-
Notifications
You must be signed in to change notification settings - Fork 77
/
INSTALL
300 lines (209 loc) · 11.1 KB
/
INSTALL
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
MrBayes 3.2.7a
This document describes how to install the most recent release of
MrBayes using Homebrew on macOS, Linux, or on Window subsystem for
Linux (WSL). It also describes how to build the development sources of
MrBayes from the GitHub repository sources.
========================================================================
Installing MrBayes on macOS using Homebrew
------------------------------------------------------------------------
MrBayes is available for macOS through the Homebrew package manager.
See https://brew.sh/ for general information about Homebrew and for
Homebrew installation instructions.
On a macOS system with Homebrew, MrBayes may be installed through the
following two commands in a terminal:
brew tap brewsci/bio
brew install mrbayes
The first command adds the "brewsci/bio" repository to your Homebrew
system. This is a Homebrew repository that contains various software
related to bioinformatics. Once the repository is available, you install
MrBayes with the second command above.
This will install MrBayes with support for the Beagle library. If you
need additional MPI support, use
brew install mrbayes --with-open-mpi
This will likely download the neccesary Homebrew packages for building
MrBayes with MPI support and then proceed to automatically build and
install it on your macOS system (this may take a bit of time).
========================================================================
Installing MrBayes on Linux or WSL using Homebrew ("Linuxbrew")
------------------------------------------------------------------------
The instructions for installing MrBayes on Linux systems are identical
to those for installing MrBayes on macOS. It relies on Homebrow
being available on the Linux system where it's being installed.
Installing Homebrew on Linux is a matter of following the instructions
at https://docs.brew.sh/Homebrew-on-Linux
We have found that the pre-compiled binaries may not work on all systems
and that you may get an "Illegal instruction (core dumped)" error when
you try starting MrBayes. In that case, install the MrBayes package
from sources instead. This can still be done through Homebrew like
this:
brew reinstall -s mrbayes
Likewise, you may possibly want to compile the Beagle library locally,
brew reinstall -s beagle
========================================================================
Installing MrBayes from the GitHub sources on Unix
------------------------------------------------------------------------
Make a shallow clone of the MrBayes repository:
git clone --depth=1 https://github.com/NBISweden/MrBayes.git
(a shallow clone requires about 27 MB of disk space, a full clone
requires about 77 MB)
Building MrBayes using the supplied "configure" script:
------------------------------------------------------------------------
To build MrBayes, you will need a C compiler (gcc or clang works well),
the "make" utility, and optionally the "pkg-config" utility. MrBayes
may also be compiled with support for the Beagle library and for
parallelization using MPI.
The code in the MrBayes Git repository comes with a standard GNU
"configure" script. On any Unix system, these are the steps required to
compile and optionally install MrBayes:
* Run "configure" in the top-level directory to create "Makefile" (see
"./configure --help" for info about enabling and disabling features of
MrBayes, or how to install in non-standard locations etc., and also
read further down in this document):
./configure
* Make (i.e. compile) the project:
make
Note that if "pdflatex" or "bibtex" could not be found by the
"configure" script, the PDF documentation in doc/manual will not
be rebuilt, even if the PDF documents are outdated or missing.
* Install it on the system (optional). This will install
the executable "mb" in /usr/local/bin, the documentation
in /usr/local/share/doc/mrbayes, and the example files in
/usr/local/share/examples/mrbayes unless the default installation
prefix ("/usr/local") is changed with the "--prefix" option when
running "configure".
make install
* We also support configuring and building the project away from the
checked out source repository. This avoids littering the source
repository checkout with temporary files. This is done through the
following steps:
1. Create and enter a build directory somewhere (its name and location
is arbitrary)
mkdir build
cd build
2. Call the "configure" script
location-of-MrBayes-checkout/configure
3. Build and optionally install the project
make
make install
Building MrBayes using the GNU autotools (Autoconf and Automake):
------------------------------------------------------------------------
MrBayes uses the GNU autotools, i.e. Automake and Autoconf, for its
configuration and build system. If you tinker with "configure.ac"
and/or any of the "Makefile.am" files and then want to regenerate the
"configure" script and associated files, there are some prerequisites
that need to be in place:
* Make sure Automake 1.15 (http://www.gnu.org/software/automake/)
is installed.
* Make sure Autoconf 2.69 (http://www.gnu.org/software/autoconf/)
is installed.
The "configure.ac" script uses the "pkg-config" tool for detection
of external libraries (Beagle) and also uses m4 macros from the
autoconf-archive collection for detection of MPI, Readline, and some
architecture-dependent compiler flags. Therefore,
* Make sure pkg-config (https://www.freedesktop.org/wiki/Software/pkg-config/)
is installed.
* Make sure autoconf-archive 2016.03.20 (or later)
(http://www.gnu.org/software/autoconf-archive/) is installed.
* On some systems that uses metaauto for wrapping multiple versions of
the GNU autotools (OpenBSD for example):
export AUTOCONF_VERSION=2.69
export AUTOMAKE_VERSION=1.15
* On Ubuntu Linux, installing the following packages installs all of the
above prerequisites:
1. automake
2. autoconf
3. pkg-config
4. autoconf-archive
These may be installed through
sudo apt install automake autoconf pkg-config autoconf-archive
When all the prerequisites are in place:
* Run "autoreconf" to generate the "configure" script:
autoreconf -i
* Then continue as outlined earlier in this document.
Disabling the SSE, AVX and FMA code paths
------------------------------------------------------------------------
MrBayes will use SSE, AVX and FMA instructions to speed up computations
on CPUs that support these instruction sets, if the compiler and build
architecture supports it. These code paths are however optional, and
if you suspect a bug in part of this code, you may use "--disable-sse",
"--disable-avx" and/or "--disable-fma" to disable it when running the
"configure" script.
Note that disabling SSE will also disable AVX and FMA, and disabling AVX
will also disable FMA.
Picking up the Beagle library:
------------------------------------------------------------------------
MrBayes uses the Beagle library
(https://github.com/beagle-dev/beagle-lib) if it is available. It will
make use of release 3.1.2 of Beagle but should also work with release
2.1.3 of the library.
Assuming Beagle was compiled and installed in a standard location, it
will be picked up by the "configure" script automatically. If it isn't
found, or the "configure" script is run with "--without-beagle", Beagle
will not be used.
If Beagle is installed in a non-default location, there are three ways
of telling the "configure" script how to find it:
* Use the flag "--with-beagle=PATH" where "PATH" is the prefix path
where the Beagle headers and libraries may be found. For example
"$HOME/local", "/opt" etc. The paths "/usr/local" and "/usr" are
tested if no path is specified.
* Point the "PKG_CONFIG_PATH" environment variable to the "pkgconfig"
directory that Beagle installed its "hmsbeagle-1.pc" file into. This
file is installed if Beagle was compiled from sources, and may be
found in the installation's "lib" directory. The detection of Beagle
will fall back on using "pkg-config" which picks up this file.
* As a last resort, it's also possible to set the "BEAGLE_CFLAGS" and
"BEAGLE_LIBS" environment variables prior to running "configure" (the
example shows how to use these variables when Beagle was installed
under the path "$HOME/local"):
env BEAGLE_CFLAGS="-I$HOME/local/include/hmsbeagle-1" \
BEAGLE_LIBS="-L$HOME/local/lib -Wl,-rpath=$HOME/local/lib -lhmsbeagle" \
./configure
Building the Beagle library for MrBayes
------------------------------------------------------------------------
Ideally, you would use a pre-built distribution of the Beagle library,
as setting up the required prerequisites for things like OpenCL etc. is
a bit cumbersome to say the least.
If you none the less want to try building and installing it, this is the
executive summary for how to do this on a Unix system, not including
installation of prerequisites (since these will differ between systems).
It's assumed that the Beagle library is being installed in the default
location, under "/usr/local". Note that the Beagle Java library is not
needed by MrBayes.
git clone --branch=v3.1.2 --depth=1 \
'https://github.com/beagle-dev/beagle-lib.git'
cd beagle-lib
./autogen.sh
./configure --without-jdk LDFLAGS=-Wl,-rpath=/usr/local/lib
make
sudo make install
See also the "INSTALL" document supplied with the Beagle library's
source distribution.
Picking up and using MPI:
------------------------------------------------------------------------
The "configure" script will find any available MPI C compiler or
compiler wrapper and use it (for example the one provided by OpenMPI
(https://www.open-mpi.org/) or MPICH (https://www.mpich.org/)) if
the "--with-mpi" flag is used. If this flag is not used, or if
"--without-mpi" is used, MrBayes will be compiled without support for
MPI parallelization.
You may set the "MPICC" environment variable to the name or path of a
specific MPI C compiler, if you have many to choose from:
env MPICC="/usr/local/bin/mpicc" ./configure --with-mpi
About support for the GNU Readline library:
------------------------------------------------------------------------
MrBayes will be compiled with support for the GNU Readline Library
(https://cnswww.cns.cwru.edu/php/chet/readline/rltop.html) (which allows
for command line history within an interactive session, and command
completion through pressing the "tab" key) if the Readline library
and its associated header files are available. However, it seems as
if the Readline library doesn't work well together with common MPI
implementations, such as OpenMPI (https://www.open-mpi.org/) and MPICH
(https://www.mpich.org/), so if MrBayes is configured with support for
MPI parallelization, Readline support will be automatically disabled.
A possible workaround is to use a "Readline wrapper", such as "rlwrap"
(https://github.com/hanslub42/rlwrap), which gives you persistent
command line history between sessions, but no command tab-completion.
To use rlwrap with an MPI-enabled MrBayes, simply start MrBayes like
this:
rlwrap mb
# vim: filetype=text