https://github.com/teuben/nemo
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README.install
Executive Summary
=================
Installation of the core version of NEMO is roughly follows (your yapp selection may vary):
git clone https://github.com/teuben/nemo
cd nemo
./configure --with-yapp=pgplot
make build check bench5
source nemo_start.sh
many more details can be found below. The biggest caveat on this scheme is the use of the pgplot
driver for the yapp plotting interface. By default it would install a safe but fairly useless
postscript-only driver. The pgplot driver is probably the most functional, but We also have (fairly)
functional plplot and giza drivers.
The configure line can be complex, for example for a Mac it could be:
CC=gcc-10 CXX=g++-10 F77=gfortran-10 ./configure --disable-shared --with-yapp=pgplot
A simple test to create and plot a 1911 Plummer sphere is the following:
mkplummer p10.dat 10
snapprint p10.dat
snapplot p10.dat
tsf p10.dat
Failing pgplot
--------------
One of the more common installation problems is with pgplot: didn't compile or link. Usually
you can find out with the command
mknemo tabplot
what is wrong/missing. Sometimes it's the X libraries, sometimes the PNG library, or something with PGPLOT alltogether.
We keep a version of pgplot for manual compilation, which might work well on a mac. Here's an example
to try in that case:
mknemo pgplot
# this needs to work, otherwise the next steps make no sense
# it will have deposited a number of pgplot things in $NEMOLIB
./configure --with-yapp=pgplot --enable-png --with-pgplot-prefix=$NEMOLIB
source nemo_start.sh
make build check
mknemo tabplot
tabgen - | tabplot - point=2,0.5
If this still fails, and you just want a non-graphical NEMO to work, use the PS driver instead:
./configure --with-yapp=ps
source nemo_start.sh
make build check
mknemo tabplot
tabgen - | tabplot - point=2,0.5
open yapp.ps
there should be a file "yapp.ps" which you might be able to open or xdg-open.
Preconditions for Installation
==============================
To build the basics of NEMO you need compilers (C/C++/Fortran). C is essential,
C++ and Fortran highly recommended. You will also need the usual build tools
C essential
C++ highly recommended (essential for gyrfalcON)
Fortran highly recommended
tcsh essential (some scripts are still in csh)
make essential
cmake highly recommended
pgplot recommended for yapp_pgplot (we also have a "mknemo pgplot" builtin option)
cfitsio recommended for some tools
hdf4 recommended for some tools
hdf5 recommended for some tools
netcdf recommended for some tools
python3 recommended (a builtin anaconda3 is one option)
boost recommended (for uns_projects)
swig recommended (for unsio)
x11, cairo essential, but depending on the selected yapp graphics driver
For debian and redhat based systems, one of these may help to install packages:
make install_apt
or
make install_dnf
based on a package requirements style file in $NEMO/src/scripts/requirements.
Depending on your packaging tools (apt, yum, dnf, brew, port, ....) these are hidden under
various package names
dpkg -L pgplot5
dpkg -S /usr/include/cpgplot.h
dpkg -l
rpm -ql pgplot
rpm -qf /usr/lib64/libpgplot.so.5.2.2
rpm -qa
or your system manager has hidden them in a module
module avail
See examples of package names in $NEMO/src/scripts/linux and $NEMO/src/scripts/brew (for Mac too)
-gfortran
-libx11-dev
-libxt-dev
-libxext-dev
-libcairo2-dev
-build-essential
-cmake
-csh
-pgplot5
-libhdf4-dev
-libhdf5-dev
-hdf5-tools
DOWNLOAD and INSTALLATION: two examples
=======================================
Perhaps the easiest way to install nemo is using the docs/install_nemo
script. The following example shows how to bootstrap this:
wget https://teuben.github.io/nemo/install_nemo
csh -f install_nemo nemo=nemo
source nemo/nemo_start.sh
if you prefer the more classic approach, we do use configure under the hood
git clone https://github.com/teuben/nemo
cd nemo
./configure ...
make build
source nemo_start.sh
The configure script has many options, use --help to review them. The
install_nemo script has a number of key=val type command line options that
will aid in using some of the configure options.
MANUAL INSTALLATION BACKGROUND:
===============================
The remainder of this document gives some more examples and background
information in case the more automated script(s) to install NEMO have
failed you.
Installation of NEMO V4.x roughly follows that of most open source
packages, except that NEMO does not install its products in an
external prefix like /usr/local, but keeps them "in-place" and
bootstraps a special NEMO shell environment by sourcing an "rc" file
where things like your search path are modified for your shell. Hence
the basic scheme is more one of (except commands are different and
detailed below!!!):
configure
make build
source nemo_start.sh
It may be handy to pre-install a few libraries and packages on your
system, if they do not exist yet. For a few common ones (e.g. pgplot,
cfitsio, gsl, hdf, hdf5) we also do have some support to install them
within the NEMO tree before the NEMO is installed. Typically you can
then use the commonly used sequence
configure --prefix=$NEMO/opt
make
make install
or
mkdir build
cd build
cmake
-DCMAKE_INSTALL_PREFIX=$NEMO/opt ..
make
make install
We generally now support this via the mknemo script, e.g.
mknemo cfitsio
would compile cfitsio under $NEMO/opt, which all Makefiles when building
NEMO programs use to compile and link.
Preconditions for INSTALLATION
==============================
a1) Installing PGPLOT - native Linux/MacOSX-brew distribution
Some distributions now keep pgplot in their package list. For example
in Ubuntu you can use
sudo apt install pgplot5
(but see below for the giza version). In this case you can use
configure --with-yapp=pgplot --with-pgplot-prefix=/usr/lib
In Centos PGPLOT is also available
sudo yum install pgplot-devel pgplot
On MacOSX, with brew, you can
brew install pgplot
If you are lucky, you can also find the proper paths via pkg-config, but
you will need to know the package name and they can vary.
a2) Installing PGPLOT (native CALTECH version)
It is recommended to install PGPLOT before you install NEMO.
We do have a simple procedure to install PGPLOT during the NEMO
install itself. You can also decide to use another plotting (YAPP)
device though, e.g. plplot (a pure C plotting library similar to PGPLOT)
is gaining in popularity.
Unless it finds the PGPLOT library in a reasonably location, or as dictated
by the PGPLOT_DIR environment variable, or via the --with-pgplot-dir= option
to configure, as a fallback NEMO would install itself with a very simple
postscript-only graphics library (a.k.a. yapp_ps),
If none of these options work, you can also try to install PGPLOT in
for example the following way
cd $NEMO/local
$NEMO/src/scripts/pgplot.install
(you may need to get the pgplot522.tar.gz, or newer, file from
Caltech (http://astro.caltech.edu/~tjp/pgplot/) or a local repository)
or the newer command in a current NEMO:
mknemo pgplot
On some older linux systems may need to create the following symbolic link
ln -s /usr/X11R6 /usr/X11
a3) Installing PGPLOT - MIRIAD pgplot git release
You can also place the pgplot source code in $NEMO/local (the default git install
uses this method), and use something like
make pgplot png=1 gif=1
a4) Install PGPLOT (giza github installation) -
The giza package is now primarily maintained on the developer's github account
(https://github.com/danieljprice/giza). The giza implementation of PGPLOT can be installed
by adding an extra parameter to the ./install_nemo script: "./install_nemo giza=1"
It can also be cloned from price's repository using git clone https://github.com/danieljprice/giza.git.
Then it can be installed using the same instructions as the sourceforge download. Here is an example
git clone https://github.com/danieljprice/giza.git
cd giza
./configure --prefix=$NEMO
make
make install
(OLD) Install PGPLOT (giza sourceforge) -
The giza package (http://giza.sourceforge.net) has its own implementation of PGPLOT,
which is compatible with cairo. Here is an example that seems to work with NEMO
cd $NEMO/local
svn co http://svn.code.sf.net/p/giza/code/ giza
cd giza
./configure --prefix=$NEMO
make
make install
After this you can use the regular
cd $NEMO
configure --with-yapp=pgplot --with-pgplot-prefix=$NEMO/lib
My experience with this version of pgplot is not ideal yet.
b1) Installing HDF4
Preferred command: mknemo hdf4
You only need the HDF library if you plan to work with the ZEUS or CMHOG
hydrocodes.
This requires:
libdf.a
libz.a (often comes with the system)
df.h -- and many others belonging to HDF4
A newer version of HDF (HDF5) is also supported, they used hdf5.h, see below.
The install package for hdf4 can be found at https://support.hdfgroup.org/products/hdf4/.
You will need to extract the package. The next command assumes you are already in HDF4 directory
One way to install this package is
configure --prefix=$NEMO
make
make install
examples:
https://support.hdfgroup.org/ftp/HDF/releases/HDF4.2.14/src/CMake-hdf-4.2.14.tar.gz
https://support.hdfgroup.org/ftp/HDF/releases/HDF4.2.14/src/hdf-4.2.14.tar.gz
b2) Installing HDF5
Preferred command: mknemo hdf5
https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6.tar.gz
This version of HDF may either be installed via the system, or in $NEMO/opt.
c) Installing CFITSIO (pending work on configure.in)
NEMO has two internal routines (fits.c and fitsio.c) that handle various
types of fits I/O. Optionally the CFITSIO library can also be used, e.g.
fitsio_nemo.c implements the fitsio.c file by providing a wrapper
that actually calls the CFITSIO library (courtesy Bill Pence)
wget ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/cfitsio3390.tar.gz
(see https://heasarc.gsfc.nasa.gov/fitsio/fitsio.html)
One way is to embed it into NEMO, so when you configure cfitsio
configure --prefix=$NEMO
make
make install
If your system has FTOOLS installed, possibly via the LHEASOFT package,
you can use their prefix, e.g.
configure --with-cfitsio-prefix=/opt/lheasoft/SunOS_5.6_sparc
d) If you are on a system where you need to install NEMO and other packages,
but don't have root access to places like /usr/local,
but plenty of disk-space, you can also host these packages inside of NEMO.
For this a directory $NEMO/opt has also been created during the installation
process,
Under $NEMO/opt you will then find the usual /usr/local hierarchy:
bin
include
info
lib
man
share
Packages that NEMO can use can then be installed under this hierarchy
easiest with the "mknemo" command:
gsl configure --prefix=$NEMO
cfitsio configure --prefix=$NEMO
plplot
netcdf4
NEMO can then use these packages as follows:
configure --with-gsl-prefix=$NEMO/opt
configure --enable-gsl
configure --disable-gsl (the default)
Peer Installations
==================
Here is a list of peer (astronomy) packages install instructions that could
well be useful in case of issues with the instructions listed above:
* cloudy: https://gitlab.nublado.org/cloudy/cloudy/-/wikis/CompilingCloudyNext
Some old notes
==============
*) pieces of configure out of date? Encountering a new machine?
1) you can update the config.guess and config.sub
wget ftp://ftp.gnu.org/pub/gnu/config/config.guess
wget ftp://ftp.gnu.org/pub/gnu/config/config.sub
chmod a+x config.guess config.sub
2) regenerate configure from configure.in
autoconf
3) replace some *.m4 files
4) replace aclocal.m4: aclocal
*) Configuration options known to work:
--with-pgplot-prefix=$NEMOLIB
expects grfont.dat and friends to be in the named directory
($NEMO/src/scripts/pgplot.install will help you
installing pgplot in $NEMOLIB if you need)
--with-hdf-prefix=PFX
expects hdf.h to be found somewhere in an {include,hdf}
subdirectory and will link with 'df', 'jpeg' and 'z' library.
Doesn't work with HDF5 yet, assumes HDF4 for ow.
--with-miriad-prefix=PFX
if $MIR is present, it will use this variable, else you need
to set it.
--disable-fortran
if you don't have a working fortran compiler (actually doesn't work)
--with-ccmalloc
use CCMALLOC to debug malloc usage
--with-yapp=ps
use a PS based yapp, on systems where you cannot get pgplot to work,
or really don't have a working fortran compiler
--with-cfitsio-prefix=PFX
--disable-cfitsio explicitly disable it
--enable-cfitsio explicitly enable it (the default)
--with-gsl-prefix=PFX
--enable-gsl
--disable-gsl (the default)