diff --git a/doc/binary_c-installation.lyx b/doc/binary_c-installation.lyx
deleted file mode 100644
index b4259364795d8d45a549bba1b306305e6195dabf..0000000000000000000000000000000000000000
--- a/doc/binary_c-installation.lyx
+++ /dev/null
@@ -1,3431 +0,0 @@
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-\def\nat{Nature} % Nature
-\def\aplett{Astrophys.~Lett.} % Astrophysics Letters
-\def\physrep{Phys.~Rep.} % Physics Reports%
-\def\na{NewA} % new astronomy%
-
-\usepackage{natbibspacing}
-\setlength{\bibspacing}{0mm}
-
-% header
-\usepackage{fancyhdr}
-\pagestyle{fancy}
-\renewcommand{\headrulewidth}{0pt}
-\fancyhead[LE,RO]{\color{Sectioncolour}\normalfont\itshape\bfseries{}} % page number in "outer" position of footer line
-\fancyhead[RE,LO]{\color{Sectioncolour}\rightmark} % other info in "inner" position of footer line
-
-\raggedbottom
-\end_preamble
-\use_default_options true
-\maintain_unincluded_children false
-\language british
-\language_package default
-\inputencoding auto
-\fontencoding global
-\font_roman "utopia" "default"
-\font_sans "default" "default"
-\font_typewriter "default" "default"
-\font_math "auto" "auto"
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-\use_geometry true
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-\use_package mathdots 1
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-\use_package stmaryrd 1
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-\cite_engine natbib
-\cite_engine_type authoryear
-\biblio_style plainnat
-\use_bibtopic false
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-\suppress_date false
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-\use_refstyle 1
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-\html_be_strict false
-\end_header
-
-\begin_body
-
-\begin_layout Title
-This document is deprecated.
- Please see binary_c2.lyx/pdf instead.
-\end_layout
-
-\begin_layout Standard
-\begin_inset CommandInset line
-LatexCommand rule
-offset "0.5ex"
-width "100col%"
-height "1pt"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Title
-
-\series bold
-Installation guide for
-\family typewriter
-binary_c
-\family default
- and
-\family typewriter
-binary_grid2
-\end_layout
-
-\begin_layout Standard
-\align center
-
-\series bold
-A guide to the installation of
-\emph on
-binary_c
-\emph default
- and
-\emph on
-binary_grid2
-\end_layout
-
-\begin_layout Standard
-\align center
-
-\series bold
-Version 2.1.4+
-\begin_inset Newline newline
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-\align center
-
-\series bold
-Warning: Version 2 of the combined
-\emph on
-binary_c
-\emph default
- and
-\emph on
-binary_grid2
-\emph default
- is currently under development.
- Details are likely to change.
-
-\end_layout
-
-\begin_layout Standard
-\align center
-Please see also other documentation, e.g.
-
-\end_layout
-
-\begin_layout Description
-binary_cV2 for information about changes in
-\emph on
-binary_c
-\emph default
- V2.0+.
-\end_layout
-
-\begin_layout Description
-binary_grid2 for population grid instructions.
-\end_layout
-
-\begin_layout Description
-getting_binary_c for instructions about how to obtain
-\emph on
-binary_c
-\emph default
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Newpage pagebreak
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-System Requirements
-\end_layout
-
-\begin_layout Standard
-\begin_inset CommandInset label
-LatexCommand label
-name "subsec:Requirements"
-
-\end_inset
-
-The following software is required on your system:
-\end_layout
-
-\begin_layout Itemize
-A
-\emph on
-C
-\emph default
- compiler.
- Binary_c has been tested on
-\emph on
-gcc
-\emph default
- and
-\emph on
-clang
-\emph default
-.
- Other options are available, but probably will not work.
-\begin_inset Separator latexpar
-\end_inset
-
-
-\end_layout
-
-\begin_deeper
-\begin_layout Itemize
-
-\emph on
-gcc
-\emph default
- (GNU compiler
-\begin_inset Flex URL
-status collapsed
-
-\begin_layout Plain Layout
-
-http://gcc.gnu.org/
-\end_layout
-
-\end_inset
-
-) this comes as standard on most Linux systems and is easily installed on
- others.
-
-\emph on
-gcc
-\emph default
-is free.
-\end_layout
-
-\begin_layout Itemize
-
-\emph on
-clang
-\emph default
- (
-\emph on
-C
-\emph default
- compiler for LLVM
-\begin_inset CommandInset href
-LatexCommand href
-target "http://clang.llvm.org/"
-literal "false"
-
-\end_inset
-
-) is also free, and may be faster than
-\emph on
-gcc
-\emph default
-.
-\end_layout
-
-\begin_layout Itemize
-
-\emph on
-icc
-\emph default
- (Intel compiler
-\begin_inset Flex URL
-status collapsed
-
-\begin_layout Plain Layout
-
-http://software.intel.com/en-us/articles/intel-compilers/
-\end_layout
-
-\end_inset
-
-) this costs money and
-\emph on
-binary_c
-\emph default
- has not been tested with it recently.
-\end_layout
-
-\begin_layout Standard
-Your system should include such a compiler unless you're using Windows.
-
-\emph on
-Binary_c
-\emph default
- has been tested on Linux and various Solaris machines.
- Note that (for an unknown reason!) it does not run (but does compile) on
- old versions of MacOS X.
- If you can fix this problem please let me know! Also, there has been trouble
- with
-\emph on
-gcc
-\emph default
-on Xeon machines.
- This is not my fault, please use
-\emph on
-icc
-\emph default
-.
-\begin_inset Foot
-status collapsed
-
-\begin_layout Plain Layout
-This information may be out of date! Please test the build and let me know.
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\end_deeper
-\begin_layout Itemize
-
-\emph on
-Python3
-\emph default
-,
-\emph on
-Meson
-\emph default
- and
-\emph on
-Ninja
-\emph default
- are required for installation.
- You can install all of these on your system, e.g.
- with the following on
-\emph on
-Ubuntu 18.04
-\emph default
-,
-\begin_inset listings
-inline false
-status open
-
-\begin_layout Plain Layout
-
-sudo apt-get install python3 meson ninja-build
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\emph on
-Perl
-\emph default
- - this is required for
-\emph on
-binary_grid2
-\emph default
-.
- Perl is usually installed on your system, and for configuration of
-\emph on
-binary_c
-\emph default
- this should be sufficient.
- You can download Perl at
-\begin_inset Flex URL
-status collapsed
-
-\begin_layout Plain Layout
-
-www.perl.com
-\end_layout
-
-\end_inset
-
-, or use your system Perl, but I recommend
-\emph on
-Perlbrew
-\emph default
- instead.
- Please try to use a version of Perl that is 5.16 or later: 5.25 is currently
- the standard.
-\end_layout
-
-\begin_layout Itemize
-
-\emph on
-Perlbrew
-\emph default
- and
-\emph on
-cpanm
-\emph default
- are
-\emph on
-essential
-\emph default
-if you want to use
-\series bold
-\emph on
-binary_grid2
-\series default
-\emph default
-.
- These are standard tools.
- I recommend downloading them on a per-user basis, but they could also be
- installed as part of your system.
-\end_layout
-
-\begin_layout Itemize
-You will want to use
-\emph on
-git
-\emph default
- to get
-\emph on
-binary_c
-\emph default
-, see the document
-\series bold
-\emph on
-getting_binary_c.pdf
-\end_layout
-
-\begin_layout Itemize
-Probably you want a debugger, e.g.
-
-\emph on
-gdb
-\emph default
-, to be installed, if you plan to modify (and hence break)
-\emph on
-binary_c
-\emph default
-.
- You may also want
-\emph on
-valgrind
-\emph default
- which is superior in many ways to
-\emph on
-gdb
-\emph default
-.
-\end_layout
-
-\begin_layout Itemize
-The
-\emph on
-GNU Scientific Library
-\emph default
- version 2.4 is required.
- You may be able to install this as a system package, or you can get it
- from
-\begin_inset Flex URL
-status collapsed
-
-\begin_layout Plain Layout
-
-https://www.gnu.org/software/gsl/
-\end_layout
-
-\end_inset
-
-.
- I have a modified version at
-\begin_inset Flex URL
-status collapsed
-
-\begin_layout Plain Layout
-
-https://gitlab.eps.surrey.ac.uk/ri0005/GSL-2.4-RGI
-\end_layout
-
-\end_inset
-
- which has minor fixes: please use this if you can.
-\end_layout
-
-\begin_layout Itemize
-
-\emph on
-libbsd
-\emph default
- is recommended.
- Please install the libbsd-devel package also.
- You can also install from the source available at
-\begin_inset Flex URL
-status collapsed
-
-\begin_layout Plain Layout
-
-https://libbsd.freedesktop.org/wiki/
-\end_layout
-
-\end_inset
-
-.
-\end_layout
-
-\begin_layout Itemize
-
-\emph on
-libbacktrace
-\emph default
- is recommended.
- See
-\begin_inset Flex URL
-status open
-
-\begin_layout Plain Layout
-
-https://github.com/ianlancetaylor/libbacktrace
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Itemize
-
-\emph on
-libbfd
-\emph default
- is recommended.
- This is part of the Linux
-\emph on
-binutils
-\emph default
- package.
-\end_layout
-
-\begin_layout Itemize
-
-\emph on
-libmemoize
-\emph default
- can be downloaded from
-\begin_inset Flex URL
-status open
-
-\begin_layout Plain Layout
-
-https://gitlab.eps.surrey.ac.uk/ri0005/libmemoize
-\end_layout
-
-\end_inset
-
- but a version is included in
-\emph on
-binary_c
-\emph default
-if you do not have it.
-\end_layout
-
-\begin_layout Itemize
-
-\emph on
-librinterpolate
-\emph default
- can be downloaded from
-\begin_inset Flex URL
-status open
-
-\begin_layout Plain Layout
-
-https://gitlab.eps.surrey.ac.uk/ri0005/librinterpolate
-\end_layout
-
-\end_inset
-
- but a version is included in
-\emph on
-binary_c
-\emph default
-if you do not have it.
-\end_layout
-
-\begin_layout Standard
-By using
-\emph on
-binary_c
-\emph default
- and
-\emph on
-binary_grid2
-\emph default
- you are part of a community.
- You are therefore jointly responsible for helping with the never-ending
- process of improvement and bug fixing.
-
-\emph on
- Binary_c
-\emph default
- (and its
-\emph on
-Perl
-\emph default
-modules, such as
-\emph on
-binary_grid
-\emph default
-2) is stored on an
-\emph on
-git
-\emph default
- server.
- Please read the
-\series bold
-\emph on
-LICENCE
-\series default
-\emph default
- file before use.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Newpage pagebreak
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-binary_c
-\end_layout
-
-\begin_layout Standard
-\begin_inset CommandInset label
-LatexCommand label
-name "sec:binary-c"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsubsection
-Getting binary_c
-\end_layout
-
-\begin_layout Itemize
-You should obtain
-\emph on
-binary_c
-\emph default
- from the
-\emph on
-git
-\emph default
- server, currently at
-\begin_inset Flex URL
-status open
-
-\begin_layout Plain Layout
-
-https://gitlab.eps.surrey.ac.uk/ri0005/binary_c
-\end_layout
-
-\end_inset
-
-.
- Please see the document
-\emph on
-getting_binary_c
-\emph default
- (available in
-\emph on
-pdf
-\emph default
- and
-\emph on
-lyx
-\emph default
- formats).
-
-\end_layout
-
-\begin_layout Itemize
-You should consider joining the mailing lists.
-\end_layout
-
-\begin_layout Subsubsection
-Building
-\end_layout
-
-\begin_layout Standard
-\begin_inset CommandInset label
-LatexCommand label
-name "subsec:Building"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsubsection
-From git
-\end_layout
-
-\begin_layout Standard
-Assuming you have checked out your branch, or the trunk, from the
-\emph on
-git
-\emph default
- repository (see section
-\begin_inset space ~
-\end_inset
-
-
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "sec:SVN-access"
-
-\end_inset
-
-), go to that directory (which will be called the
-\family typewriter
-binary_c
-\family default
- directory below).
-\end_layout
-
-\begin_layout Subsubsection
-From a zip file or tarball
-\end_layout
-
-\begin_layout Standard
-If have been given a file zip file
-\family typewriter
-binary_c.zip,
-\family default
- or a tarball e.g.
-
-\family typewriter
- binary_c.tar.gz
-\family default
- or
-\family typewriter
-binary_c.tar.bz2,
-\family default
- you should copy it to a directory (hereafter
-\family typewriter
-binary_c
-\family default
-, usually I put everything in
-\family typewriter
-
-\begin_inset Formula $\sim$
-\end_inset
-
-/progs/stars/binary_c
-\family default
- where
-\begin_inset Formula $\sim$
-\end_inset
-
- is your home directory – if you put it there then all the scripts will
- work) and
-\emph on
-unzip
-\emph default
- it with one of the following commands (depending on the file you were given):
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-unzip binary_c.zip
-\family default
-
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-tar -xvzf binary_c.tar.gz
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-tar -xvjf binary_c.tar.bz2
-\end_layout
-
-\begin_layout Standard
-which will unzip the files in the appropriate places.
-\end_layout
-
-\begin_layout Subsubsection
-Build with meson
-\end_layout
-
-\begin_layout Standard
-From inside
-\end_layout
-
-\begin_layout Standard
-Now, from the
-\family typewriter
-binary_c
-\family default
- directory, you need to run the configuration script with
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-./configure
-\end_layout
-
-\begin_layout Standard
-which creates the
-\family typewriter
-Makefile
-\family default
-.
- Now type
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-./make
-\end_layout
-
-\begin_layout Standard
-to build the code.
- The make script is a wrapper around GNU make that executes the build on
- as many CPUs as you have, and pretties up the output so that it is more
- readable..
-\begin_inset Newline newline
-\end_inset
-
-Note that you may need to use
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-gmake
-\end_layout
-
-\begin_layout Standard
-from the
-\family typewriter
-src
-\family default
- directory if
-\emph on
-GNU
-\emph default
- make is not your default (e.g.
- you are on something like Solaris).
-
-\begin_inset Newline newline
-\end_inset
-
-The code will now build, assuming
-\family typewriter
-configure
-\family default
- worked ok.
- If configure does
-\emph on
-not
-\emph default
- work then please try to fix it before running to me with complaints.
- It works on Linux and will revert to
-\family typewriter
-gcc
-\family default
- as the default compiler if something goes wrong - it
-\emph on
-might
-\emph default
- detect
-\family typewriter
-icc
-\family default
- if it's on your system.
- It is up to you to make your compiler work properly!
-\end_layout
-
-\begin_layout Standard
-The executable is called
-\family typewriter
-binary_c.
-\end_layout
-
-\begin_layout Standard
-Note:
-\family typewriter
-binary_c
-\family default
- is built as a single, possibly
-\emph on
-large
-\emph default
- (many MB) executable.
- The reason for this is purely ease of use when transferring the executable
- from one machine to another.
- It is possible to build a shared library instead.
-\end_layout
-
-\begin_layout Subsubsection
-Building the shared library
-\end_layout
-
-\begin_layout Standard
-To build the shared library, run
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-./configure
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-make libbinary_c.so
-\end_layout
-
-\begin_layout Standard
-This makes the
-\family typewriter
-libbinary_c.so
-\family default
- shared library which can be used, for example, by the
-\emph on
-C
-\emph default
- backend to
-\emph on
-binary_grid
-\emph default
-2, or to access
-\emph on
-binary_c
-\emph default
- through its
-\emph on
-API
-\emph default
-.
-\end_layout
-
-\begin_layout Subsubsection
-Alternative compiler
-\end_layout
-
-\begin_layout Standard
-You can build with another compiler, e.g.
-
-\emph on
-clang
-\emph default
-, by doing
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-export CC=clang
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-./configure
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-./make
-\end_layout
-
-\begin_layout Subsubsection
-Debugging build
-\end_layout
-
-\begin_layout Standard
-To enable full debugging, run
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-./configure debug
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-./make
-\end_layout
-
-\begin_layout Subsubsection
-Testing binary_c
-\end_layout
-
-\begin_layout Standard
-Run the
-\emph on
-bash
-\emph default
- script to
-\begin_inset Quotes eld
-\end_inset
-
-test binary star evolution
-\begin_inset Quotes erd
-\end_inset
-
- called
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-tbse
-\family default
-\series default
-
-\begin_inset Newline newline
-\end_inset
-
-You should see output.
-
-\begin_inset Newline newline
-\end_inset
-
-You may have to symbolically link src/binary_c to binary_c in the directory
- to make this work, e.g.
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-cd
-\emph on
-<binary_c_directory>
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-ln -s src/binary_c
-\end_layout
-
-\begin_layout Subsubsection
-tbse commands
-\end_layout
-
-\begin_layout Standard
-
-\emph on
-tbse
-\emph default
-can take extra arguments, which are usually passed to
-\emph on
-binary_c
-\emph default
- directly.
-\end_layout
-
-\begin_layout Standard
-There are also many commands which can be given to
-\emph on
-tbse
-\emph default
-, e.g.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-echo This outputs (to
-\emph on
-stdout
-\emph default
-) the arguments that would have been sent to
-\emph on
-binary_c
-\emph default
-.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-args Ignores settings in the
-\emph on
-tbse
-\emph default
-file and runs only with the extra arguments given on the command line.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-debug This runs
-\emph on
-binary_c
-\emph default
-with the gdb debugger
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-valgrind This runs
-\emph on
-binary_c
-\emph default
- through
-\emph on
-Valgrind
-\emph default
-'s
-\emph on
-memcheck
-\emph default
- tool to detect memory leaks.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-massif This runs
-\emph on
-binary_c
-\emph default
- through
-\emph on
-Valgrind
-\emph default
-'s
-\emph on
-massif
-\emph default
- heap checker.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-callgrind This runs
-\emph on
-binary_c
-\emph default
- through
-\emph on
-Valgrind
-\emph default
-'s
-\emph on
-callgrind
-\emph default
-tool.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-cachegrind This runs
-\emph on
-binary_c
-\emph default
- through
-\emph on
-Valgrind
-\emph default
-'s
-\emph on
-cachegrind
-\emph default
- tool.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-ptrcheck This runs
-\emph on
- binary_c
-\emph default
- through
-\emph on
-Valgrind
-\emph default
-'s
-\emph on
-ptrcheck
-\emph default
- tool.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-sgcheck This runs
-\emph on
- binary_c
-\emph default
- through
-\emph on
-Valgrind
-\emph default
-'s
-\emph on
-sgcheck
-\emph default
- tool.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-drd This runs
-\emph on
- binary_c
-\emph default
- through
-\emph on
-Valgrind
-\emph default
-'s
-\emph on
-drd
-\emph default
- tool.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-gprof This runs
-\emph on
-binary_c
-\emph default
- through
-\emph on
-gprof
-\emph default
-, the
-\emph on
-GNU
-\emph default
- profiler.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-gprof_lines This runs
-\emph on
-binary_c
-\emph default
- through
-\emph on
-gprof
-\emph default
-, the
-\emph on
-GNU
-\emph default
- profiler, doing line-by-line accounting.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-gprof_with_stdout This runs
-\emph on
-binary_c
-\emph default
- through
-\emph on
-gprof
-\emph default
-, the
-\emph on
-GNU
-\emph default
- profiler, showing
-\emph on
-stdout
-\emph default
-.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-pgo Profile guided optimization.
- This builds
-\emph on
-binary_c
-\emph default
- once, runs a number of systems, then rebuilds with extra optimization based
- on the profile generated by the runs.
- This works for
-\emph on
-GCC
-\emph default
- and probably also
-\emph on
-clang
-\emph default
-.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-bug This runs
-\emph on
-binary_c
-\emph default
- and outputs information which is suitable for reporting a bug to Rob.
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-multicore This runs
-\emph on
-binary_c
-\emph default
- on many CPU cores at once.
- Exits immediately on failure, so this is useful for testing e.g.
- Monte carlo kicks.
-
-\end_layout
-
-\begin_layout Description
-tbse
-\begin_inset space ~
-\end_inset
-
-
-\emph on
-<filename>
-\emph default
- This runs the set of arguments specified in the file given by
-\emph on
-filename
-\emph default
-.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Newpage pagebreak
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsubsection
-binary_grid2
-\end_layout
-
-\begin_layout Standard
-This section describes in some detail the installation of
-\emph on
-binary_grid2
-\emph default
-.
- Note that sometimes you will require the latest version of pieces of software,
- in particular
-\emph on
-Perl
-\emph default
- which should be at least version 5.16.
- I show you how to do this
-\emph on
-without
-\emph default
- requiring root permissions on your machine.
- Should you require packages to be installed that require root permission,
- you can always set up
-\emph on
-binary_c
-\emph default
- and
-\emph on
-binary_grid2
-\emph default
- on a
-\emph on
-virtual machine
-\emph default
- which runs as a guest on your operating system, I do this with
-\emph on
-Virtualbox
-\emph default
- (
-\begin_inset CommandInset href
-LatexCommand href
-target "https://www.virtualbox.org/"
-literal "false"
-
-\end_inset
-
-).
- This would be my advice if you are running on a non-standard operating
- system, e.g.
-
-\emph on
-Micro$oft Windows
-\emph default
-.
- You will have the root password for your virtual machine, so there are
- never permissions problems.
-\end_layout
-
-\begin_layout Standard
-You will need some basic tools installed to make everything work:
-\emph on
-bash
-\emph default
-,
-\emph on
-subversion
-\emph default
-,
-\emph on
-perl
-\emph default
-,
-\emph on
-gmake
-\emph default
-,
-\emph on
-wget
-\emph default
-,
-\emph on
-gcc
-\emph default
-.
- These are available on all good operating systems, and come by default
- – or after a simple install – with most flavours of Linux/Unix and MacOSX.
-\end_layout
-
-\begin_layout Standard
-Some
-\emph on
-Perl
-\emph default
-modules also require some other system libraries and development files.
- It is difficult to know exactly what these would be for every operating
- system.
- You may have to use a web search to find out, but that's fine because you
- are smart!
-\end_layout
-
-\begin_layout Paragraph
-Latest
-\emph on
-Perl
-\emph default
-: use
-\emph on
-perlbrew
-\end_layout
-
-\begin_layout Standard
-I highly recommend that you install the latest version of
-\emph on
-Perl
-\emph default
-using
-\series bold
-\emph on
-perlbrew
-\series default
-\emph default
- and install modules using
-\series bold
-\emph on
-cpanm
-\series default
-.
-
-\emph default
- I describe how to do this below, but also please see
-\begin_inset CommandInset href
-LatexCommand href
-target "http://perlbrew.pl/"
-literal "false"
-
-\end_inset
-
- and
-\begin_inset CommandInset href
-LatexCommand href
-target "http://perlbrew.pl/Perlbrew-and-Friends.html "
-literal "false"
-
-\end_inset
-
-for further instructions and documentation.
-\end_layout
-
-\begin_layout Paragraph
-Installing
-\emph on
-binary_c
-\end_layout
-
-\begin_layout Standard
-Please see Sec.
-\begin_inset space ~
-\end_inset
-
-
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "sec:binary-c"
-
-\end_inset
-
- above for details about how to install
-\emph on
-binary_c
-\emph default
-.
-
-\end_layout
-
-\begin_layout Paragraph
-Installing
-\emph on
-binary_grid2
-\end_layout
-
-\begin_layout Standard
-\begin_inset CommandInset label
-LatexCommand label
-name "subsec:installing binary_grid"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
-
-\emph on
-binary_grid2
-\emph default
- is written in
-\emph on
-Perl
-\emph default
- (
-\begin_inset CommandInset href
-LatexCommand href
-target "http://www.perl.org/"
-literal "false"
-
-\end_inset
-
-) which is available on almost every modern operating system, although to
- my knowledge
-\emph on
-binary_grid2
-\emph default
- has never been tested on anything other than
-\emph on
-Linux
-\emph default
- (
-\begin_inset CommandInset href
-LatexCommand href
-target "http://www.linux.org/"
-literal "false"
-
-\end_inset
-
-),
-\emph on
-Solaris
-\emph default
- and
-\emph on
-MacOSX
-\emph default
- (which is [currently] really
-\emph on
- BSD Unix
-\emph default
-).
-\end_layout
-
-\begin_layout Standard
-The newest
-\emph on
-binary_grid2
-\emph default
- uses features from the latest
-\emph on
-Perl
-\emph default
- (5.16 or above, currently testing on 5.25) so you'll need a recent
-\emph on
-Perl
-\emph default
- to be installed.
- Unfortunately most versions of
-\emph on
-Linux
-\emph default
- run an older
-\emph on
-Perl
-\emph default
- without support for many of the required features.
- You will also need to have the latest versions of a number of
-\emph on
-Perl
-\emph default
- modules which come from either from the online resource
-\emph on
-CPAN
-\emph default
-
-\begin_inset Foot
-status open
-
-\begin_layout Plain Layout
-
-\emph on
-Comprehensive Perl Archive Network
-\end_layout
-
-\end_inset
-
- (
-\begin_inset CommandInset href
-LatexCommand href
-target "http://www.cpan.org/"
-literal "false"
-
-\end_inset
-
-) or as part of the
-\emph on
-binary_c
-\emph default
- package.
-\end_layout
-
-\begin_layout Standard
-My recommendation is to use
-\series bold
-\emph on
-perlbrew
-\series default
-
-\emph default
-to make your own
-\emph on
-Perl
-\emph default
- and
-\emph on
-cpanminus
-\emph default
- (the command is
-\family typewriter
-cpanm
-\family default
-) to install the modules.
-
-\end_layout
-
-\begin_layout Standard
-You can find
-\emph on
-perlbrew
-\emph default
- at
-\begin_inset CommandInset href
-LatexCommand href
-target "http://perlbrew.pl/"
-literal "false"
-
-\end_inset
-
- : please follow the instructions on that page to install the latest
-\emph on
-Perl
-\emph default
- on your system if you do not trust my instructions below.
- Typically do the following, but remember you
-\emph on
-must
-\emph default
- install
-\emph on
-perlbrew
-\emph default
- with
-\begin_inset Quotes eld
-\end_inset
-
-
-\family typewriter
--Dusethreads
-\family default
-
-\begin_inset Quotes erd
-\end_inset
-
- otherwise
-\emph on
-Perl
-\emph default
- will not use threads and you will lose the multi-CPU features of
-\emph on
-binary_grid
-\emph default
-2.
- Please note that I assume you are using the
-\emph on
-bash
-\emph default
- shell.
-\end_layout
-
-\begin_layout Enumerate
-
-\family typewriter
-\series bold
-wget --no-check-certificate -O - http://install.perlbrew.pl | bash
-\begin_inset Newline newline
-\end_inset
-
-
-\family default
-\series default
-\emph on
-or
-\emph default
-
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
-\series bold
-curl -kL http://install.perlbrew.pl | bash
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\family default
-\series default
-If you have problems with
-\series bold
-\emph on
-wget
-\series default
-\emph default
-, try removing the
-\series bold
-\emph on
-–no-check-certificate
-\series default
-\emph default
-.
-\end_layout
-
-\begin_layout Enumerate
-Run
-\family typewriter
-perlbrew available
-\family default
- to find a list of available versions, you should choose the newest, e.g.
-
-\family typewriter
-perl-5.25
-\family default
-, and then run the following command to install
-\emph on
-Perl
-\emph default
-:
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
-
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Box Frameless
-position "t"
-hor_pos "c"
-has_inner_box 1
-inner_pos "t"
-use_parbox 0
-use_makebox 0
-width "95col%"
-special "none"
-height "1in"
-height_special "totalheight"
-thickness "0.4pt"
-separation "3pt"
-shadowsize "4pt"
-framecolor "black"
-backgroundcolor "none"
-status open
-
-\begin_layout Plain Layout
-
-\family typewriter
-\series bold
-perlbrew -v install perl-5.25 --thread --multi --64bitall --notest -Dusethreads
- -Duselargefiles -Dcccdlflags=-fPIC -Dpager=/usr/bin/sensible-pager -Doptimize="
--O3 -march=native -mtune=native" -Duseshrplib -j 8
-\end_layout
-
-\end_inset
-
-
-\family default
-
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-You can use
-\family typewriter
-\series bold
--march=native -mtune=native
-\family default
-\series default
- if you are quite sure you will not use this version of
-\emph on
-Perl
-\emph default
-, or its modules, on a machine with a different architecture.
- If you are building for use with an
-\emph on
-HTCondor
-\emph default
- grid, I highly recommend using the
-\family typewriter
-generic
-\family default
- option and this is now the default.
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-Note that the final
-\emph on
-8
-\emph default
- should be replaced by the number of CPUs you wish to use for the build
- (it is an option passed to
-\emph on
-make
-\emph default
-).
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-Note also that
-\family typewriter
--Duseshrplib
-\family default
- may no longer be required.
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-I have recently added
-\family typewriter
---thread –-multi –-64bitall
-\family default
- so if you have trouble, please remove these and try again.
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-In
-\emph on
-Perl
-\emph default
- 5.25.5 there is a (known) bug in the test routines which may (or may not)
- stop your installation.
- For this reason the
-\family typewriter
---notest
-\family default
- flag if set.
- Remove this if you want testing back (beware it is slow).
-\series bold
-
-\begin_inset Newline newline
-\end_inset
-
-
-\series default
-
-\begin_inset Newline newline
-\end_inset
-
-The installation process can take a long time, go and have lunch\SpecialChar ldots
- then:
-\end_layout
-
-\begin_layout Enumerate
-Do what
-\emph on
-perlbrew
-\emph default
- suggests with your
-\family typewriter
-.bashrc
-\family default
- (or whatever shell initialization script you use) to fix the
-\family typewriter
-PERLBREW_PATH
-\family default
-.
-\end_layout
-
-\begin_layout Enumerate
-Restart your shell (e.g.
- close your terminal and open a new one, or just run
-\family typewriter
-bash
-\family default
- again) to update your environment and
-\family typewriter
-$PATH
-\family default
-.
-\end_layout
-
-\begin_layout Enumerate
-Check you're using the correct
-\emph on
-Perl
-\emph default
- with
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
-\series bold
-perl -v
-\family default
-\series default
-
-\begin_inset Newline newline
-\end_inset
-
-This should say something like
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
-\size small
-This is perl 5, version 25, subversion 0 (v5.25.0) built for x86_64-linux-thread-m
-ulti
-\size default
-
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\family default
-Check that the
-\family typewriter
--thread-
-\family default
- is there – without threads,
-\emph on
-binary_grid2
-\emph default
- multi-CPU options will not function.
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-If you have a previous version of
-\emph on
-Perl
-\emph default
- installed by
-\emph on
-perlbrew
-\emph default
-, you will have to do something like
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
-\series bold
-perlbrew switch perl-5.25
-\end_layout
-
-\begin_layout Enumerate
-If the installation was successful, but you see an older
-\emph on
-Perl
-\emph default
-, check that your
-\family typewriter
-$PATH
-\family default
- variable points to the new
-\emph on
-Perl
-\emph default
-, and check that
-\family typewriter
-$PERLBREW_PATH
-\family default
- exists.
-\end_layout
-
-\begin_layout Enumerate
-Install
-\emph on
-cpanminus
-\emph default
- by running
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
-\series bold
-perlbrew install-cpanm
-\end_layout
-
-\begin_layout Standard
-Now you have the latest
-\emph on
-Perl
-\emph default
- and
-\emph on
-cpanm
-\emph default
- installed, you can start to install the modules needed for
-\emph on
-binary_grid
-\emph default
-2.
- (Un?)fortunately, there are many of them, so I have made a script to do
- it for you
-\end_layout
-
-\begin_layout Enumerate
-From the
-\emph on
-binary_c
-\emph default
- directory, go to
-\family typewriter
-src/perl
-\family default
- with
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
-\series bold
-cd src/perl
-\end_layout
-
-\begin_layout Enumerate
-Run the install script which uses
-\emph on
-cpanminus
-\emph default
- to install the modules
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
-\series bold
-./install_modules.pl
-\end_layout
-
-\begin_layout Enumerate
-Wait.
- Watch the output flow past your eyes.
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-Note that you can
-\emph on
-also
-\emph default
- install the modules yourself from their tarballs in
-\family typewriter
-src/perl/modules_targz
-\family default
-., e.g.
-
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
-\series bold
-cd src/perl/modules_targz
-\begin_inset Newline newline
-\end_inset
-
-cpanm ./<modname>.tar.gz
-\begin_inset Newline newline
-\end_inset
-
-
-\family default
-\series default
-but please note the
-\family typewriter
-\series bold
-./
-\family default
-\series default
- in the filename is
-\emph on
-required
-\emph default
-.
-\end_layout
-
-\begin_layout Enumerate
-In case of errors, try installing the module with verbose logging switched
- on
-\family typewriter
-\series bold
-
-\begin_inset Newline newline
-\end_inset
-
-cpanm -v ./<modname>.tar.gz
-\end_layout
-
-\begin_layout Enumerate
-Check the output.
- If there is a failure, it should say.
- You will have to fix it by looking at the output to see where it went wrong.
- The most common cause of failure is that you need some kind of development
- (
-\emph on
--dev
-\emph default
- or
-\emph on
--devel
-\emph default
-) packages to be installed on your system, e.g.
- through
-\emph on
-apt
-\emph default
-,
-\emph on
-yum
-\emph default
- or
-\emph on
-synaptic
-\emph default
- or the system package manager.
- This may require root permission.
-\begin_inset Newline newline
-\end_inset
-
-If all else fails, you can ask Rob for help.
-\end_layout
-
-\begin_layout Enumerate
-Your installed modules are usually in (for
-\emph on
-Perl
-\emph default
- 5.25)
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
- $HOME/perl5/perlbrew/perls/5.25.0/lib/site_perl/5.25.
-\family default
-0
-\begin_inset Newline newline
-\end_inset
-
-You should not have to set the
-\emph on
-PERL5LIB
-\emph default
- environment variable when installing with a modern cpanminus.
-\begin_inset Newline newline
-\end_inset
-
-If you
-\emph on
-do
-\emph default
- have trouble, try
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
-\series bold
-export PERL5LIB=$HOME/perl5/perlbrew/perls/5.25.0/lib/site_perl/5.25.0
-\family default
-\series default
-
-\begin_inset Newline newline
-\end_inset
-
-(or similar).
-
-\end_layout
-
-\begin_layout Standard
-Now you should have everything installed and be able to run a
-\emph on
-binary_grid
-\emph default
- script.
-\end_layout
-
-\begin_layout Paragraph
-Troubleshooting
-\emph on
-Perl
-\end_layout
-
-\begin_layout Description
-Module
-\begin_inset space ~
-\end_inset
-
-not
-\begin_inset space ~
-\end_inset
-
-found Check the
-\family typewriter
-PERL5LIB
-\family default
- environment variable.
- When it is empty,
-\emph on
-cpanm/perlbrew
-\emph default
- should find your modules automatically,
-\emph on
-if
-\emph default
- they are installed correctly by
-\emph on
-cpanm
-\emph default
- (in the
-\emph on
-site_perl
-\emph default
- directory, see above).
- You can try installing modules again with
-\family typewriter
-\series bold
-cpanm --force --reinstall
-\family default
-\series default
- to force a reinstallation, and with
-\family typewriter
-\series bold
--v
-\family default
-\series default
- for extra logging.
-\end_layout
-
-\begin_layout Description
-Module
-\begin_inset space ~
-\end_inset
-
-fails
-\begin_inset space ~
-\end_inset
-
-to
-\begin_inset space ~
-\end_inset
-
-build Try
-\family typewriter
-\series bold
-cpanm --notests
-\family default
-\series default
- to not run all tests.
- Sometimes these fail for spurious reasons, e.g.
- in the case of
-\emph on
-binary_grid
-\emph default
- because there are
-\emph on
- no tests,
-\emph default
- but
-\emph on
-
-\emph default
-the module still functions.
-\end_layout
-
-\begin_layout Description
-Perlbrew
-\begin_inset space ~
-\end_inset
-
-build
-\begin_inset space ~
-\end_inset
-
-flags I would recommend at least
-\begin_inset Newline newline
-\end_inset
-
-
-\family typewriter
--Dusethreads -Duselargefiles -Doptimize="-O3 -march=native -mtune=native"
-\begin_inset Newline newline
-\end_inset
-
-
-\family default
-although you may wish to use
-\family typewriter
--O2
-\family default
- if you feel mathematical precision is key to your application (I have never
- noticed a problem with the above).
-\begin_inset Newline newline
-\end_inset
-
-I also recommend
-\family typewriter
--Dcccdlflags=-fPIC
-\family default
-so that module code is position independent and
-\family typewriter
--Duseshrplib
-\family default
- so that the appropriate threading library is used.
- (These flags are passed to the
-\emph on
-C
-\emph default
- compiler that builds
-\emph on
-Perl
-\emph default
-.)
-\end_layout
-
-\begin_layout Description
-Rebuild
-\begin_inset space ~
-\end_inset
-
-modules
-\begin_inset space ~
-\end_inset
-
-for
-\begin_inset space ~
-\end_inset
-
-new
-\begin_inset space ~
-\end_inset
-
-
-\emph on
-Perl
-\emph default
- Let's say you had an old
-\emph on
-perl
-\emph default
-built with perlbrew, have installed a shiny new
-\emph on
-perl
-\emph default
- version with perlbrew, and now you want to rebuild all your existing modules.
- Try this after the install, but before switching to the new
-\emph on
-perl
-\emph default
-, replacing
-\family typewriter
-5.xx.yy
-\family default
- with the new
-\emph on
-perl
-\emph default
- version:
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Box Frameless
-position "t"
-hor_pos "c"
-has_inner_box 1
-inner_pos "t"
-use_parbox 0
-use_makebox 0
-width "100col%"
-special "none"
-height "1in"
-height_special "totalheight"
-thickness "0.4pt"
-separation "3pt"
-shadowsize "4pt"
-framecolor "black"
-backgroundcolor "none"
-status open
-
-\begin_layout Plain Layout
-
-\family typewriter
-\series bold
-perlbrew list-modules | perlbrew exec --with 5.xx.yy cpanm
-\end_layout
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Paragraph
-
-\emph on
-binary_grid2
-\emph default
- backends
-\end_layout
-
-\begin_layout Standard
-The
-\begin_inset Quotes eld
-\end_inset
-
-backend
-\begin_inset Quotes erd
-\end_inset
-
- is a set of interface code between
-\emph on
-binary_c
-\emph default
- and
-\emph on
-binary_grid2
-\emph default
-.
-
-\end_layout
-
-\begin_layout Paragraph
-Perl backend
-\end_layout
-
-\begin_layout Standard
-In
-\emph on
-binary_grid
-\emph default
-version 1, the only backend available was the Perl backend which communicates
- with
-\emph on
-binary_c
-\emph default
- via a series of Unix pipes.
- This is portable and flexible, and hence for many years was the default.
- It does not, however, scale very well in multi-CPU architectures.
- In binary_grid2 a pure
-\emph on
-Perl
-\emph default
-module is also provided, both for backwards compatibility and because the
- code is well tested and stable.
- The
-\emph on
-Perl
-\emph default
-backend is installed by default with
-\emph on
-binary_grid2
-\emph default
-.
-
-\end_layout
-
-\begin_layout Standard
-It is a simple matter of changing the
-\family typewriter
-prog
-\family default
- grid variable if you want to use a different version of
-\emph on
-binary_c
-\emph default
- with each grid script.
-\end_layout
-
-\begin_layout Paragraph
-C backend
-\end_layout
-
-\begin_layout Standard
-New to
-\emph on
-binary_grid2
-\emph default
- is the
-\emph on
-C
-\emph default
- backend.
- This features simpler code and uses
-\emph on
-binary_c
-\emph default
-'s
-\emph on
-API
-\emph default
- to access data directly, hence it is a lot faster than the
-\emph on
-Perl
-\emph default
- backend, and scales
-\series bold
-much
-\series default
-better on multi-core architectures.
- The down side is that installation is more difficult, especially if you
- have multiple projects.
-
-\end_layout
-
-\begin_layout Standard
-If you see errors like:
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-perl: symbol lookup error: /.../perl5/perlbrew/perls/perl-5.25.0/lib/site_perl/5.25.0/x
-86_64-linux-thread-multi/auto/binary_grid/C/C.so: undefined symbol: new_system
-\end_layout
-
-\begin_layout Standard
-then you have failed to build the shared library as required and you are
- trying to use the
-\emph on
-C
-\emph default
- backend.
-\begin_inset Newline newline
-\end_inset
-
-To make the
-\emph on
-C
-\emph default
- backend work, you have to
-\series bold
-\emph on
-first
-\series default
-\emph default
- install
-\emph on
-libbinary_c.so
-\emph default
- and
-\series bold
-\emph on
-then
-\series default
-\emph default
- install
-\emph on
-binary_grid2
-\emph default
-.
- Essentially:
-\end_layout
-
-\begin_layout Enumerate
-Build
-\emph on
-binary_c
-\emph default
- as normal
-\end_layout
-
-\begin_layout Enumerate
-Make the shared library,
-\emph on
-libbinary_c.so
-\emph default
- (with
-\family typewriter
-\series bold
-make libbinary_c.so
-\family default
-\series default
-)
-\end_layout
-
-\begin_layout Enumerate
-Install
-\emph on
-binary_grid2
-\end_layout
-
-\begin_layout Standard
-Because this module is written partly in
-\emph on
-C
-\emph default
- and partly in
-\emph on
-Perl
-\emph default
-, there are more things that can go wrong and it is harder to share installation
-s (you cannot just copy the shared library to another filename).
- The shared library
-\emph on
-libbinary_c.so
-\emph default
-must match with
-\emph on
-binary_grid2
-\emph default
-
-\series bold
-at compile time
-\series default
-, and if you change anything in
-\emph on
-binary_c
-\emph default
- you probably have to follow the above instructions to reinstall the
-\emph on
-C
-\emph default
- backend.
-
-\end_layout
-
-\begin_layout Standard
-There are ways around this problem.
- You can change the name of the shared library by setting the environment
- variable
-\family typewriter
-BINARY_C_LIB
-\family default
- to the name of the library, and pointing
-\family typewriter
-BINARY_C_SRC
-\family default
- to the
-\family typewriter
-src
-\family default
- directory in your
-\emph on
-binary_c
-\emph default
- tree.
- Then rebuild, e.g.,
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-export BINARY_C_LIB=binary_c_custom
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-export BINARY_C_SRC=$HOME/binary_c/src
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-./configure
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-make libbinary_c_custom.so
-\end_layout
-
-\begin_layout Standard
-
-\family typewriter
-\series bold
-cpanm binary_grid2.tar.gz
-\end_layout
-
-\begin_layout Standard
-The
-\emph on
-binary_grid2
-\emph default
- module respects the
-\family typewriter
-BINARY_C_LIB
-\family default
- environment variable.
-
-\end_layout
-
-\begin_layout Standard
-I do not yet know how to have custom
-\emph on
-C
-\emph default
- backend modules with different shared libraries.
- It is quite possible that you could use the
-\family typewriter
-PERL_INLINE_DIRECTORY
-\family default
- environment variable to have multiple builds, and point to the appropriate
- one.
- Please read
-\begin_inset CommandInset href
-LatexCommand href
-target "http://search.cpan.org/~ingy/Inline-0.44/Inline.pod"
-literal "false"
-
-\end_inset
-
- especially the section
-\emph on
-The Inline DIRECTORY
-\emph default
- for instructions on how it is best to set up production code for multiple
- projects.
- Let Rob know if it works, so better instructions can be put in here.
-\end_layout
-
-\begin_layout Standard
-There are a number of environment variables which can be set when installing
-
-\emph on
-binary_grid2
-\emph default
-'s
-\emph on
-C
-\emph default
- backend:
-\end_layout
-
-\begin_layout Description
-BINARY_GRID2_LIB The name of the shared library.
- Usually this is 'binary_c'.
-\end_layout
-
-\begin_layout Description
-BINARY_GRID2_CC The name of the compiler used to build the C backend.
- Usually 'gcc'.
-\end_layout
-
-\begin_layout Description
-BINARY_GRID2_LD The name of the linker used to build the C backend.
- Usually 'ld'.
-\end_layout
-
-\begin_layout Description
-BINARY_GRID2_INC Include flags for the build.
- Defaults to
-\family typewriter
--I
-\emph on
-srcdir
-\family default
-
-\emph default
-where
-\emph on
-srcdir
-\emph default
- is the
-\emph on
-binary_c
-\emph default
-
-\family typewriter
-src
-\family default
- directory (e.g.
- set by
-\family typewriter
-BINARY_C_SRC
-\family default
-)
-\end_layout
-
-\begin_layout Description
-BINARY_GRID2_EXTRAINC Include flags to be postfixed to the
-\emph on
-inc
-\emph default
- flags set above.
-\end_layout
-
-\begin_layout Description
-BINARY_GRID2_LIBS Library flags.
- Defaults to
-\family typewriter
--Lsrcdir -lbinary_c -lbfd
-\family default
-.
-\end_layout
-
-\begin_layout Description
-BINARY_GRID2_EXTRALIBS Library flags postfixed to the
-\emph on
-libs
-\emph default
- flags set above.
-\end_layout
-
-\begin_layout Description
-BINARY_GRID2_CCFLAGS Compiler flags.
- Defaults to
-\family typewriter
--march=native -mtune=native -lm -lc -fPIC -ffunction-sections -lbfd
-\end_layout
-
-\begin_layout Description
-BINARY_GRID2_EXTRACCFLAGS C compiler flags postfixed to the
-\emph on
-ccflags
-\emph default
-set above.
-\end_layout
-
-\begin_layout Standard
-\begin_inset Newpage pagebreak
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsubsection
-when proxies/authentication get in the way
-\end_layout
-
-\begin_layout Standard
-Many thanks to George Angelou for this guide to installing at the Max-Planck
- Institiut f
-\begin_inset ERT
-status open
-
-\begin_layout Plain Layout
-
-
-\backslash
-
-\begin_inset Quotes erd
-\end_inset
-
-
-\end_layout
-
-\end_inset
-
-ur Astronomie in Garching.
-\begin_inset Newline newline
-\end_inset
-
-We want the
-\family typewriter
--k
-\family default
- flag when getting
-\emph on
-perlbrew
-\emph default
- and to write to a file
-\end_layout
-
-\begin_layout Standard
-\begin_inset listings
-inline false
-status open
-
-\begin_layout Plain Layout
-
-
-\backslash
-curl -kL -o perlbrew.sh https://install.perlbrew.pl | bash
-\end_layout
-
-\end_inset
-
-Make it executable
-\end_layout
-
-\begin_layout Standard
-\begin_inset listings
-inline false
-status open
-
-\begin_layout Plain Layout
-
-chmod +x perlbrew.sh
-\end_layout
-
-\end_inset
-
-Edit
-\family typewriter
-perlbrew.sh
-\family default
-.
- Find:
-\end_layout
-
-\begin_layout Standard
-\begin_inset listings
-inline false
-status open
-
-\begin_layout Plain Layout
-
-echo
-\end_layout
-
-\begin_layout Plain Layout
-
-if type curl >/dev/null 2>&1; then
-\end_layout
-
-\begin_layout Plain Layout
-
-PERLBREWDOWNLOAD="curl -f -sS -Lo $LOCALINSTALLER $PERLBREWURL"
-\end_layout
-
-\end_inset
-
-And add the ignore certificate flag
-\end_layout
-
-\begin_layout Standard
-\begin_inset listings
-inline false
-status open
-
-\begin_layout Plain Layout
-
-if type curl >/dev/null 2>&1; then
-\end_layout
-
-\begin_layout Plain Layout
-
-PERLBREWDOWNLOAD="curl -kf -sS -Lo $LOCALINSTALLER $PERLBREWURL"
-\end_layout
-
-\end_inset
-
-Execute
-\family typewriter
-perlbrew.sh
-\family default
- and we should get an error about
-\emph on
-patchperl
-\emph default
-Add the following to your
-\family typewriter
-tcshrc
-\family default
- (it will print out the
-\emph on
-bash
-\emph default
- equivalent on screen)
-\end_layout
-
-\begin_layout Standard
-\begin_inset listings
-inline false
-status open
-
-\begin_layout Plain Layout
-
-source ~/perl5/perlbrew/etc/cshrc
-\end_layout
-
-\end_inset
-
-Close the terminal and open a new window.
-
-\begin_inset Newline newline
-\end_inset
-
-Get
-\emph on
-patchperl
-\emph default
- manually:
-\end_layout
-
-\begin_layout Standard
-\begin_inset listings
-inline false
-status open
-
-\begin_layout Plain Layout
-
-
-\backslash
-curl -kL https://raw.github.com/gugod/patchperl-packing/master/patchperl
-\backslash
-
-\end_layout
-
-\begin_layout Plain Layout
-
- > $PERLBREW_ROOT/bin/patchperl
-\end_layout
-
-\begin_layout Plain Layout
-
-chmod 755 $PERLBREW_ROOT/bin/patchperl
-\end_layout
-
-\end_inset
-
-
-\family typewriter
-$PERLBREW_ROOT
-\family default
- is the path where
-\emph on
-perlbrew
-\emph default
- has been installed.
- Follow Rob’s command for installing
-\emph on
-perl
-\emph default
- in
-\emph on
-multithread
-\emph default
- mode.
- Hopefully this will install with no problems.
-
-\end_layout
-
-\begin_layout Standard
-Make
-\emph on
-perl
-\emph default
- point to your new
-\emph on
-perlbrew
-\end_layout
-
-\begin_layout Standard
-\begin_inset listings
-inline false
-status open
-
-\begin_layout Plain Layout
-
-perlbrew switch perl.x.x.x
-\end_layout
-
-\end_inset
-
-Install
-\emph on
-cpanminus
-\emph default
- manually
-\end_layout
-
-\begin_layout Standard
-\begin_inset listings
-inline false
-status open
-
-\begin_layout Plain Layout
-
-curl -kL https://cpanmin.us | perl - App::cpanminus
-\end_layout
-
-\end_inset
-
-Make sure all is fine
-\end_layout
-
-\begin_layout Standard
-\begin_inset listings
-inline false
-status open
-
-\begin_layout Plain Layout
-
-perlbrew list-modules
-\end_layout
-
-\end_inset
-
-And hopefully you see
-\family typewriter
-App::cpanminus
-\family default
- and
-\family typewriter
- Perl
-\end_layout
-
-\begin_layout Standard
-Good luck!
-\begin_inset Newline newline
-\end_inset
-
-
-\begin_inset Newline newline
-\end_inset
-
-
-\series bold
-Installing robs perl modules
-\end_layout
-
-\begin_layout Standard
-Running his script it failed on
-\family typewriter
-Inline::C.
-
-\family default
- Its on the list twice anyway so I reran and got as far as Sys::Info
-\emph on
-.
- MPA
-\emph default
- has its own OS that the module does not like and thinks is fake.
- I edited the install_modules.pl file and commented out this module.
- Rob says he doesn’t use it anymore so hopefully that will be fine.
-
-\end_layout
-
-\begin_layout Standard
-It also failed at binning so I went into
-\family typewriter
-modules_targz
-\family default
- and used the install script there.
- At first there are errors at it searches for the packages online then it
- installs them locally.
-
-\family typewriter
-perlbrew list-modules
-\family default
- suggests they are installed.
- Going to scripts and testing the
-\family typewriter
-CNgrids.pl
-\family default
- I seem to get output.
- So I assume all worked.
-\end_layout
-
-\end_body
-\end_document
diff --git a/doc/binary_c-installation.pdf b/doc/binary_c-installation.pdf
deleted file mode 100644
index 1a02d23883300fe36d40b02b4cf26afa1e6c1eae..0000000000000000000000000000000000000000
Binary files a/doc/binary_c-installation.pdf and /dev/null differ
diff --git a/doc/binary_c2.lyx b/doc/binary_c2.lyx
index 425cb50dae0abb583bd3a01627a712e95e175b5c..5bb03af5f242519a55a229a696db21851c436b93 100644
--- a/doc/binary_c2.lyx
+++ b/doc/binary_c2.lyx
@@ -1180,7 +1180,7 @@ Ubuntu
status open
\begin_layout Plain Layout
-ubuntu_install.sh
+ubuntu_install_binary_c.sh
\end_layout
\end_inset
@@ -1210,17 +1210,17 @@ status open
\begin_layout Plain Layout
-wget http://personal.ph.surrey.ac.uk/~ri0005/ubuntu_install.sh
+wget http://personal.ph.surrey.ac.uk/~ri0005/ubuntu_install_binary_c.sh
\end_layout
\begin_layout Plain Layout
-chmod +x ubuntu_install.sh
+chmod +x ubuntu_install_binary_c.sh
\end_layout
\begin_layout Plain Layout
-./ubuntu_install.sh
+./ubuntu_install_binary_c.sh
\end_layout
\end_inset
@@ -3661,7 +3661,7 @@ noprefix "false"
\begin_inset Formula $\binaryc$
\end_inset
- is describe in section
+ is described in section
\begin_inset space ~
\end_inset
diff --git a/doc/getting_binary_c.lyx b/doc/getting_binary_c.lyx
index 3eb0002b74567be8cc8faad9ae596ac51db590d9..076b92264e1083887cfa7a6b99e529d7506a1d0a 100644
--- a/doc/getting_binary_c.lyx
+++ b/doc/getting_binary_c.lyx
@@ -391,7 +391,155 @@ End
\begin_body
\begin_layout Subsubsection
-Getting the source code
+Getting the
+\begin_inset Formula $\binaryc$
+\end_inset
+
+ source code
+\end_layout
+
+\begin_layout Description
+With
+\begin_inset space ~
+\end_inset
+
+git download the source code from
+\begin_inset CommandInset href
+LatexCommand href
+target "https://gitlab.eps.surrey.ac.uk/ri0005/binary_c"
+literal "false"
+
+\end_inset
+
+, e.g.
+\begin_inset space ~
+\end_inset
+
+from the command line,
+\begin_inset listings
+inline false
+status open
+
+\begin_layout Plain Layout
+
+git clone https://gitlab.eps.surrey.ac.uk/ri0005/binary_c.git
+\end_layout
+
+\end_inset
+
+or, if you have set up
+\begin_inset Flex Software
+status open
+
+\begin_layout Plain Layout
+SSH
+\end_layout
+
+\end_inset
+
+ keys on the
+\begin_inset Flex Software
+status open
+
+\begin_layout Plain Layout
+gitlab
+\end_layout
+
+\end_inset
+
+ server,
+\begin_inset listings
+inline false
+status open
+
+\begin_layout Plain Layout
+
+git clone gitlab@gitlab.eps.surrey.ac.uk:ri0005/binary_c.git
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Description
+As
+\begin_inset space ~
+\end_inset
+
+a
+\begin_inset space ~
+\end_inset
+
+zip
+\begin_inset space ~
+\end_inset
+
+file you can either download a release, e.g.,
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Flex URL
+status open
+
+\begin_layout Plain Layout
+
+https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/archive/2.1.6/binary_c-2.1.6.zip
+\end_layout
+
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Flex URL
+status open
+
+\begin_layout Plain Layout
+
+https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/archive/2.1.6/binary_c-2.1.6.tar.gz
+\end_layout
+
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+
+\begin_inset Flex URL
+status open
+
+\begin_layout Plain Layout
+
+https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/archive/2.1.6/binary_c-2.1.6.tar.bz2
+\end_layout
+
+\end_inset
+
+
+\begin_inset Newline newline
+\end_inset
+
+or get the latest master branch from
+\begin_inset Flex URL
+status open
+
+\begin_layout Plain Layout
+
+https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/archive/master/binary_c-master.zip
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsubsection
+Editing the source code
\end_layout
\begin_layout Standard
@@ -417,8 +565,8 @@ literal "false"
\end_inset
.
- Access requires permission which is done on a user-by-user basis and currently
- only works easily if you have a Gmail account.
+ Write access requires permission which is done on a user-by-user basis
+ and currently only works easily if you have a Gmail account.
If you don't, we can probably arrange something.
\end_layout
@@ -454,7 +602,16 @@ your account is locked!
\end_layout
\begin_layout Enumerate
-Email me at r.izzard@surrey.ac.uk and tell me your account is
+Email me at
+\begin_inset CommandInset href
+LatexCommand href
+name "r.izzard@surrey.ac.uk"
+type "mailto:"
+literal "false"
+
+\end_inset
+
+ and tell me your account is
\begin_inset Quotes eld
\end_inset
@@ -596,9 +753,17 @@ You can access
\emph default
through
+\begin_inset Flex Software
+status open
+
+\begin_layout Plain Layout
+
\emph on
docker
-\emph default
+\end_layout
+
+\end_inset
+
\begin_inset Foot
status open
@@ -620,14 +785,30 @@ target "https://www.docker.com/"
\begin_layout Enumerate
I assume you have installed and signed in to
+\begin_inset Flex Software
+status open
+
+\begin_layout Plain Layout
+
\emph on
docker
-\emph default
+\end_layout
+
+\end_inset
+
.
I cannot provide support for
+\begin_inset Flex Software
+status open
+
+\begin_layout Plain Layout
+
\emph on
Docker
-\emph default
+\end_layout
+
+\end_inset
+
!
\end_layout
@@ -702,8 +883,18 @@ docker pull robizzard/binary_c:master2.0pre32
\end_layout
\begin_layout Enumerate
-When you run Docker it inherits your stack settings, which may be too small
- for binary_c to run.
+When you run
+\begin_inset Flex Software
+status open
+
+\begin_layout Plain Layout
+Docker
+\end_layout
+
+\end_inset
+
+ it inherits your stack settings, which may be too small for binary_c to
+ run.
Use
\begin_inset listings
lstparams "language=bash"
diff --git a/ubuntu_install.sh b/ubuntu_install.sh
deleted file mode 100644
index d6c6cf8bca6d22f17d607010fa24ab194c96b8c5..0000000000000000000000000000000000000000
--- a/ubuntu_install.sh
+++ /dev/null
@@ -1,110 +0,0 @@
-#!/bin/bash
-
-############################################################
-#
-# script to install binary_c
-#
-# tested on Ubuntu 20.10
-#
-# Note: this will ask you to choose python3.9
-# as your default python. You do NOT have to
-# do this, but some software is only tested
-# on python3.9.
-#
-# We default to using gcc-10 for the compilation.
-#
-############################################################
-
-
-
-# update and install a KDE desktop :)
-#sudo apt-get install synaptic kubuntu-desktop
-#balooctl disable
-
-# update system
-sudo apt-get update
-sudo apt-get upgrade
-
-# install required packages
-sudo apt-get install bash zip gcc-10 libgcc-10-dev gdb valgrind gawk python3.9 pipenv kcachegrind meson ninja-build emacs perl libgsl-dev global libbsd-dev binutils-dev libiberty-dev libjemalloc-dev zlib1g-dev unzip wget curl
-sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.9 1
-sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.8 2
-sudo update-alternatives --config python # >>> choose python3.9 <<<
-pip install --upgrade meson
-pip install --upgrade ninja
-
-# set up environment
-export CC=gcc-10
-export BINARY_C=$HOME/progs/stars/binary_c
-
-if [ ! grep -q 'binary_c paths do not alter' ~/.bashrc ]
-then
- # set up bash paths : do this only once!
- echo '# binary_c paths do not alter' >> ~/.bashrc
- echo 'export LD_LIBRARY_PATH=$HOME/lib:$BINARY_C:$BINARY_C/src' >> ~/.bashrc # do this only once!
- echo 'export PATH=$HOME/bin:$PATH' >> ~/.bashrc # do this only once!
-fi
-export LD_LIBRARY_PATH=$HOME/lib:$BINARY_C:$BINARY_C/src
-export PATH=$HOME/bin:$PATH
-
-# Install librinterpolate, libmemoize, librchash
-cd $HOME
-mkdir git
-cd $HOME/git
-wget https://gitlab.eps.surrey.ac.uk/ri0005/librinterpolate/-/archive/master/librinterpolate-master.zip -O librinterpolate-master.zip
-unzip -o librinterpolate-master.zip
-cd librinterpolate-master/
-meson --prefix=$HOME --buildtype=release builddir
-ninja -C builddir install
-cd ..
-
-wget https://gitlab.eps.surrey.ac.uk/ri0005/libmemoize/-/archive/master/libmemoize-master.zip -O libmemoize-master.zip
-unzip -o libmemoize-master.zip
-cd libmemoize-master/
-meson --prefix=$HOME --buildtype=release builddir
-ninja -C builddir install
-cd ..
-
-wget https://gitlab.eps.surrey.ac.uk/ri0005/librchash/-/archive/master/librchash-master.zip -O librchash-master.zip
-unzip -o librchash-master.zip
-cd librchash-master/
-meson --prefix=$HOME --buildtype=release builddir
-ninja -C builddir install
-cd ..
-
-# download and install binary_c
-mkdir -p $BINARY_C
-cd $BINARY_C/..
-wget http://personal.ph.surrey.ac.uk/~ri0005/binary_c-master.zip -O binary_c-master.zip
-unzip -o binary_c-master.zip
-rmdir binary_c
-mv binary_c-master binary_c
-cd binary_c
-meson -Dbuildtype=release -Dvalgrind=true builddir
-ninja -C builddir binary_c_install
-./tbse
-
-
-# install perlbrew and binary_grid
-cd $HOME
-\curl -L https://install.perlbrew.pl | bash
-
-if [ ! grep -q 'perlbrew paths do not alter' ~/.bashrc ]
-then
- echo "# perlbrew paths do not alter" >> ~/.bashrc
- echo "source ~/perl5/perlbrew/etc/bashrc" >> ~/.bashrc # only do this once!
-fi
-source ~/perl5/perlbrew/etc/bashrc
-
-
-export NTHREADS=`cat /proc/cpuinfo |grep cpu\ famil|wc -l`
-export LATEST_PERL=`perlbrew available | grep "^[[:space:]]\+perl" | head -1`
-perlbrew -v install $LATEST_PERL --thread --multi --64bitall --notest -Dusethreads -Duselargefiles -Dcccdlflags=-fPIC -Dpager=/usr/bin/sensible-pager -Doptimize="-O3 -mtune=generic" -Duseshrplib -j $NTHREADS
-perlbrew switch $LATEST_PERL
-perlbrew install-cpanm
-cd $BINARY_C/src/perl/modules_targz
-./install_all.pl
-
-# run a test population
-cd $BINARY_C
-LD_PRELOAD=./src/libbinary_c.so ./src/perl/scripts2/template.pl
diff --git a/ubuntu_install_binary_c.sh b/ubuntu_install_binary_c.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5160d4de2068ac7466b607d6446415a3c36d3eaa
--- /dev/null
+++ b/ubuntu_install_binary_c.sh
@@ -0,0 +1,401 @@
+#!/bin/bash
+
+############################################################
+#
+# script to install binary_c
+#
+# tested on Ubuntu 20.10/21.04, binary_c 2.2
+#
+# Note: this will ask you to choose python3.9
+# as your default python. You do NOT have to
+# do this, but some software is only tested
+# on python3.9.
+#
+# Environment variables:
+#
+# CC : the C compiler, we default to gcc-10, but
+# gcc should be fine.
+#
+# BINARY_C : the location of the binary_c root directory.
+#
+# GITROOT : the location in which we download the source code
+# of libraries we require.
+#
+############################################################
+set -e # fail -> exit
+
+# Defaults for the environment variables that control
+# installation locations, compiler etc.
+
+# set up compiler
+: "${CC:="gcc-10"}"
+# set up location of binary_c
+: "${BINARY_C:="$HOME/binary_c"}"
+# git download location
+: "${GITROOT:="$HOME/git"}"
+
+export CC
+export BINARY_C
+export GITROOT
+
+echo
+echo "#########################################################"
+echo "Binary_c installation script for Ubuntu/Kubuntu 20/21+"
+echo "#########################################################"
+echo
+echo "Press CTRL-C to exit at any time"
+echo
+echo "C compiler is set in CC"
+echo "CC = $CC"
+echo
+echo "BINARY_C is the directory where binary_c will be installed"
+echo "BINARY_C = $BINARY_C"
+echo
+echo "GITROOT is where source code for support libraries is downloaded"
+echo "GITROOT = $GITROOT"
+echo
+echo "#########################################################"
+echo
+echo "Does the above look correct? (y/n)"
+select s in "Yes" "No"; do
+ case $s in
+ "Yes" ) break;;
+ "No" ) exit; break;;
+ esac
+done
+
+# Install librinterpolate, libmemoize, librchash
+mkdir -p $GITROOT
+cd $GITROOT
+
+############################################################
+versionsorter() {
+ [ "$1" = "`echo -e "$1\n$2" | sort -V | head -n1`" ]
+}
+
+function setup_bash
+{
+ # set up bash and .bashrc
+ BASHRC="$HOME/.bashrc"
+ if ! grep -q 'binary_c paths do not alter' $BASHRC
+ then
+ # set up bash paths : do this only once!
+ echo '# binary_c paths do not alter' >> $BASHRC
+ echo 'export LD_LIBRARY_PATH=$HOME/lib:$BINARY_C:$BINARY_C/src' >> $BASHRC # do this only once!
+ echo 'export PATH=.:$HOME/bin:$HOME/.local/bin:$PATH' >> $BASHRC # do this only once!
+ echo "export BINARY_C=\"$BINARY_C\"" >> $BASHRC
+
+ # psb, psbb, git functions etc. and completion of binary_c arguments
+ printf '%s' '
+
+# source perlbrew
+source $HOME/perl5/perlbrew/etc/bashrc
+
+# function to switch to progs/stars/binary_c
+function psb
+{
+ cd $BINARY_C
+}
+function psbb
+{
+ cd $BINARY_C/builddir
+}
+
+# git function for review number
+git_rev ()
+{
+ d=`date +%Y%m%d`
+ c=`git rev-list --full-history --all --abbrev-commit | /usr/bin/wc -l | /bin/sed -e "s/^ *//"`
+ h=`git rev-list --full-history --all --abbrev-commit | head -1`
+ echo ${c}:${d}:${h}
+}
+
+alias new="ls -lrt |head -10"
+
+# git function to find the repository url
+git_url ()
+{
+ git config --get remote.origin.url
+}
+
+# source autocompletion library
+if [ -n "$BASH_VERSION" ]; then
+ [ -f /etc/bash_completion ] && . /etc/bash_completion
+fi
+
+# completion of binary_c arguments
+_binary_c()
+{
+ COMPREPLY=()
+ cmd="${COMP_WORDS[0]}"
+ cur="${COMP_WORDS[COMP_CWORD]}"
+ prev="${COMP_WORDS[COMP_CWORD-1]}"
+ binaryc_opts=$($BINARY_C_ROOT/binary_c help |/bin/grep -A2 "where the arguments are a selection of :"|tail -1|tr " " "\n")
+ # check if we match a binary_c argument
+ subcmd=( $(compgen -W "$binaryc_opts" "$prev") )
+ if [[ $subcmd ]] ; then
+ # we do match an argument : try to get sub options
+ subopts=$($BINARY_C_ROOT/binary_c argopts $subcmd)
+ COMPREPLY=( $(compgen -W "$subopts" -- ${cur}) )
+ else
+ # we do not, so list the arguments
+ COMPREPLY=( $(compgen -W "$binaryc_opts" -- ${cur}) )
+ fi
+ return 0
+}
+complete -F _binary_c binary_c
+complete -F _binary_c tbse
+complete -F _binary_c tbse.mint
+complete -F _binary_c tbse.IRAS
+' >> $BASHRC
+ fi
+
+ # some of the above we require now
+ export LD_LIBRARY_PATH=$HOME/lib:$BINARY_C:$BINARY_C/src
+ export PATH=$HOME/bin:$HOME/.local/bin:$PATH
+ if [ -f $HOME/perl5/perlbrew/etc/bashrc ];
+ then
+ source $HOME/perl5/perlbrew/etc/bashrc
+ fi
+}
+
+
+function install_from_surrey_git
+{
+ PACKAGE=$1
+
+ # download and install $PACKAGE
+ mkdir -p $GITROOT
+ cd $GITROOT
+ wget https://gitlab.eps.surrey.ac.uk/ri0005/$PACKAGE/-/archive/master/$PACKAGE-master.zip -O $PACKAGE-master.zip
+ unzip -o $PACKAGE-master.zip
+ cd $PACKAGE-master/
+ if [ -d builddir ];
+ then
+ rm -r builddir
+ fi
+ meson --prefix=$HOME --buildtype=release builddir
+ ninja -C builddir install
+}
+
+function install_binary_c_from_zip
+{
+ # download and install binary_c
+ if [ -d $BINARY_C ];
+ then
+ echo "Directory $BINARY_C already exists: please remove any old binary_c installation before installing a new one"
+ exit
+ fi
+ cd /tmp # work from /tmp
+ wget https://gitlab.eps.surrey.ac.uk/ri0005/binary_c/-/archive/master/binary_c-master.zip -O binary_c-master.zip
+ unzip -o binary_c-master.zip
+ rm binary_c-master.zip
+ mv binary_c-master $BINARY_C
+ cd $BINARY_C
+ meson -Dbuildtype=release -Dvalgrind=true builddir
+ ninja -C builddir binary_c_install
+ ./tbse
+ cd $HOME
+}
+
+function install_binary_c_from_git_https
+{
+ # download and install binary_c
+ echo "Install to BINARY_C=$BINARY_C"
+ git clone --branch master --single-branch https://gitlab.eps.surrey.ac.uk/ri0005/binary_c.git $BINARY_C
+ rm -rf $BINARY_C/builddir 2>/dev/null
+ cd $BINARY_C
+ meson -Dbuildtype=release -Dvalgrind=true $BINARY_C/builddir
+ ninja -C $BINARY_C/builddir binary_c_install
+ $BINARY_C/binary_c-config version
+}
+
+
+function install_binary_c_from_git_ssh
+{
+ # download and install binary_c
+ cd $BINARY_C/..
+ git clone gitlab@gitlab.eps.surrey.ac.uk:ri0005/binary_c.git
+ cd binary_c
+ meson -Dbuildtype=release -Dvalgrind=true builddir
+ ninja -C builddir binary_c_install
+ ./binary_c-config version
+}
+
+function run_test_population
+{
+ # run a test population
+ cd $BINARY_C
+ LD_PRELOAD=./src/libbinary_c.so ./src/perl/scripts2/template.pl
+}
+
+function install_binary_c_perl_modules
+{
+ # install the binary_c Perl modules
+ cd $BINARY_C/src/perl/modules_targz
+ ./install_all.pl
+}
+
+function install_perl
+{
+ # install perlbrew and binary_grid
+ cd $HOME
+ \curl -L https://install.perlbrew.pl | bash
+
+ if ! grep -q 'perlbrew paths do not alter' ~/.bashrc
+ then
+ echo "# perlbrew paths do not alter" >> ~/.bashrc
+ echo "source ~/perl5/perlbrew/etc/bashrc" >> ~/.bashrc # only do this once!
+ fi
+ source ~/perl5/perlbrew/etc/bashrc 2>&1 || true
+ export NTHREADS=`cat /proc/cpuinfo |grep cpu\ famil|wc -l`
+ export CURRENT_PERL=`perl -e '$v=$^V;$v=~s/v//;print "perl-$v\n";'`
+ export LATEST_PERL=`perlbrew available | grep "^[[:space:]i]\+perl" | sed s/^i// | sed s/^[[:space:]]*// | sed s/[[:space:]]*\\$// | head -1`
+ echo "CURRENT_PERL = \"$CURRENT_PERL\""
+ echo "LATEST_PERL = \"$LATEST_PERL\""
+
+ if [ "$CURRENT_PERL" == "$LATEST_PERL" ];
+ then
+ echo "You already have the latest Perl"
+ else
+ NEWER_PERL=`echo -e "$CURRENT_PERL\n$LATEST_PERL" | sort -Vr | head -1`
+ if [ "$NEWER_PERL" == "$LATEST_PERL" ];
+ then
+ echo "Installing $LATEST_PERL"
+ perlbrew -v install $LATEST_PERL --thread --multi --64bitall --notest -Dusethreads -Duselargefiles -Dcccdlflags=-fPIC -Dpager=/usr/bin/sensible-pager -Doptimize="-O3 -mtune=generic" -Duseshrplib -j $NTHREADS
+ # clean the build
+ echo "Cleaning perlbrew/build"
+ rm -rf $HOME/perl5/perlbrew/build 2>/dev/null
+ else
+ echo "No newer Perl has been found : sticking with $CURRENT_PERL"
+ fi
+ echo "Source perlbrew"
+ source ~/perl5/perlbrew/etc/bashrc 2>&1 || true
+ echo "Switch to use $LATEST_PERL"
+ perlbrew switch $LATEST_PERL
+ fi
+
+ source ~/perl5/perlbrew/etc/bashrc 2>&1 || true
+ echo "Install cpanm"
+ perlbrew -f install-cpanm
+}
+
+function update_packages
+{
+ # update and install a KDE desktop :)
+ #sudo apt-get install synaptic kubuntu-desktop
+ #balooctl disable
+
+ # update system
+ sudo apt-get update
+ sudo apt-get upgrade
+
+ # install required packages
+ sudo apt-get install bash zip gcc-10 libgcc-10-dev gdb valgrind gawk python3.9 pipenv kcachegrind meson ninja-build emacs perl libgsl-dev global libbsd-dev binutils-dev libiberty-dev libjemalloc-dev zlib1g-dev unzip wget curl git
+ sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.9 1
+# sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.8 2 2>/dev/null
+ echo "You should normally choose Python 3.9"
+ sudo update-alternatives --config python # >>> choose python3.9 <<<
+ sudo apt-get clean
+ pip install --upgrade meson
+ pip install --upgrade ninja
+}
+
+function download_MINT_data
+{
+ # download MINT data
+ mkdir -p $HOME/data/MINT
+ cd $HOME/data/MINT
+ rm -f sync
+ wget http://personal.ph.surrey.ac.uk/~ri0005/MINT/sync
+ chmod +x sync
+ ./sync
+}
+
+############################################################
+
+# set up bash (always do this)
+setup_bash
+
+# install/check system packages
+echo "Do you wish to check and, if necessary, install system packages? (requires sudo permissions)"
+select yn in "Yes" "No"; do
+ case $yn in
+ Yes ) update_packages; break;;
+ No ) break;;
+ esac
+done
+
+# install perl from perlbrew
+echo "Install perlbrew and custom Perl?"
+select yn in "Yes" "No"; do
+ case $yn in
+ Yes ) install_perl; break;;
+ No ) break;;
+ esac
+done
+
+# install librinterpolate
+echo "Install librinterpolate?"
+select yn in "Yes" "No"; do
+ case $yn in
+ Yes ) install_from_surrey_git librinterpolate; break;;
+ No ) break;;
+ esac
+done
+
+# install libmemoize
+echo "Install libmemoize?"
+select yn in "Yes" "No"; do
+ case $yn in
+ Yes ) install_from_surrey_git libmemoize; break;;
+ No ) break;;
+ esac
+done
+
+# install librchash
+echo "Install librchash?"
+select yn in "Yes" "No"; do
+ case $yn in
+ Yes ) install_from_surrey_git librchash; break;;
+ No ) break;;
+ esac
+done
+
+# install binary_c
+echo "Install binary_c from ... ?"
+select s in "git (https)" "git (ssh, keys must be set up)" "git (zip, no version control)" "No";
+ do case $s in
+ "git (https)" ) install_binary_c_from_git_https; break;;
+ "git (ssh, keys must be set up)" ) install_binary_c_from_git_ssh; break;;
+ "git (zip, no version control)" ) install_binary_c_from_zip; break;;
+ "No" ) break;;
+ esac
+done
+
+# install binary_c's perl modules
+echo "Install binary_c Perl modules?"
+select yn in "Yes" "No"; do
+ case $yn in
+ Yes ) install_binary_c_perl_modules; break;;
+ No ) break;;
+ esac
+done
+
+# install MINT data?
+echo "Download MINT data?"
+select yn in "Yes" "No"; do
+ case $yn in
+ Yes ) download_MINT_data; break;;
+ No ) break;;
+ esac
+done
+
+# run test population
+echo "Run a test stellar population to make sure everything works?"
+select yn in "Yes" "No"; do
+ case $yn in
+ Yes ) run_test_population; break;;
+ No ) break;;
+ esac
+done