most aggressive optimisation level available.
If the HEALPIX configuration file is sourced as described in § 4.1.1, the full path to the F90 executables will be added to the environment PATH variable.


IDL/GDL configuration

You will be asked for the external applications you want to use to visualize the Postscript and PNG files created by IDL (or GDL).
If the HEALPix configuration file is sourced as described in § 4.1.1, the aliases hidl, hidlde, hgdl and hgdlde are also defined to give you access to HEALPIX routines from IDL (and GDL).
See the HEALPix IDL Document for more information on using HEALPix IDL/GDL together with other IDL libraries.

Java installation

The configuration and installation of the Healpix Java package is currently handled separately. See table 1 for more information.

Python (healpy) installation

The ./configure script will ask for the Python command you want to use (in case many coexist on your computer) and will check that its version number meets the healpy requirements (see above). Note that during the compilation with make (see below), the src/healpy/setup.py Python script will be invoked to automatically prompt a fresh compilation of the src/cxx/* libraries, with all the options necessary to Python linkage, and can be done independently of the C++ installation described above.

Compilation and installation

The
     make     
command will compile one or several of the C, C++, F90 and Python packages depending on what was configured with the ./configure script. Specific packages can be compiled with the respective commands

   make c-all
   make cpp-all
   make f90-all
   make healpy-all

To perform several compilation jobs simultaneously, the command make -j [jobs] can be used.

Please neglect any possible warnings at compile time. If you run into trouble please refer to the section Troubleshooting and further information.

After running make, the user must re-login to ensure that the new profiles built by the installation procedure are correctly sourced. Only then will the user have full access to the specific HEALPix environment variables etc.

Testing the installation

All installed libraries and executables can be tested with

   make test

while specific tests of the C, C++ and Fortran products can be performed with, respectively

   make c-test
   make cpp-test
   make f90-test
For the latter, Table 2 lists the codes tested with the parameter files used, as well as the data files produced and the respective reference files.


Table 2: Data files and images produced by the Fortran codes during the tests, and the respective reference files to which they can be compared. All the files listed are located or produced in the Healpix_3.31/test directory. The GIF images of full sky maps were produced using map2gif. NA: No image available, because the data set is not a sky map
code & parameter file output data reference data output image reference image
synfast syn.par test_map.fits map.fits test_map.gif map.gif
test_alm.fits alm.fits NA NA
smoothing smo.par test_sm.fits map_sm.fits test_sm.gif map_sm.gif
ud_grade udg.par test_LOres.fits map_LOres.fits test_LOres.gif map_LOres.gif
hotspot hot.par test_ext.fits map_ext.fits test_ext.gif map_ext.gif
test_max.asc max.asc NA NA
test_min.asc min.asc NA NA
anafast ana.par test_cl.fits cl_out.fits NA NA
alteralm alt.par test_almdec.fits almdec.fits NA NA
median_filter med.par test_mf.fits map_mf.fits test_mf.gif map_mf.gif
sky_ng_sim ngfs.par test_ngfs.fits map_ngfs.fits test_ngfs.gif map_ngfs.gif
process_mask prmask.par test_distmask.fits distmask.fits test_distmask.gif distmask.gif


Notes:

* the input power spectrum (in Healpix_3.31/test/cl.fits) used to generate the Fortran90 test maps is currently the WMAP 1yr best fit, in $(\mu$K)2, and is therefore different from the one included in releases 1.* (that can still be found in cl_old.fits).
* Other input fiducial $C(\ell)$, all in $(\mu$K)2 and defined on the multipole range $[0, \ell_{\rm max}]$, have been included for convenience in Healpix_3.31/test/ in a HEALPix compatible format.
File name alias Origin $\ell_{\rm max}$
wmap_lcdm_pl_model_yr1_v1.fits cl.fits WMAP-1yr (2005) 3000
wmap_lcdm_sz_lens_wmap5_cl_v3.fits cl_wmap5.fits WMAP-5yr (2008) 2000
wmap_lcdm_sz_lens_wmap7_cl_v4.fits cl_wmap7.fits WMAP-7yr (2011) 3726
planck2013ext_lcdm_cl_v1.fits cl_planck1.fits Planck 2013 4500
planck2015_lcdm_cl_v2.fits cl_planck2.fits Planck 2015 4900

For more information on their respective origin and underlying model see their FITS header, or Healpix_3.31/test/README

In order to test the new HEALPix profile set-up one can then attempt to run any C++ or F90 facility from any directory on your system. Similarly, IDL (and/or GDL) can be tested by invoking hidl or hidlde (resp. hgdl or hgdlde).

Cleaning up

Three levels of cleaning are available:
  make clean
will remove the intermediate files created during compilation, such as object files, (Fortran) modules files, ... found in the source or build directories;
  make tidy
same as above, and will also remove the HEALPix executables, libraries and module and/or include files;
  make distclean
will return the HEALPix directory to its original 'distribution' state by discarding the same files as above, as well as the executable and library directories and the top level Makefile.

As a consequence, make clean can be used after a successful compilation and installation in order to remove now useless intermediate files while keeping the codes functional, while make tidy should be used between consecutive (failed) attempts with different compilers, compiler versions or compiler options, to avoid any conflict between new and pre-existing files.

A Note on Re-installation

As a result of the line added to your shell profile which explicitly sources the HEALPix profile, care must be taken if the package is reinstalled in a different directory. If such reinstallation is desired, the included line must be removed from your system profile, allowing the corrected version to be added.


Pkg-config files

Starting with HEALPix 3.12, pkg-config (.pc) files are generated during the configuration of the C, C++ and F90 packages, and are initially located respectively in ${HEALPIX}/lib/chealpix.pc, install_lib_directory/pkgconfig/healpix_cxx.pc and ${HEALPIX}/libsuffix/healpix.pc. If the pkg-config software is available on your system (see http://www.freedesktop.org/wiki/Software/pkg-config/ to download, install and use it) and if the location of the HEALPix pkg-config files above are known to it (either by moving/copying them to one of the standard locations returned by
pkg-config -variable pc_path pkg-config
or by customizing the environment variable PKG_CONFIG_PATH3) then linking your own code with the C, C++, F90 HEALPix library simply becomes
cc `pkg-config -cflags -libs chealpix` mycode.c -o mycode
c++ `pkg-config -cflags -libs healpix_cxx` mycode.cpp -o mycode
FC `pkg-config -cflags -libs healpix` mycode.f90 -o mycode
(where FC has to be replaced by the Fortran compiler used to generate the HEALPix library).


Troubleshooting and further information

This section contains a list of difficulties which we have dealt with. It is by no means exhaustive. In case of problems, see http://healpix.sourceforge.net/support.php or contact healpix-support at lists.sourceforge.net


Free Fortran90/95 Compilers

The free Fortran90/95 compilers that can be used to compile HEALPix include:
* Intel Fortran Compiler for Linux based computers (versions 11.* to 16.*4)
https://software.intel.com/en-us/fortran-compilers
* GNU Fortran 95 compiler (gfortran) included in GNU Compiler Collection GCC version 4.0.0 and up and available for Linux, Mac OSX, Windows, Sun ... platforms
http://www.gnu.org/software/gcc/fortran/.
GFortran binaries for all platforms can also be downloaded from
http://gcc.gnu.org/wiki/GFortranBinaries.
Please note that only recent versions of gfortran (Aug 2005 and later) compile HEALPix correctly, and v4.2.1 and more have given satisfying results so far, including native OpenMP support.
* G95 compiler available for Linux, Mac OSX, Windows, Sun and HP platforms with 32 and 64 bit architectures (eg, x86 and x86-64). In the latter case, the '32bit default integer' (32bit DI) version of g95 must be used.
http://www.g95.org


Installation under Microsoft Windows

Detailed instructions to install HEALPix on Windows 7 using Cygwin, kindly provided by John Arballo, are available in §7.2.1, while other configurations are discussed in §7.2.2.


Installation on Windows 7 with Cygwin

The three steps (installation of Cygwin, cfitsio and HEALPix respectively) must be done in that order.

A: Install Cygwin

  1. Go to https://www.cygwin.com/ and click on `Install Cygwin' in the menu on the left.

  2. Click on setup-x86.exe (for 32-bit installation) or setup-x86_64.exe (for 64-bit installation) and then `Save File' when prompted.

  3. Go to your Downloads folder (or wherever you saved setup-x86*.exe) and double-click on the setup-x86*.exe file to run it.

  4. Accept all defaults, except:

    1. You have to `Choose A Download Site'. (eg: ftp://ftp.gtlib.gatech.edu).
    2. When prompted to `Select Packages', expand `Default' (if you see a `+' to the left of it), expand `Devel', then find and add the following packages (click on `Skip' for each of them so it changes to the version number and a checkbox appears in the `Bin' column):
           gcc-core     
           gcc-fortran     
           gcc-g++     
           make     
  The installation will take a few minutes.

B: Install CFITSIO Library

  1. Get the latest source code package from NASA's HEASARC website (http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio_latest.tar.gz). When prompted to save the file, in the Save dialog window, navigate to C:\cygwin64\usr\local (assuming you accepted the defaults when installing Cygwin), click on `New folder' and  name it `src', go into that folder and `Save'.
  2. Open a Cygwin terminal (via the new Desktop icon or through your Start menu).
  3. Enter the following commands at the '$' prompt:
         $ cd /usr/local/src     
         $ tar zxvf cfitsio_latest.tar.gz     
         $ cd cfitsio     
         $ ./configure -prefix=/usr     
         $ make     
         $ make install     
         $ cd ../     
  4. Leave the Cygwin terminal open.

C: Install HEALPix

  1. Get the latest version of HEALPix from SourceForge (https://sourceforge.net/projects/healpix/files/latest/download). When prompted to save the file, save it in C:\cygwin64\usr\local\src.
  2. In Windows Explorer, navigate to C:\cygwin64\usr\local\src, right-click on Healpix_*.zip and `Extract all...'. Accept the default location.
  3. In the Cygwin terminal, type the following commands at the '$' prompt
    (use the names of the Healpix directories for the version you installed):
         $ cd Healpix_3.30_2015Oct08     
         $ cd Healpix_3.30     
         $ ./configure     
    Select an option from the menu (e.g., `2' for the C package) and accept all of the defaults except that the first time you run configure, you'll be prompted at the end to modify your home shell profile ('.profile'). Enter `y' at this prompt.
    If you want to install the C++ package of HEALPix (option 4), pick generic_gcc when prompted for a C++ configuration.
         $ make     
         $ make test     
         $ make tidy     


Other Windows configurations

Installation on Windows versions other than 7 should be very similar to the one detailed above.
In step A above, replacing Cygwin with MinGW (http://www.mingw.org/) together with the MSYS collection of GNU utilities (see http://www.mingw.org/wiki/msys and https://sourceforge.net/projects/mingw/files) is also possible. The Unix/Linux tools required include sh, make, awk, grep, sed, ls, wc, cat, more, nm, ar, as well as C, C++ and Fortran compilers.
The latest gfortran binaries for Cygwin and/or MinGW can be found at, eg
https://cygwin.com/cgi-bin2/package-grep.cgi?grep=gcc-fortran&arch=x86_64, following the tips found at http://gcc.gnu.org/wiki/GFortranBinaries.

Problems with CFITSIO

Compilation of CFITSIO Fortran wrappers

The most common problem with the Fortran HEALPix compilation will produce messages like:
  ld: Undefined symbols:
   _ftbnfm_
   _ftclos_
   _ftcrhd_
   _ftdkey_
   ...
or
  fitstools.f90: undefined reference to `ftdkey_'
  fitstools.f90: undefined reference to `ftbnfm_'
  fitstools.f90: undefined reference to `ftclos_'
  ...
or
 Undefined symbols:
  "_ftghbn_", referenced from:
      ___fitstools_MOD_read_fits_cut4.clone.2 in libhealpix.a(fitstools.o)
      ___fitstools_MOD_getsize_fits.clone.1 in libhealpix.a(fitstools.o)
      ___fitstools_MOD_getsize_fits in libhealpix.a(fitstools.o)
   ...
 ld: symbol(s) not found
 collect2: ld returned 1 exit status
and occurs when the CFITSIO installation script could not find a valid fortran compiler.
To solve this problem
  1. Go into the CFITSIO directory.
    Assuming that ifort is available on your system (it can be replaced below by gfortran, g95, f77, f2c, $\ldots$) type:
         ./configure FC=ifort     
         make     
         make install      (optional).
  2. Then go back into the HEALPix directory and do
         ./configure      (making sure that you are using the newly created libcfitsio.a library)
         make     
         make test     
See also the note below on 64 bit architectures.

CFITSIO problems on systems with 64 bit architecture

  1. Linux, Mac OS X

    If the HEALPix codes are compiled in 64 bits, and the GNU C Compiler (gcc) is used to compiled CFITSIO, then issue the following commands in the CFITSIO directory:

      ./configure FC='gcc -m64'
      make
    

    You can then force compilation to the same binary format by entering -m64 when asked for the optimisation options in the HEALPix configure script.

  2. IRIX64

    On a 64-bit architecture such as IRIX64, CFITSIO will have to be compiled in the same binary format as the HEALPix codes. This can be achieved by typing the following on the command line in the CFITSIO directory:

      rm config.cache    
      setenv CC 'cc -n32'
      ./configure
      make
    

    Alternatively you can replace the -n32 with -64. You can then force compilation to the same binary format by entering either -n32 or -64 when asked for the optimisation options in the HEALPix configure script.

CFITSIO linking problems

A particular problem encountered with the CFITSIO Version 2.0 release relates to the inclusion of various libraries within the system release for a given machine. This led to some modifications to the Makefile to include the specific library links -lm -lnsl -lsocket on SunOS, but only -lm for IRIX64. If your OS is not completely supported by the distribution, you may find this as one source of errors. The CFITSIO developers recommend compilation of the testprog routine. Inspection of the libraries linked after executing the make testprog statement will reveal those you need to include in the Makefile.

CFITSIO and Debian/Linux

Some problems have been reported on Debian/Linux systems during the linking to the CFITSIO library shipped with Linux. If these problems occur, try to recompile the CFITSIO library from scratch before linking to HEALPix .

diff shows that the test files are different from the supplied files

This by itself is no cause for concern. When comparing using a diff on the test files will most likely report a difference even when the installation has been successful. This may be due to the fact that different installations have different floating point representations. Also, the FITS files carry date information.

Try unlimit

If you have unforeseen problems at runtime, try unlimit (under csh or tcsh) or ulimit (under sh or bash), in order to increase the heap and stack memory size. It sometimes helps.

hidl usage

We have found that in very rare cases the alias hidl is not recognised by the user's system. Usually, this is related to the local system's IDL script. A quick-fix is achieved by setting the environment variable IDL_STARTUP to be equal to the HEALPix startup file HEALPix_startup including the directory path to the file. This enables the user to access the HEALPix IDL procedures simply by invoking IDL. For example, in the typical installation documented above for a user running the tcsh shell, the command
setenv IDL_STARTUP /disk1/user1/HEALPix_3.31/src/idl/HEALPix_startup
should be issued (or added to the user's shell profile).

If the user already has an IDL startup file, then this should be merged with HEALPix_startup. This temporary solution does mean that the HEALPix IDL procedures are available in the IDL_PATH at all times, which may lead to conflicts with user-defined procedures. The hidl invocation was intended to circumvent these issues, allowing HEALPix IDL procedures to be available only when desired.

A proper fix requires the user to ask the local system administrator to adjust the local IDL script.

Using HEALPix IDL together with other IDL libraries

See the eponymous section in the ``IDL Facilities Overview''


Mac OS X, X11 and IDL cursor

If the IDL cursor does not work correctly on X11 windows under Mac OS X, and the 2nd and 3rd button clicks are ineffective, type
* with Apple's X11:
* under Tiger (10.4.*):
defaults write com.apple.x11 wm_click_through -bool true
* under Leopard (10.5.*), Snow Leopard (10.6.*) and Lion (10.7.*):
defaults write org.x.x11 wm_click_through -bool true
* with Xquartz (default under Moutain Lion (10.8.*), Mavericks (10.9.*) and Yosemite (10.10.*), available for download for El Capitan (10.11.*) and Sierra (10.12.*)):
defaults write org.macosforge.xquartz.X11 wm_click_through -bool true
* with MacPort's X11 (package xorg-server):
defaults write org.macports.X11 wm_click_through -bool true
at your X11 prompt and restart X11.
Note that the command ls -lrt $HOME/Library/Preferences/*[xX]11*plist can be used to determine the X window system installed on your Mac. See also http://www.idlcoyote.com/misc_tips/maccursor.html and mollcursor documentation in ''IDL Facilities'').


Using GDL instead of IDL

GNU Data Language (GDL), is a free clone of IDL 6.0 (for more information see http://gnudatalanguage.sourceforge.net). Both the source code and precompiled executables for various platforms are available.

When used to run IDL-Healpix routines, GDL 0.9.6 or more gives very satisfactory results5. The calculations agree with those done under IDL, with comparable computation times, but a few minor features are missing in the production of Postscript, GIF and PNG files, as described below.

GDL+HEALPix specific requirements

To fully enjoy GDL capabilities
* HEALPix 3.31 or more must be installed6.

* Besides the mandatory requirements (plplot, gsl, readline and zlib) GDL must also have been (pre-)compiled with links to
* ImageMagick (or GraphicsMagick) to produce PNG and JPEG output files,
* pslib to produce PostScript and PDF files (in the latter case, a recent version of ghostscript, i.e. 9.07 or more, is also recommended).

Impact of GDL limitations on HEALPix

* When run under GDL 0.9.6, and if the requirements stated above are met, the visualization routines azeqview, cartview, gnomview, mollview and orthview will produce correct screen (X) outputs and PS, PDF, PNG and JPEG images, with the following caveats:
* they won't produce GIF files (because GDL's write_gif is not yet functional);
* the transparent keyword will be ignored in the production of PNG files under GDL (except when TrueColors is set and Nx3 map is provided), and for the same reason, the hpx2gs routine won't mark missing pixels as transparent in the output PNG file;
* and finally, the pfonts keyword will not allow the selection of other fonts than Hershey vectorial fonts (pfonts[0]=-1).
All other features work properly, including the Latex keyword.


Appendix I: Recent Changes and New Features

Bug corrections and Improvements in Version 3.31

General

* Detailed HOWTO for installation under Windows;
* Interactive configure script now supports MINGW environment (for Windows), and better detects gcc and python versions;
* Improved cross-document linking in PDF documentation.


C++

* Removal of C++11 features inadvertently introduced in Version 3.30 (see http://sourceforge.net/p/healpix/bugs/72)

Fortran 90 facilities and subroutines

* Bug correction in input_map routine for reading of polarized multi-HDU cut sky FITS files;
* Introduction of winfiledir_* and windowfile_* qualifiers in alteralm facility.


IDL

* Improved support for GDL;
* update of the required IDL-astron library routines, and Coyote library routines (2016-08-19).


Python

* Switch to healpy 1.9.1 (CHANGELOG)
* Removed C++ 11 features
* Streamlined setup.py
* Plotting fixes for Python 3
* Numpy 1.10 fix

Appendix II: Older changes (versions 3.00 to 3.30)

Bug corrections and Improvements in Version 3.30 (2015-10)C++

* support for multi-order coverages (MOC);
* allow generation of $a_{\ell m}$ from 6-component power spectra;
* moved from alice2 to alice3, which produces FITS HEALPix maps as output. These can be visualized more flexibly with external tools.
* switch from custom xcomplex class to std::complex;
* rangeset class has been redesigned.

Fortran 90 facilities and subroutines

* anafast facility now produces nine spectra (TT, EE, BB, TE, TB, EB, ET, BT and BE), instead of six previously, when analyzing two polarized maps;
* alm2cl subroutine can now produces nine spectra (TT, EE, BB, TE, TB, EB, ET, BT and BE), instead of six previously, when called with two sets of polarized $a_{\ell m}$ and can also symmetrize the output $C(\ell)$ if requested;
* the $a_{\ell m}$ generated by create_alm subroutine can now take into account non-zero (exotic) TB and EB cross-spectra (option polar=2) if the input FITS file contains the relevant information
* new routines nest2uniq and uniq2nest for conversion of standard pixel index to/from Unique ID number. See ''The Unique Identifier scheme'' section in ''HEALPix Introduction Document'' for more details.
* improved repeat behavior in write_bintabh routine
* edited map2alm_iterative routine to avoid a bug specific to Intel's Ifort 15.0.2
* CFITSIO version 3.20 (August 2009) or more now required;

IDL

* azeqview, cartview, gnomview, mollview, orthview visualization routines:
* addition of PDF keyword for production of Adobe PDF outputs;
* addition of LATEX keyword for genuine or emulated LATEX processing of character strings;
* addition of PFONTS keyword to select origin and type of character font;
* the CROP keyword now has the same behavior for all output media (GIF, JPEG, PDF, PNG, PS, ... and X); the NOBAR keyword now removes the color bar or the polarization color wheel, as applicable; correct EQUINOX date in header of output FITS map; the double precision maps and those with constant value are now correctly handled.
* fits2cl: addition of /PLANCK2 keyword to read best fit $C(\ell)$ model to Planck 2015 data.
* new routines nest2uniq and uniq2nest for conversion of standard pixel index to/from Unique ID number. See ''The Unique Identifier scheme'' section in ''HEALPix Introduction Document'' for more details.
* HEALPix enabled GDL commands (hgdl and hgdlde) are defined during the configuration process.
* update of the required IDL-astron library routines, and Coyote library routines (2015-09-23).

Java

* deprecated parts of the library have been removed;
* MOC support (see http://ivoa.net/documents/MOC/ for high-level description);
* queries for arbitrary polygons (using MOC);
* new targets in build.xml which allow compilation without external JARs.

Python

* switch to healpy 1.9.0
* same C++ source code as HEALPix 3.30
* drop support for Python 2.6
* support for astropy.fits
* improvements to read_map and write_map
* renamed get_neighbours to get_interp_weights
* several bug fixes in build and installation processes

Bug corrections and Improvements in Version 3.20 (2014-12)

General

* Generation of pkg-config files during the configuration of the C, C++ and F90 packages. See Section 6 of ''HEALPix Installation'' for details.
C
* Top configure script now proposes compilation with or without CFITSIO-related functions
* Improved autotools support

C++

* automatic workaround for bugs in older versions of GNU g++ compiler (bug reports 37, 45, 48, 51)
* workaround for possible bug in Intel icc 14.0 compiler
* bug fix in Mollweide projection in map2tga when not looking at (0,0)
* autotools updates
* deprecation warnings in alice2, soon to be replaced

Fortran 90 facilities and subroutines

* HEALPix-F90 routines and facilities can now also be compiled with the free Fortran95 compiler g95 (http://www.g95.org/). See Section 7.1 of ''HEALPix Installation'' for details.
* A separate build directory is used to store the objects, modules, ... produced during the compilation of the source codes
* improved handling of long FITS keywords, now producing FITS files fully compatible with the PyFITS and Astropy (www.astropy.org) Python libraries
* improved FITS file parsing in generate_beam, affecting the external B(l) reading in the F90 facilities alteralm, synfast, sky_ng_sim, smoothing.

IDL

* addition of ialteralm to modify Spherical Harmonics coefficients (alm).
* addition of planck_colors to modify current color table to one used in Planck 2013 publications.
* cartview, gnomview, mollview, orthview:
* addition of BAD_COLOR, BG_COLOR and FG_COLOR keywords to change the color of the missing pixels, background and foreground labels and lines.
* support for COLT='planck1' and COLT='planck2' to use the Planck color tables defined in planck_colors
* Bugs correction in bin_llcl, query_disc.
* update of the required IDL-astron library routines, and their supporting Coyote routines (2014-11-10).

Java

* explicit deprecation warnings in the source codes

Python

* switch to healpy 1.8.1
* fixes bugs in monopole removal,
* adds orthographic projection,
* easier install on MacOSX

Bug corrections and Improvements in Version 3.11 (2013-04)

General

* libsharp C library used for Spherical Harmonics Transforms in Fortran and C++ since HEALPix 3.10 can now be compiled with any gcc version.

C++

* See General section above
Fortran 90 facilities and subroutines
* bug correction in query_disc routine in inclusive mode
* bug correction in alm2map_spin routine, which had its spin value set to 2
* See General section above
IDL
* ang2pix_ring and pix2ang_nest routines now accept scalar arguments

Bug corrections and Improvements in Version 3.10 (2013-03) General N/AC

* experimental GNU autotools support (undocumented); the standard configuration script remains available

C++

* Spherical Harmonics Transform library libpsht replaced by libsharp (Reinecke & Seljebotn, 2013).
Note that some gcc versions (4.4.1 to 4.4.6) crash with an internal compiler error during compilation of libsharp. The problem has been fixed in gcc 4.4.7, 4.5.*, 4.6.*, 4.7.* and newer versions and was not present in versions 4.2.* and 4.3.*.
* added boundaries() method to T_Healpix_Base
* experimental GNU autotools support (undocumented); the standard configuration script remains available

Fortran 90 facilities and subroutines

* all Fortran facilities now support most of cfitsio's ``Extended File Name Syntax'' features, allowing the reading and processing of an arbitrary HDU and table column out of remote, compressed FITS files. For example, setting
infile = ftp://url/file.fits.gz[extn][col colname]
in anafast will download the FITS file file.fits.gz from url, uncompress it, open the HDU (extension) featuring keyword EXTNAME=extn, or the one with 1-based rank number extn, read the table column with TTYPE*=colname out of it and will analyze it.
It is also possible to perform a remote anafast analysis of a Planck Legacy Archive (PLA) sky map named map.fits via the PLA AIO Subsystem by simply setting infile=http://pla.esac.esa.int/pla/aio/product-action?MAP.MAP_ID=map.fits as input map file.
* yet faster synfast, anafast, smoothing thanks to libsharp routines (see warning on gcc releases above).

IDL

* bug corrections: query_disc: correct handling of empty disc; bin_llcl: correct handling of optional argument.
* double precision of input now preserved in gaussbeam and euler_matrix_new.
* fits2cl: addition of /PLANCK1 keyword to read best fit C(l) model to Planck 2013 + external data.
* it is now possible to read a specific FITS file extension identified by its (0-based) number or its case-insensitive EXTNAME value with the Extension keyword added to fits2cl, getsize_fits, read_fits_map, read_fits_s and read_tqu.
* update of the required IDL-astron library routines, and their supporting Coyote routines (2013-02-08).

Java N/APython

* switch to healpy 1.5.0: addition of gauss_beam to generate Gaussian beam window function.

Bug corrections and Improvements in Version 3.0 (2012-11)

General Introduction of the script healpix_doc for easy access to the HEALPix PDF and HTML documentation.

C

* Interface has remained unchanged, but the code has been replaced by a C port of the relevant Healpix C++ functions, resulting in significant speedups.
* Additional functions are provided which support Nside values up to 229. They have the same name as the traditional functions, with a ``64'' suffix appended.

C++

* Query routines: query_polygon() and query_polygon_inclusive() added. Query routines now return lists of pixel ranges instead of lists of pixels, which is much more economic. Inclusive query routines: tradeoff between performance and number of false positives is tuneable. Queries now work natively in both NESTED and RING schemes. Operations on the NESTED scheme are typically slower than in RING, but still much faster than computing the query in RING and converting all pixel numbers to NESTED afterwards.

* Healpix_Base: Healpix_Base and Healpix_Base2 have been merged into the templated class T_Healpix_Base; functionality is still available under the old names. Various performance improvements to T_Healpix_Base functionality

* User-friendliness: module parameters can now optionally be passed on the command line instead of using a parameter file. For example:
anafast_cxx nlmax=500 infile=test.fits iter_order=3 $\langle\ldots\rangle$
Facilities now check input maps for undefined pixels before calling map2alm(). If undefined pixels are found, a warning is printed, and the pixels are set to zero. udgrade_cxx refuses downgrading of polarised maps (which would produce unphysical results)
* Bug fixes: accuracy of pix2ang near the poles at high resolutions has been improved.
* Configuration: optional autoconf support
* Interface changes:
* Healpix_Base::query_*(): new interface
* cxxutils.h has been split up into announce.h (dealing with module banners), share_utils.h (dealing with subdividing tasks between multiple workers) and string_utils.h (dealing with string manipulation and file parsing)
* psht.h: interface to alm_info changed in order to add MPI support
* ylmgen_c.h: Ylmgen_init() interface has changed
* bluestein.h: bluestein_i() interface changed

Fortran 90 facilities and subroutines

* Compressed and/or remote (ftp or http) FITS files can now be read. CFITSIO 3.14 or more is now required;
* introduction of the process_mask facility to compute the angular distance of valid pixels to the closest invalid pixels for a input binary mask, and of the supporting routines dist2holes_nest, fill_holes_nest, maskborder_nest, size_holes_nest;
* the pixel query routine query_disc has been improved and will return fewer false positive pixels in the inclusive mode;
* improved accuracy of the co-latitude calculation in the vicinity of the poles at high resolution in nest2ring, ring2nest, pix2ang_*, pix2vec_*, $\ldots$;
* sky_ng_sim now allows the computation of the spatial derivatives of the non Gaussian map being produced, and the output of the alm coefficients of that map;
* anafast now allows the pro/down-grading of the input mask to match the resolution of the map(s) being analyzed;
* the median filter routine medfiltmap, used by the facility median_filter is now parallelized.

IDL

* New routines to go from circular beam profile to transfer function (beam2bl), and back (bl2beam); to go from indexed list of alm to a(l,m) 2D table (alm_i2t), and back (alm_t2i); and to compute the angular distance between pairs of vectors (angulardistance).
* addition of iprocess_mask interface to F90 process_mask facility to compute the angular distance of valid pixels to the closest invalid pixels for a input binary mask.
* creation of hpx2dm routine to generate DomeMaster images of HEALPix maps that can be projected on planetariums.
* the pixel query routines query_triangle, query_polygon, and in particular query_disc, have been improved and will return fewer false positive pixels in the inclusive mode
* improved accuracy of the co-latitude calculation in the vicinity of the poles at high resolution in nest2ring, ring2nest, pix2ang_*, pix2vec_*, $\ldots$
* cartview, gnomview, mollview, orthview: the length and spacing of the headless vectors used to represent polarization is now user-controlled via POLARIZATION keyword. The COLT keyword now allows the use of an interactively modified color table.
* orthview now accepts STAGGER keyword to overplot staggered spheres (with a twist) in order to detect periodic boundary conditions on the sky
* fits2cl: addition of WMAP7 keyword to read best fit C(l) model to WMAP 7yr data.
* read_fits_map can now read ${N_{\rm side}}$=8192 HEALPix maps and is generally faster than previously for smaller maps
* update of astron library routines (01-Feb-2012).

Java

* Core functionality has been reimplemented from scratch in the form of the "healpix.essentials" package. It is strongly recommended to use this package directly in future projects making use of Java HEALPix. "healpix.essentials" is a port of the Healpix C++ library and presents a very similar interface.

The "healpix.core" package is still provided. It uses "healpix.essentials" internally, and its interface has been kept stable as much as possible. Some adaptations in user code will still be necessary, however. Please note that using "healpix.core" will result in slightly lower performance than calling "healpix.essentials" methods directly, because of the necessary data conversion.

* New features and improvements introduced with the HealpixBase class, compared to the HealpixIndex, Healpix and PixTools classes:
* close similarities with Healpix_Base_T class from Healpix C++, which allows simultaneous development and bug fixes for both.
* support for arbitrary positive Nside values in RING scheme; no longer limited to powers of 2
* maximum supported Nside value: 229
* significant performance improvements: most methods have been accelerated by integral factors, some by more than an order of magnitude.
* re-implementation of queryDisc and queryPolygon, with same new features as the C++ implementation (see above).
* the HealpixProc class offers a procedural (instead of object-oriented) interface to the HealpixBase functionality, which simplifies transition for users of the "Healpix" and "PixTools" classes. NOTE: this only works for Nside parameters which are powers of 2
* many bug fixes
* no external library dependencies, except for "nom.tam.fits" if FITS I/O is required

Python

* the healpy package (C. Rosset, A. Zonca et al.) is now part of HEALPix

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HEALPix Facility Installation Guidelines

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