-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathlofar-2.def
255 lines (224 loc) · 16.5 KB
/
lofar-2.def
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
Bootstrap: shub
From: tikk3r/lofar-grid-hpccloud:lofarbase
# If building from a base image locally enable this instead.
#Bootstrap: localimage
#From: lofar_base.simg
%environment
export PYTHONPATH=
export INSTALLDIR=/opt/lofar
. $INSTALLDIR/init.sh
ulimit -n 4096
%post
# General environment settings.
export J=4
export INSTALLDIR=/opt/lofar
export PYTHON_VERSION=2.7
# Path to where the patch for python-casacore setup is stored.
export PYTHON_CASACORE_PATCH=$INSTALLDIR/python-casacore/python_casacore_setup_patch.patch
export PATCH_LOFAR=$INSTALLDIR/lofar/lofar.patch
# Settings relevant to the installed software.
export AOFLAGGER_VERSION=latest
export CASACORE_VERSION=v2.4.1
# Leave at latest, release versions crash for some reason.
export CASAREST_VERSION=latest
export DYSCO_VERSION=v1.0.1
export LOFAR_VERSION=3_2_9
export LOSOTO_VERSION=2.0
export PYBDSF_VERSION=v1.8.15
export PYTHON_CASACORE_VERSION=v2.2.1
export WSCLEAN_VERSION=latest
export HDF5_USE_FILE_LOCKING=FALSE
yum -y install vim
yum -y install libsigc++20-devel gtkmm30-devel
scl enable devtoolset-7 bash
export CC=`which gcc`
export CXX=`which g++`
export CXXFLAGS="-std=c++11"
export make=$INSTALLDIR/make/bin/make
pip install xmlrunner
pip install aplpy
mkdir -p $INSTALLDIR
#
# Install CASAcore
#
mkdir -p ${INSTALLDIR}/casacore/build
mkdir -p ${INSTALLDIR}/casacore/data
cd $INSTALLDIR/casacore && git clone https://github.com/casacore/casacore.git src
if [ "${CASACORE_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/casacore/src && git checkout tags/${CASACORE_VERSION}; fi
cd ${INSTALLDIR}/casacore/data && wget --retry-connrefused ftp://[email protected]/outgoing/Measures/WSRT_Measures.ztar
cd ${INSTALLDIR}/casacore/data && tar xf WSRT_Measures.ztar
export CMAKE_PREFIX_PATH=$INSTALLDIR/hdf5
cd ${INSTALLDIR}/casacore/build && cmake -DCMAKE_INSTALL_PREFIX=${INSTALLDIR}/casacore/ -DDATA_DIR=${INSTALLDIR}/casacore/data -DWCSLIB_ROOT_DIR=/${INSTALLDIR}/wcslib/ -DCFITSIO_ROOT_DIR=${INSTALLDIR}/cfitsio/ -DBUILD_PYTHON=True -DUSE_OPENMP=True -DUSE_FFTW3=TRUE -DUSE_HDF5=True -DBLAS_blas_LIBRARY=$INSTALLDIR/openblas/lib/libopenblas.so -DBOOST_LIBRARYDIR=$INSTALLDIR/boost/lib -DBOOST_INCLUDEDIR=$INSTALLDIR/boost/include ../src/
cd ${INSTALLDIR}/casacore/build && $make -j ${J}
cd ${INSTALLDIR}/casacore/build && $make install
#
# install-python-casacore
#
# Finding libraries is broken, patch the setup to include the previously installed boost and casacore libraries.
export PYTHON_VERSION=2.7
mkdir ${INSTALLDIR}/python-casacore
cd ${INSTALLDIR}/python-casacore && git clone https://github.com/casacore/python-casacore && wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/master/patches/python_casacore_setup_patch.patch
if [ "$PYTHON_CASACORE_VERSION" != "latest" ]; then cd ${INSTALLDIR}/python-casacore/python-casacore && git checkout tags/${PYTHON_CASACORE_VERSION}; fi
cd ${INSTALLDIR}/python-casacore/python-casacore && patch setup.py $PYTHON_CASACORE_PATCH && ./setup.py build_ext -I${INSTALLDIR}/wcslib/include:${INSTALLDIR}/casacore/include/:${INSTALLDIR}/cfitsio/include:${INSTALLDIR}/boost/include -L${INSTALLDIR}/wcslib/lib:${INSTALLDIR}/casacore/lib/:${INSTALLDIR}/cfitsio/lib/:${INSTALLDIR}/boost/lib:/usr/lib64/
mkdir -p ${INSTALLDIR}/python-casacore/lib/python${PYTHON_VERSION}/site-packages/
mkdir -p ${INSTALLDIR}/python-casacore/lib64/python${PYTHON_VERSION}/site-packages/
export PYTHONPATH=${INSTALLDIR}/python-casacore/lib/python${PYTHON_VERSION}/site-packages:${INSTALLDIR}/python-casacore/lib64/python${PYTHON_VERSION}/site-packages:$PYTHONPATH && cd ${INSTALLDIR}/python-casacore/python-casacore && ./setup.py install --prefix=${INSTALLDIR}/python-casacore/
#
# Install Dysco
#
mkdir -p $INSTALLDIR/dysco/build
cd $INSTALLDIR/dysco && git clone https://github.com/aroffringa/dysco.git src
cd $INSTALLDIR/dysco/build && cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/dysco -DCASACORE_ROOT_DIR=$INSTALLDIR/casacore -DBoost_LIBRARY_DIR=$INSTALLDIR/boost/lib -DBoost_INCLUDE_DIR=$INSTALLDIR/boost/include -DPORTABLE=True ../src && $make -j $J && $make install
#
# install-aoflagger
#
mkdir -p ${INSTALLDIR}/aoflagger/build
if [ "${AOFLAGGER_VERSION}" = "latest" ]; then cd ${INSTALLDIR}/aoflagger && git clone git://git.code.sf.net/p/aoflagger/code aoflagger && cd ${INSTALLDIR}/aoflagger/aoflagger; fi
if [ "${AOFLAGGER_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/aoflagger && git clone git://git.code.sf.net/p/aoflagger/code aoflagger && cd ${INSTALLDIR}/aoflagger/aoflagger && git checkout tags/${AOFLAGGER_VERSION}; fi
cd ${INSTALLDIR}/aoflagger/build && cmake -DCMAKE_INSTALL_PREFIX=${INSTALLDIR}/aoflagger/ -DCASACORE_ROOT_DIR=${INSTALLDIR}/casacore -DCFITSIO_ROOT_DIR=${INSTALLDIR}/cfitsio -DBUILD_SHARED_LIBS=ON -DBOOST_INCLUDEDIR=$INSTALLDIR/boost/include -DBOOST_LIBRARYDIR=$INSTALLDIR/boost/lib -DBOOST_ROOT=$INSTALLDIR/boost/ -DBoost_INCLUDE_DIR=$INSTALLDIR/boost/include -DBoost_LIBRARY_DIR=$INSTALLDIR/boost/lib -DBLAS_atlas_LIBRARY=$INSTALLDIR/openblas/lib/libopenblas.so -DBLAS_f77blas_LIBRARY=$INSTALLDIR/openblas/lib/libopenblas.so -DBLAS_goto2_LIBRARY=$INSTALLDIR/openblas/lib/libopenblas.so -DPORTABLE=True ../aoflagger
cd ${INSTALLDIR}/aoflagger/build && $make -j ${J}
cd ${INSTALLDIR}/aoflagger/build && $make install
#
# install-pybdsf
#
mkdir -p ${INSTALLDIR}/pybdsf
if [ "${PYBDSF_VERSION}" = "latest" ]; then cd ${INSTALLDIR}/pybdsf && git clone https://github.com/lofar-astron/pybdsf pybdsf && cd pybdsf; fi
if [ "${PYBDSF_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/pybdsf && git clone https://github.com/lofar-astron/pybdsf && cd ${INSTALLDIR}/pybdsf/pybdsf && git checkout tags/${PYBDSF_VERSION}; fi
mkdir -p ${INSTALLDIR}/pybdsf/lib/python${PYTHON_VERSION}/site-packages/ && mkdir -p ${INSTALLDIR}/pybdsf/lib64/python${PYTHON_VERSION}/site-packages/ && export PYTHONPATH=${INSTALLDIR}/pybdsf/lib/python${PYTHON_VERSION}/site-packages:${INSTALLDIR}/pybdsf/lib64/python${PYTHON_VERSION}/site-packages:$PYTHONPATH && cd ${INSTALLDIR}/pybdsf/pybdsf && python setup.py install --prefix=${INSTALLDIR}/pybdsf/
#pip install https://github.com/lofar-astron/PyBDSF/archive/v1.8.14.tar.gz
#
# install-lofar
#
mkdir -p ${INSTALLDIR}/lofar
mkdir -p ${INSTALLDIR}/lofar/build
mkdir -p ${INSTALLDIR}/lofar/build/gnucxx11_opt
ls ${INSTALLDIR}
ls ${INSTALLDIR}/lofar
ls ${INSTALLDIR}/lofar/build/gnucxx11_opt
if [ "${LOFAR_VERSION}" = "latest" ]; then cd ${INSTALLDIR}/lofar && svn checkout https://svn.astron.nl/LOFAR/trunk src; fi
if [ "${LOFAR_VERSION}" != "latest" ]; then cd ${INSTALLDIR}/lofar && svn checkout https://svn.astron.nl/LOFAR/tags/LOFAR-Release-${LOFAR_VERSION} src; fi
cd $INSTALLDIR/lofar && svn update --depth=infinity $INSTALLDIR/lofar/src/CMake
wget https://raw.githubusercontent.com/tikk3r/lofar-grid-hpccloud/master/patches/lofar.patch
patch $INSTALLDIR/lofar/src/CMake/variants/GNUCXX11.cmake $PATCH_LOFAR
#cd ${INSTALLDIR}/lofar/build/gnucxx11_opt && cmake -DBUILD_PACKAGES=Offline -DCMAKE_INSTALL_PREFIX=${INSTALLDIR}/lofar/ -DARMADILLO_LIBRARY=$INSTALLDIR/armadillo/lib64/libarmadillo.so -DARMADILLO_INCLUDE_DIR=$INSTALLDIR/armadillo/include -DWCSLIB_ROOT_DIR=${INSTALLDIR}/wcslib/ -DCFITSIO_ROOT_DIR=${INSTALLDIR}/cfitsio/ -DCASACORE_ROOT_DIR=${INSTALLDIR}/casacore/ -DCASAREST_ROOT_DIR=${INSTALLDIR}/casarest/ -DAOFLAGGER_LIBRARY=$INSTALLDIR/aoflagger/lib/libaoflagger.so -DAOFLAGGER_LIBRARY_DIR=${INSTALLDIR}/aoflagger/lib -DAOFLAGGER_INCLUDE_DIR=$INSTALLDIR/aoflagger/include -DLOG4CPLUS_ROOT_DIR=${INSTALLDIR}/log4cplus/ -DPYTHON_BDSF=${INSTALLDIR}/pybdsf/lib/python${PYTHON_VERSION}/site-packages/ -DUSE_OPENMP=True -DBUILD_Imager=OFF -DBLAS_blas_LIBRARY=$INSTALLDIR/openblas/lib/libopenblas.so -DBLAS_f77blas_LIBRARY=$INSTALLDIR/openblas/lib/libopenblas.so -DBLAS_goto2_LIBRARY=$INSTALLDIR/openblas/lib/libopenblas.so -DBoost_LIBRARY_DIR=$INSTALLDIR/boost/lib -DBoost_INCLUDE_DIR=$INSTALLDIR/boost/include ${INSTALLDIR}/lofar/src/
export LD_LIBRARY_PATH=$INSTALLDIR/superlu/lib64:$LD_LIBRARY_PATH
export CMAKE_PREFIX_PATH=$INSTALLDIR/aoflagger:$INSTALLDIR/armadillo:$INSTALLDIR/boost:$INSTALLDIR/casacore:$INSTALLDIR/casarest:$INSTALLDIR/cfitsio:$INSTALLDIR/dysco:$INSTALLDIR/openblas:$INSTALLDIR/superlu:$INSTALLDIR/wcslib:$INSTALLDIR/hdf5
export LD_LIBRARY_PATH=$INSTALLDIR/aoflagger/lib:$INSTALLDIR/armadillo/lib64:$INSTALLDIR/boost/lib:$INSTALLDIR/casacore/lib:$INSTALLDIR/cfitsio/lib:$INSTALLDIR/dysco/lib:$INSTALLDIR/openblas/lib:$INSTALLDIR/superlu/lib64:$INSTALLDIR/wcslib/lib
#cd ${INSTALLDIR}/lofar/build/gnucxx11_opt && cmake -DCMAKE_PREFIX_PATH=$INSTALLDIR/aoflagger:$INSTALLDIR/armadillo:$INSTALLDIR/boost:$INSTALLDIR/casacore:$INSTALLDIR/casarest:$INSTALLDIR/cfitsio:$INSTALLDIR/dysco:$INSTALLDIR/openblas:$INSTALLDIR/superlu:$INSTALLDIR/wcslib -DBUILD_PACKAGES="DPPP DP3 StationResponse pystationresponse ParmDB pyparmdb Pipeline" -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/lofar/ -DUSE_LOG4CPLUS=OFF -DUSE_OPENMP=True ${INSTALLDIR}/lofar/src/
cd ${INSTALLDIR}/lofar/build/gnucxx11_opt && cmake -DCMAKE_PREFIX_PATH=$INSTALLDIR/aoflagger:$INSTALLDIR/armadillo:$INSTALLDIR/boost:$INSTALLDIR/casacore:$INSTALLDIR/casarest:$INSTALLDIR/cfitsio:$INSTALLDIR/dysco:$INSTALLDIR/openblas:$INSTALLDIR/superlu:$INSTALLDIR/wcslib -DBUILD_PACKAGES="DPPP DP3 StationResponse pystationresponse ParmDB pyparmdb Pipeline MS" -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/lofar/ -DUSE_LOG4CPLUS=OFF -DUSE_OPENMP=True ${INSTALLDIR}/lofar/src/
$make -j $J
$make install
#
# Install the standalone StationResponse libraries.
#
echo Installing LOFARBeam...
mkdir -p $INSTALLDIR/LOFARBeam/build
cd $INSTALLDIR/LOFARBeam
git clone https://github.com/lofar-astron/LOFARBeam.git src
cd build && cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/LOFARBeam ../src && $make -j $J && $make install
#
# Install DPPP
#
#export CMAKE_PREFIX_PATH=$INSTALLDIR/aoflagger:$INSTALLDIR/armadillo:$INSTALLDIR/boost:$INSTALLDIR/casacore:$INSTALLDIR/cfitsio:$INSTALLDIR/hdf5:$INSTALLDIR/superlu:$INSTALLDIR/lofar:$INSTALLDIR/LOFARBeam:$INSTALLDIR/hdf5
#export LD_LIBRARY_PATH=$INSTALLDIR/hdf5/lib:$INSTALLDIR/superlu/lib64:$INSTALLDIR/LOFARBeam/lib:$LD_LIBRARY_PATH
#mkdir -p $INSTALLDIR/DPPP/build
#git clone https://github.com/lofar-astron/DP3.git $INSTALLDIR/DPPP/src
#cd $INSTALLDIR/DPPP/build
#cmake3 -DCMAKE_CXX_FLAGS="-D_GLIB_USE_CXX_ABI=1 -DBOOST_NO_CXX11_SCOPED_ENUMS" -DCMAKE_INSTALL_PREFIX:PATH=$INSTALLDIR/DPPP -DLOFAR_STATION_RESPONSE_DIR:PATH=$INSTALLDIR/LOFARBeam/include -DLOFAR_STATION_RESPONSE_LIB:FILEPATH=$INSTALLDIR/LOFARBeam/lib/libstationresponse.so ../src
#$make -j $J && $make install
#
# install-RMextract
#
export PYTHONPATH=$INSTALLDIR/RMextract/lib64/python2.7/site-packages:$PYTHONPATH
echo ${PYTHONPATH}
mkdir ${INSTALLDIR}/RMextract
mkdir ${INSTALLDIR}/RMextract/build
mkdir ${INSTALLDIR}/RMextract/lib64
mkdir ${INSTALLDIR}/RMextract/lib64/python2.7
mkdir ${INSTALLDIR}/RMextract/lib64/python2.7/site-packages
cd ${INSTALLDIR}/RMextract/build && git clone https://github.com/lofar-astron/RMextract.git src && cd src && python setup.py build --add-lofar-utils && python setup.py install --add-lofar-utils --prefix=${INSTALLDIR}/RMextract
ls ${INSTALLDIR}
#
# Install-Losoto
#
export PYTHONPATH=/opt/lofar/losoto/lib/python2.7/site-packages/:$PYTHONPATH
mkdir ${INSTALLDIR}/losoto
mkdir ${INSTALLDIR}/losoto/build
mkdir ${INSTALLDIR}/losoto/lib
mkdir ${INSTALLDIR}/losoto/lib/python2.7
mkdir ${INSTALLDIR}/losoto/lib/python2.7/site-packages
export PYTHONPATH=$INSTALLDIR/losoto/lib/python2.7/site-packages:$PYTHONPATH
cd ${INSTALLDIR}/losoto/build && git clone https://github.com/revoltek/losoto.git src && cd src && python setup.py build && python setup.py install --prefix=${INSTALLDIR}/losoto
#
# Install LSMTool.
#
mkdir -p $INSTALLDIR/lsmtool/lib/python2.7/site-packages
export PYTHONPATH=$INSTALLDIR/lsmtool/lib/python2.7/site-packages:$PYTHONPATH
cd $INSTALLDIR/lsmtool && git clone https://github.com/darafferty/LSMTool.git lsmtool
cd $INSTALLDIR/lsmtool/lsmtool && python setup.py install --prefix=$INSTALLDIR/lsmtool
#
# Install-WSClean
#
export CPATH=${INSTALLDIR}/casacore/include:$INSTALLDIR/LOFARBeam/include:$CPATH
export CMAKE_PREFIX_PATH=$INSTALLDIR/armadillo:$INSTALLDIR/boost:$INSTALLDIR/casacore:$INSTALLDIR/cfitsio:$INSTALLDIR/dysco:$INSTALLDIR/idg:$INSTALLDIR/lofar:$INSTALLDIR/LOFARBeam:$INSTALLDIR/openblas:$INSTALLDIR/superlu:$INSTALLDIR/wcslib:$INSTALLDIR/hdf5:/usr/lib64
mkdir ${INSTALLDIR}/wsclean
if [ "$WSCLEAN_VERSION" != "latest" ]; then cd ${INSTALLDIR}/wsclean && wget http://downloads.sourceforge.net/project/wsclean/wsclean-${WSCLEAN_VERSION}/wsclean-${WSCLEAN_VERSION}.tar.bz2 && tar -xjf wsclean-${WSCLEAN_VERSION}.tar.bz2 && cd wsclean-${WSCLEAN_VERSION}; fi
if [ "$WSCLEAN_VERSION" = "latest" ]; then cd ${INSTALLDIR}/wsclean && git clone git://git.code.sf.net/p/wsclean/code src && cd src/wsclean; git checkout 5b7bdce; fi
mkdir build && cd build && cmake -DCMAKE_INSTALL_PREFIX=$INSTALLDIR/wsclean -DPORTABLE=True -DLOFAR_STATION_RESPONSE_DIR:PATH=$INSTALLDIR/LOFARBeam/include -DLOFAR_STATION_RESPONSE_LIB:FILEPATH=$INSTALLDIR/LOFARBeam/lib/libstationresponse.so ..
$make -j ${J}
$make install
#
# Install DS9
#
mkdir -p $INSTALLDIR/ds9/bin
cd $INSTALLDIR/ds9 && wget http://ds9.si.edu/download/centos7/ds9.centos7.8.0.1.tar.gz
tar xf ds9*.tar.gz -C $INSTALLDIR/ds9/bin
echo "Installation directory contents:"
ls ${INSTALLDIR}
rm -rf ${INSTALLDIR}/lofar/src
rm -rf ${INSTALLDIR}/lofar/build/gnu_opt
rm -rf ${INSTALLDIR}/casacore/src
rm -rf ${INSTALLDIR}/casarest/src
yum -y clean all
#
# init-lofar
#
#ln -s /opt/lofar/DPPP/bin/DPPP /opt/lofar/lofar/bin/NDPPP
echo export INSTALLDIR=$INSTALLDIR > $INSTALLDIR/init.sh
echo export HDF5_USE_FILE_LOCKING=FALSE >> $INSTALLDIR/init.sh
echo source \$INSTALLDIR/lofar/lofarinit.sh >> $INSTALLDIR/init.sh
echo export PYTHONPATH=\$INSTALLDIR/dppp:\$INSTALLDIR/lofar/lib64/python2.7/site-packages:\$INSTALLDIR/losoto/lib/python2.7/site-packages:\$INSTALLDIR/lsmtool/lib/python2.7/site-packages:\$INSTALLDIR/pybdsf/lib/python2.7/site-packages:\$INSTALLDIR/pybdsf/lib64/python2.7/site-packages:\$INSTALLDIR/python-casacore/lib/python2.7/site-packages/:\$INSTALLDIR/python-casacore/lib64/python2.7/site-packages/:\$INSTALLDIR/RMextract/lib64/python2.7/site-packages:\$INSTALLDIR/DPPP/lib64/python2.7/site-packages/:/usr/lib64/python2.7/site-packages >> $INSTALLDIR/init.sh
echo export PATH=\$INSTALLDIR/aoflagger/bin:\$PATH >> $INSTALLDIR/init.sh
echo export PATH=\$INSTALLDIR/casacore/bin:\$PATH >> $INSTALLDIR/init.sh
echo export PATH=\$INSTALLDIR/ds9/bin:\$PATH >> $INSTALLDIR/init.sh
echo export PATH=\$INSTALLDIR/DPPP/bin:\$PATH >> $INSTALLDIR/init.sh
echo export PATH=\$INSTALLDIR/dysco/bin:\$PATH >> $INSTALLDIR/init.sh
echo export PATH=\$INSTALLDIR/lofar/bin:\$PATH >> $INSTALLDIR/init.sh
echo export PATH=\$INSTALLDIR/losoto/bin:\$PATH >> $INSTALLDIR/init.sh
echo export PATH=\$INSTALLDIR/pybdsf/bin:\$PATH >> $INSTALLDIR/init.sh
echo export PATH=\$INSTALLDIR/RMextract/bin:\$PATH >> $INSTALLDIR/init.sh
echo export PATH=\$INSTALLDIR/wsclean/bin:\$PATH >> $INSTALLDIR/init.sh
echo export LD_LIBRARY_PATH=\$INSTALLDIR/aoflagger/lib:\$INSTALLDIR/armadillo/lib64:\$INSTALLDIR/boost/lib:\$INSTALLDIR/casacore/lib:\$INSTALLDIR/cfitsio/lib:\$INSTALLDIR/DPPP/lib:\$INSTALLDIR/dysco/lib:\$INSTALLDIR/hdf5/lib:\$INSTALLDIR/lofar/lib64:\$INSTALLDIR/LOFARBeam/lib:\$INSTALLDIR/openblas/lib:\$INSTALLDIR/superlu/lib64:\$INSTALLDIR/wcslib/:\$LD_LIBRARY_PATH >> $INSTALLDIR/init.sh
echo export OPENBLAS_NUM_THREADS=1 >> $INSTALLDIR/init.sh
echo export OPENBLAS_MAX_THREADS=1 >> $INSTALLDIR/init.sh
echo export OMP_NUM_THREADS=1 >> $INSTALLDIR/init.sh
echo export OMP_MAX_THREADS=1 >> $INSTALLDIR/init.sh
#
# entrypoint
#
%runscript
. $INSTALLDIR/init.sh
ulimit -n 4096
%help
This Singularity image contains an install of LOFAR ${LOFAR_VERSION}. In order to run your pipelines, you may need to know where the software is installed. The root directory is /opt/lofar, with all software installed as follows:
* AOFlagger: $INSTALLDIR/aoflagger
* Casacore: $INSTALLDIR/casacore
* Dysco: $INSTALLDIR/dysco
* LOFAR: $INSTALLDIR/lofar
* LoSoTo: $INSTALLDIR/losoto
* PyBDSF: $INSTALLDIR/pybdsf
* RMextract: $INSTALLDIR/RMextract
To execute a command, use
singularity exec -B <paths,that,need,to,be,accessible> <path to image> <command> <arguments>
for example:
#singularity exec lofar.simg genericpipeline.py -d -c pipeline.cfg pipeline.parset