forked from saopicc/DDFacet
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathDockerfile
268 lines (238 loc) · 8.05 KB
/
Dockerfile
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
#From Ubuntu 18.04
FROM ubuntu:18.04
MAINTAINER Ben Hugo "bhugo@ska.ac.za"
#Package dependencies
COPY apt.sources.list /etc/apt/sources.list
#Setup environment
ENV DDFACET_TEST_DATA_DIR /test_data
ENV DDFACET_TEST_OUTPUT_DIR /test_output
# Support large mlocks
RUN echo "* - memlock unlimited" > /etc/security/limits.conf
ENV DEBIAN_FRONTEND noninteractive
ENV DEBIAN_PRIORITY critical
ENV GNUCOMPILER 7
ENV DEB_SETUP_DEPENDENCIES \
dpkg-dev \
g++-$GNUCOMPILER \
gcc-$GNUCOMPILER \
libc-dev \
cmake \
gfortran-$GNUCOMPILER \
git \
wget \
subversion
ENV DEB_DEPENCENDIES \
python3-pip \
libfftw3-dev \
python3-numpy \
libfreetype6 \
libfreetype6-dev \
libpng-dev \
pkg-config \
python3-dev \
libboost-all-dev \
libcfitsio-dev \
libhdf5-dev \
wcslib-dev \
libatlas-base-dev \
liblapack-dev \
python3-tk \
libreadline6-dev \
subversion \
liblog4cplus-dev \
libhdf5-dev \
libncurses5-dev \
libsofa1-dev \
flex \
bison \
libbison-dev \
# Reference image generation dependencies
make
RUN apt-get update
RUN apt-get install -y $DEB_SETUP_DEPENDENCIES
RUN apt-get install -y $DEB_DEPENCENDIES
RUN python3 -m pip install -U pip setuptools wheel
ENV PATH /usr/local/bin:$PATH
ENV LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH
ENV PYTHONPATH /usr/local/lib/python2.7/site-packages:$PYTHONPATH
# Latest GCC segfaults when compiling casacore
RUN rm /usr/bin/gcc /usr/bin/g++ /usr/bin/cpp /usr/bin/cc
RUN ln -s /usr/bin/gcc-$GNUCOMPILER /usr/bin/gcc
RUN ln -s /usr/bin/g++-$GNUCOMPILER /usr/bin/g++
RUN ln -s /usr/bin/gcc-$GNUCOMPILER /usr/bin/cc
RUN ln -s /usr/bin/g++-$GNUCOMPILER /usr/bin/cpp
RUN ln -s /usr/bin/gfortran-$GNUCOMPILER /usr/bin/gfortran
#####################################################################
## BUILD CASACORE FROM SOURCE
#####################################################################
RUN mkdir /src
WORKDIR /src
RUN wget https://github.com/casacore/casacore/archive/v3.3.0.tar.gz
RUN tar xvf v3.3.0.tar.gz
RUN mkdir casacore-3.3.0/build
WORKDIR /src/casacore-3.3.0/build
RUN cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release -DBUILD_DEPRECATED=ON -DBUILD_PYTHON=OFF -DBUILD_PYTHON3=ON ../
RUN make -j 4
RUN make install
RUN ldconfig
WORKDIR /src
RUN rm v3.3.0.tar.gz
RUN wget https://github.com/casacore/python-casacore/archive/v3.3.0.tar.gz
RUN tar xvf v3.3.0.tar.gz
WORKDIR /src/python-casacore-3.3.0
RUN python3 -m pip install .
WORKDIR /
RUN python3 -c "from pyrap.tables import table as tbl"
#####################################################################
## Get CASACORE ephem data
#####################################################################
RUN mkdir -p /usr/share/casacore/data/
WORKDIR /usr/share/casacore/data/
RUN apt-get install -y rsync
RUN rsync -avz rsync://casa-rsync.nrao.edu/casa-data .
#####################################################################
## BUILD MAKEMS FROM SOURCE AND TEST
#####################################################################
RUN mkdir -p /src/
WORKDIR /src
ENV BUILD /src
RUN wget https://github.com/ska-sa/makems/archive/1.5.3.tar.gz
RUN tar xvf 1.5.3.tar.gz
RUN mkdir -p $BUILD/makems-1.5.3/LOFAR/build/gnu_opt
WORKDIR $BUILD/makems-1.5.3/LOFAR/build/gnu_opt
RUN cmake -DCMAKE_MODULE_PATH:PATH=$BUILD/makems-1.5.3/LOFAR/CMake \
-DUSE_LOG4CPLUS=OFF -DBUILD_TESTING=OFF -DCMAKE_BUILD_TYPE=Release ../..
RUN make -j 16
RUN make install
ENV PATH=/src/makems-1.5.3/LOFAR/build/gnu_opt/CEP/MS/src:${PATH}
WORKDIR $BUILD/makems-1.5.3/test
RUN makems WSRT_makems.cfg
#####################################################################
## BUILD CASArest from source
#####################################################################
WORKDIR /src
RUN git clone https://github.com/casacore/casarest
WORKDIR /src/casarest
RUN mkdir -p build
WORKDIR /src/casarest/build
RUN cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
RUN make -j 4
RUN make install
RUN ldconfig
#####################################################################
## BUILD MEQTREES FROM SOURCE AND TEST
#####################################################################
# Owlcat
WORKDIR /src
RUN wget https://github.com/ska-sa/owlcat/archive/v1.6.0.tar.gz
RUN tar -xvf v1.6.0.tar.gz
WORKDIR /src/owlcat-1.6.0
RUN python3 -m pip install .
# kittens
WORKDIR /src
RUN wget https://github.com/ska-sa/kittens/archive/v1.4.3.tar.gz
RUN tar -xvf v1.4.3.tar.gz
WORKDIR /src/kittens-1.4.3
RUN python3 -m pip install .
# purr
WORKDIR /src
RUN wget https://github.com/ska-sa/purr/archive/v1.5.0.tar.gz
RUN tar -xvf v1.5.0.tar.gz
WORKDIR /src/purr-1.5.0
RUN python3 -m pip install .
# tigger-lsm
WORKDIR /src
RUN rm v1.6.0.tar.gz
RUN wget https://github.com/ska-sa/tigger-lsm/archive/v1.6.0.tar.gz
RUN tar -xvf v1.6.0.tar.gz
WORKDIR /src/tigger-lsm-1.6.0
RUN python3 -m pip install .
# Cattery
WORKDIR /src
RUN wget https://github.com/ska-sa/meqtrees-cattery/archive/v1.7.0.tar.gz
RUN tar -xvf v1.7.0.tar.gz
WORKDIR /src/meqtrees-cattery-1.7.0
RUN python3 -m pip install .
# blitz
WORKDIR /src
RUN wget https://github.com/blitzpp/blitz/archive/1.0.1.tar.gz
RUN tar -xvf 1.0.1.tar.gz
WORKDIR /src/blitz-1.0.1
RUN ./configure --enable-shared
RUN make -j16
RUN make install
RUN ldconfig
# timba
RUN apt-get install -y libqdbm-dev
WORKDIR /src
RUN wget https://github.com/ska-sa/meqtrees-timba/archive/v1.8.0.tar.gz
RUN tar -xvf v1.8.0.tar.gz
RUN mkdir /src/meqtrees-timba-1.8.0/build
WORKDIR /src/meqtrees-timba-1.8.0/build
RUN cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_PYTHON_3=ON ..
RUN make -j4
RUN make install
RUN ldconfig
# get the test from pyxis
WORKDIR /src
RUN rm v1.7.0.tar.gz
RUN wget https://github.com/ska-sa/pyxis/archive/v1.7.0.tar.gz
RUN tar -xvf v1.7.0.tar.gz
WORKDIR /src/pyxis-1.7.0
RUN python3 -m pip install .
RUN cp -r /src/pyxis-1.7.0/Pyxis/recipies /usr/local/lib/python3.6/dist-packages/Pyxis/
# run test when built
RUN apt-get install -y python3-pyqt4
RUN python3 -m pip install nose
WORKDIR /usr/local/lib/python3.6/dist-packages/Pyxis/recipies/meqtrees-batch-test
RUN python3 -m "nose"
#####################################################################
## BUILD LOFAR FROM SOURCE
#####################################################################
WORKDIR /src
RUN git clone -b 'v4.1.1' https://github.com/lofar-astron/LOFARBeam.git
WORKDIR LOFARBeam
RUN mkdir -p build/gnucxx11_opt
WORKDIR build/gnucxx11_opt
RUN cmake -DCMAKE_INSTALL_PREFIX=/usr -DPYTHON_EXECUTABLE=$(which python3) ../../
RUN make -j16
RUN make install
WORKDIR /
RUN touch /usr/lib/python3.6/site-packages/lofar/__init__.py
ENV PYTHONPATH "/usr/lib/python3.6/site-packages:$PYTHONPATH"
RUN python3 -c "import lofar.stationresponse as lsr"
RUN apt-get update
RUN apt-get install -y gfortran
#####################################################################
## BUILD DDF FROM SOURCE
#####################################################################
#Copy DDFacet and SkyModel into the image
ADD DDFacet /src/DDFacet/DDFacet
ADD SkyModel /src/DDFacet/SkyModel
ADD MANIFEST.in /src/DDFacet/MANIFEST.in
ADD setup.py /src/DDFacet/setup.py
ADD setup.cfg /src/DDFacet/setup.cfg
ADD README.rst /src/DDFacet/README.rst
ADD pyproject.toml /src/DDFacet/pyproject.toml
ADD .git /src/DDFacet/.git
ADD .gitignore /src/DDFacet/.gitignore
ADD .gitmodules /src/DDFacet/.gitmodules
RUN cd /src/DDFacet/ && git submodule update --init --recursive && cd /
# Finally install DDFacet
RUN rm -rf /src/DDFacet/DDFacet/cbuild
RUN python3 -m pip install -U "/src/DDFacet/[dft-support,moresane-support,testing-requirements,fits-beam-support,kms-support]"
# Set MeqTrees Cattery path to installation directory
ENV MEQTREES_CATTERY_PATH /usr/local/lib/python3.6/dist-packages/Cattery/
ENV PYTHONPATH $MEQTREES_CATTERY_PATH:$PYTHONPATH
RUN python3 -c "import Siamese"
RUN python3 -c "import bdsf"
# perform some basic tests
RUN DDF.py --help
RUN MakeMask.py --help
RUN MakeCatalog.py --help
RUN MakeModel.py --help
RUN MaskDicoModel.py --help
RUN ClusterCat.py --help
# set as entrypoint - user should be able to run docker run ddftag and get help printed
ENTRYPOINT ["DDF.py"]
CMD ["--help"]