Tuesday, 19 July 2016
New LOFAR baseline comparison tool
I've written a new tool for comparing the lengths of different baselines to a single LOFAR station. It should be useful when looking for delay and rate solutions with FRING or a similar task. The tool is located at http://www.colmcoughlan.com/lofar.html.
Tuesday, 24 May 2016
Installing AIPS on Ubuntu 16.04
I've recently installed AIPS (version 31DEC16) on Ubuntu 16.04. Here are my notes on the installation experience. Due to recent compiler work on AIPS this was a much better experience than on recent new versions of Ubuntu. Note that this was a "text" (compile-from-source) install - if you just need to use AIPS you will likely get a faster experience using the pre-compiled binaries available from the binary installation (see http://www.aips.nrao.edu/dec16.shtml for full instructions)
As before, the Ubuntu dependencies are:
libx11-dev and its dependancies
x11proto-xext-dev
libxext-dev
libxpm-dev
libncurses5-dev
libncursesw5-dev
libbsd-dev
libedit-dev
I use gcc and gfortran to compile AIPS - you need to specify their location in the AIPS installer (/usr/bin/gfortran is both the fortran compiler and the linker for me, while /usr/bin/gcc compiles for C). I also have trouble with the fortran compiler flags -axWPT and -ip options, so I turn them off both for gfortran and gcc. XAS isn't built using these directives however, so you need to go to Y/SERVERS and edit XAS.SHR to remove the use of the axWPT and -ip flags when compiling the TV server.
A new problem with this combination of Ubuntu and AIPS is an errant "-c" ending up in the link command for making XAS after XAS.SHR is run. This means you will get an error that XAS failed to link, but if you open the makefile at Y/SERVERS/XAS/makefile and remove the "-c" option from the LOCALOPTS_LNX64 variable, then you can just type "make" to correctly make and set up XAS (I did this in a separate terminal while the rest of the installation was proceeding). Make sure the executable xas file has been successfully moved to LNX64/LOAD.
Make sure to add
sssin 5000/tcp SSSIN # AIPS TV
ssslock 5002/tcp SSSLOCK # AIPS TV Lock
msgserv 5008/tcp MSGSERV # AIPS Message Server
tekserv 5009/tcp TEKSERV # AIPS TekServer
aipsmt0 5010/tcp AIPSMT0
aipsmt1 5011/tcp AIPSMT1
aipsmt2 5012/tcp AIPSMT2
aipsmt3 5013/tcp AIPSMT3
aipsmt4 5014/tcp AIPSMT4
aipsmt5 5015/tcp AIPSMT5
aipsmt6 5016/tcp AIPSMT6
aipsmt7 5017/tcp AIPSMT7
to /etc/services to get AIPS to run properly. To do this you may need to open the file as root.
One last thing - add the aips path to your profile so you can run it straight from the terminal. For me the line was ". /home/colm/aips/LOGIN.SH; $CDTST". The CDTST bit at the end is needed if you intend to compile custom AIPS tasks.
As before, the Ubuntu dependencies are:
libx11-dev and its dependancies
x11proto-xext-dev
libxext-dev
libxpm-dev
libncurses5-dev
libncursesw5-dev
libbsd-dev
libedit-dev
I use gcc and gfortran to compile AIPS - you need to specify their location in the AIPS installer (/usr/bin/gfortran is both the fortran compiler and the linker for me, while /usr/bin/gcc compiles for C). I also have trouble with the fortran compiler flags -axWPT and -ip options, so I turn them off both for gfortran and gcc. XAS isn't built using these directives however, so you need to go to Y/SERVERS and edit XAS.SHR to remove the use of the axWPT and -ip flags when compiling the TV server.
A new problem with this combination of Ubuntu and AIPS is an errant "-c" ending up in the link command for making XAS after XAS.SHR is run. This means you will get an error that XAS failed to link, but if you open the makefile at Y/SERVERS/XAS/makefile and remove the "-c" option from the LOCALOPTS_LNX64 variable, then you can just type "make" to correctly make and set up XAS (I did this in a separate terminal while the rest of the installation was proceeding). Make sure the executable xas file has been successfully moved to LNX64/LOAD.
Make sure to add
sssin 5000/tcp SSSIN # AIPS TV
ssslock 5002/tcp SSSLOCK # AIPS TV Lock
msgserv 5008/tcp MSGSERV # AIPS Message Server
tekserv 5009/tcp TEKSERV # AIPS TekServer
aipsmt0 5010/tcp AIPSMT0
aipsmt1 5011/tcp AIPSMT1
aipsmt2 5012/tcp AIPSMT2
aipsmt3 5013/tcp AIPSMT3
aipsmt4 5014/tcp AIPSMT4
aipsmt5 5015/tcp AIPSMT5
aipsmt6 5016/tcp AIPSMT6
aipsmt7 5017/tcp AIPSMT7
to /etc/services to get AIPS to run properly. To do this you may need to open the file as root.
One last thing - add the aips path to your profile so you can run it straight from the terminal. For me the line was ". /home/colm/aips/LOGIN.SH; $CDTST". The CDTST bit at the end is needed if you intend to compile custom AIPS tasks.
Monday, 9 May 2016
New website
I've made a website, where I hope to include information about some of the work that I'm doing. You can see it at www.colmcoughlan.com
Thursday, 19 November 2015
Negative diagonal elements in the covariance matrix returned by numpy.polyfit
I ran into a strange issue fitting a line to a small number of data points using numpy.polyfit that I thought was worth documenting.
I ran a command of the form:
p, cov = np.polyfit(x,y,1,w,cov=True),
where x, y and w were arrays of length 3.
The command returned the correct slope and y-intercept values, however the covariance matrix, cov, had strictly negative diagonal terms. This is apparantly because numpy scales the covariance matrix as described in here.
The scaling applied is a factor such that
factor = resids / (len(x) - order - 2.0)
If, like me, you are making a first order polynomial fit to a dataset of 3 values, the denominator has the effect of multiplying the expected matrix by -1. If I was unlucky enough to have 4 points, it would have thrown bigger errors.
In my case, looking at the results here, I could recover the correct values just by multiplying the matrix by minus one. This is a strange weighting to apply to a small dataset - I assume it makes sense if you have many points and the developers wanted to keep numpy.polyfit consistent.
I ran a command of the form:
p, cov = np.polyfit(x,y,1,w,cov=True),
where x, y and w were arrays of length 3.
The command returned the correct slope and y-intercept values, however the covariance matrix, cov, had strictly negative diagonal terms. This is apparantly because numpy scales the covariance matrix as described in here.
The scaling applied is a factor such that
factor = resids / (len(x) - order - 2.0)
If, like me, you are making a first order polynomial fit to a dataset of 3 values, the denominator has the effect of multiplying the expected matrix by -1. If I was unlucky enough to have 4 points, it would have thrown bigger errors.
In my case, looking at the results here, I could recover the correct values just by multiplying the matrix by minus one. This is a strange weighting to apply to a small dataset - I assume it makes sense if you have many points and the developers wanted to keep numpy.polyfit consistent.
Monday, 5 October 2015
Fixing AIPS after upgrading to El Capitan on OSX
I recently ran into some AIPS trouble after upgrading from Mavericks to El Capitan. My installation of AIPS complained about X11 and about being unable to find some libraries that normally come with the binary distribution I had actually installed.
The library fix should have been the easiest - AIPS was looking for:
The library fix should have been the easiest - AIPS was looking for:
- libsvml.dylib
- libirc.dylib
- libimf.dylib
All of these come with the binary and are located in 31DEC14/MACINT/LIBR/INTELCMP of the AIPS directory (note I'm still using the frozen AIPS from December 2014).
AIPS automatically adds this location to DYLD_LIBRARY_PATH when you run LOGIN.SH, but even though the libraries are on the path, AIPS does not seem to be able to find them when it needs them. I fixed this temporarily by making a simlink for each of the three libraries in 31DEC14/MACINT/LOAD, where all the AIPS executables are stored. Now when the tasks look for the libraries it appears as though they are in the same directory. Unfortunately this means having to launch AIPS from 31DEC14/MACINT/LOAD, but it works for now. I'll update this if I get around to finding out why the libraries on DYLD_LIBRARY_PATH aren't being found.
The second problem was that the El Capitan upgrade broke the X11 installation I had. I reinstalled X11 from http://xquartz.macosforge.org/landing/, but AIPS still complained. Reading the error message, it looked like AIPS was looking for X11 in /usr/X11R6, whereas I had it installed in /usr/X11. Again I fixed this with a simlink (ln -s /usr/X11 /usr/X11R6), but because of some changes in El Capitan I could not edit /usr even with superuser privileges. I restarted the computer in recovery mode (holding cmd+r) and used the terminal to enable changes to /usr with the command "csrutil disable" and rebooted. I then made the simlink, rebooted into recovery mode and re-enabled protected mode with "csrutil enable" (the steps are detailed at http://stackoverflow.com/questions/32590053/copying-file-under-root-got-failed-in-os-x-el-capitan-10-11/32590885#32590885).
AIPS is now working fine on the upgraded OS. It's likely that these issues will be taken care of automatically in a fresh install of AIPS when Eric Greisen updates the Mac binaries for El Capitan, so hopefully these steps will only be necessary if you're keeping an old version.
Tuesday, 14 October 2014
Installing LOFAR software on a mac (Mavericks)
I've installed some of the LOFAR data reduction software on a macbook pro running OSX 10.9 (Mavericks). This is probably not the best method in the world to install the LOFAR software, but it works reasonably well and I haven't seen any other documentation for a mac installation so it might be useful to someone.
I roughly followed the same procedure as for Ubuntu, but with a few differences.
First I used macports to download as many of the dependencies I listed here as I could find. The full list of macports I installed is
Boost:
Probably unnecessary patches:
The first three patches are probably redundant if you remember to include the DUSE_SHMEM=OFF compiler option.
I roughly followed the same procedure as for Ubuntu, but with a few differences.
First I used macports to download as many of the dependencies I listed here as I could find. The full list of macports I installed is
binutils @2.24_0 (active)
boost @1.56.0_1+no_single+no_static+python27 (active)
bzip2 @1.0.6_0 (active)
cctools @855_1+llvm35 (active)
cctools-headers @855_0 (active)
cfitsio @3.340_0 (active)
cloog @0.18.2_0 (active)
cmake @3.0.2_0 (active)
curl @7.38.0_0+ssl (active)
curl-ca-bundle @7.38.0_0 (active)
cython_select @0.1_0 (active)
db48 @4.8.30_3 (active)
db_select @0.1_2 (active)
expat @2.1.0_0 (active)
fftw-3 @3.3.4_0 (active)
gcc49 @4.9.1_0 (active)
gcc_select @0.1_8 (active)
gettext @0.19.2_0 (active)
gmp @6.0.0_1 (active)
hdf5 @1.8.13_0+cxx (active)
icu @53.1_1 (active)
isl @0.13_0 (active)
ld64 @236.3_1+llvm35 (active)
libarchive @3.1.2_0 (active)
libcxx @183506_1 (active)
libedit @20121213-3.0_0 (active)
libffi @3.1_4 (active)
libgcc @4.9.1_0 (active)
libiconv @1.14_0 (active)
libidn @1.29_0 (active)
libmpc @1.0.2_0 (active)
libxml2 @2.9.1_0 (active)
llvm-3.5 @3.5-r216817_0+assertions (active)
llvm_select @1.0_0 (active)
lzo2 @2.06_0 (active).
mpfr @3.1.2-p10_0 (active)
ncurses @5.9_2 (active)
nosetests_select @0.1_0 (active)
openssl @1.0.1i_0 (active)
pcre @8.35_0 (active)
py27-cython @0.21_0 (active)
py27-nose @1.3.1_0 (active)
py27-numpy @1.9.0_0 (active)
py27-pyfits @3.3_0 (active)
py27-pywcs @1.11-4.8.2_1 (active)
py27-scipy @0.14.0_0+gcc48 (active)
py27-setuptools @6.0.2_0 (active)
python27 @2.7.8_2 (active)
python_select @0.3_3 (active)
sqlite3 @3.8.6_0 (active)
SuiteSparse @4.2.1_3 (active)
swig @3.0.2_0 (active)
swig-python @3.0.2_0 (active)
wcslib @4.23_1 (active)
xz @5.0.7_0 (active)
zlib @1.2.8_0 (active)
I then downloaded and compiled FFTW and boost manually. This was required for boost because macports has trouble building boost with the gnu compiler suite and the version of boost built with clang doesn't seem to work with the LOFAR software. I thought something similar was happening with FFTW, but it might have turned out to be a linking error on my behalf - so you can try to link the macports-provided installation of FFTW instead of building your own if you prefer.
The commands I used were:
The commands I used were:
Boost:
./bootstrap.sh
--prefix=/Users/admin/boost --withpython=/opt/local/bin/python2.7
--with-toolset=gcc
./b2
./b2
install
FFTW
./configure
--prefix=/Users/admin/fftw --enable-threads
make -j 8
make install
./configure
--prefix=/Users/admin/fftwf --enable-float --enable-threads
make -j 8
make
install
Issues
There were lots of failures the first time I tried to compile the LOFAR software. Refer to the Ubuntu instructions for the gist of what I was doing. I installed everything LOFAR-related into the /opt/lofar-software directory.
cmake
-DBUILD_TESTING=NO -DCMAKE_INSTALL_PREFIX=/opt/lofar-software
-DUSE_FFTW3=Yes -DUSE_THREADS=YES -DUSE_HDF5=YES -DUSE_OPENMP=YES
-DDATA_DIR=/opt/lofar-software/data -DFFTW3_ROOT_DIR=/usr/local/lib
../..
Installed
as usual
export
LOFAR_ROOT="/opt/lofar-software"
export
PATH="${PATH}:${LOFAR_ROOT}/bin/"
export
LD_LIBRARY_PATH="${LOFAR_ROOT}/lib/"
export
PYTHONPATH="{LOFAR_ROOT}/lib/python/"
Next is the installation of PYRAP. PYRAP has not been updated in a while and you need to apply the patch indicated here to make sure it installs correctly on a mac (the bug reporter links the patch, the plus lines in the diff file indicate new lines to be added, the minuses lines that need to be taken away). Basically you need to ensure it only tries to build for one architecture. I did this manually by going to the affected setup.py files (you'll spot them if you try to build), but you might be able to do this a lot faster if you know more about patching than me. Then build with
./batchbuild-trunk.py
--casacore-root=/opt/lofar-software/ --prefix=/opt/lofar-software/
--python-prefix=/opt/lofar-software/lib/python
--extra-root=/opt/local/ --boost-lib=boost_python-mt
–universal=x86_64
(You might notice the boost_python-mt library here. That is from the macports boost install (clang) which caused no problems in this step.)
Compiled
and installed CASAREST as usual
Added
data folder as usual.
I needed to patch some LOFAR files to get them to compile successfully. I now suspect some of these patches might have been unnecessary as I was using incorrect settings.
Necessary patches:
1. LCS/pytools. tconvert.cc needs to have the python.h library included at the start (#include <python.h>.
2. Baselinefitting.cc needs to have sincosf replaced with separate calls to sin and cos (apparently sincosf is not available in OSX's version of the standard math library?). I commented out the original function and replaced it as follows:
//sincosf(phase_ij_obs - phase_ij_model, &sin_dphase, &cos_dphase); sin_dphase = sin(phase_ij_obs - phase_ij_model); cos_dphase = cos(phase_ij_obs - phase_ij_model);
Probably unnecessary patches:
The first three patches are probably redundant if you remember to include the DUSE_SHMEM=OFF compiler option.
1. LCS/common. dlmalloc.c. Comment out reference around Have_usr_include_malloc_h, thus forcing the code to define its own.
2. shmem_alloc.cc comment out def of "union semum".
3. shmem_alloc.h comment out inclusion of malloc.h.
I don't know why these didn't re-occur:
4. image2d.cpp needs to have #include <cstring> added.
5. tickset.h needs to have exp10 functions replaced with pow(10,x) functions.
6. imagewidget.cpp same exp10 patch as above.
7. processcommander.cpp. Add definition for HOST_NAME_MAX (a large long).
Note that the CMAKE/variants/GNU.cmake file needs to be edited to point to the macports compilers as follows:
set(GNU_C /opt/local/bin/gcc) # GNU C compiler
set(GNU_CXX /opt/local/bin/g++) # GNU C++ compiler
set(GNU_Fortran /opt/local/bin/gfortran) # GNU Fortran compiler
set(GNU_ASM /opt/local/bin/gcc) # GNU assembler
Note that the CMAKE/variants/GNU.cmake file needs to be edited to point to the macports compilers as follows:
set(GNU_C /opt/local/bin/gcc) # GNU C compiler
set(GNU_CXX /opt/local/bin/g++) # GNU C++ compiler
set(GNU_Fortran /opt/local/bin/gfortran) # GNU Fortran compiler
set(GNU_ASM /opt/local/bin/gcc) # GNU assembler
After applying the necessary patches above, the following compilation command should work when called from /build/gnu_opt.
cmake
-DCASACORE_ROOT_DIR=/opt/lofar-software/ -DBUILD_SHARED_LIBS=ON
-DUSE_OPENMP=ON -DBUILD_PACKAGES="ParmDB Calibration DP3
Pipeline MSLofar LofarFT GSM"
-DCMAKE_INSTALL_PREFIX:PATH=/opt/lofar-software/
-DCMAKE_C_COMPILER=/opt/local/bin/gcc
-DCMAKE_CXX_COMPILER=/opt/local/bin/g++
-DFFTW3_LIBRARY=/Users/admin/fftw/lib/libfftw3.a
-DFFTW3F_LIBRARY=/Users/admin/fftwf/lib/libfftw3f.a
-DFFTW3F_THREADS_LIBRARY=/Users/admin/fftwf/lib/libfftw3f_threads.a
-DPYTHON_EXECUTABLE:FILEPATH=/opt/local/bin/python2.7
-DF2PY_EXECUTABLE=/opt/local/bin/f2py-2.7 -DUSE_LOG4CPLUS=OFF
-DUSE_SHMEM=OFF -DBOOST_ROOT=/Users/admin/boost -Wno-dev ../..
Then run make and make install to finish up.
One final thing to do is to add the following lines to the .profile file in your home directory.
One final thing to do is to add the following lines to the .profile file in your home directory.
source /opt/lofar-software/lofarinit.sh
export DYLD_LIBRARY_PATH="$LD_LIBRARY_PATH"
This should allow LOFAR commands to be run from any terminal.
Tuesday, 7 October 2014
Installing LOFAR software on Ubuntu 12.04
Installing LOFAR software on Ubuntu 12.04
These are some notes on how I installed some LOFAR software on Ubuntu 12.04. They are based on some notes I found on the LOFAR wiki at http://www.lofar.org/operations/doku.php?id=engineering:user_software:ubuntu_12_4.
Install main LOFAR suite
===============================================
N.B. Notes below install to strange directory. Build in one directory, and install everything else into the CASACORE directory (binary)
Dependencies:
libgtkmm-2.4-dev python-matplotlib python-pyfits libatlas-base-dev
mpi-default-bin mpi-default-dev libfreetype6-dev python-setuptools
libxml2-dev libpng12-dev libcfitsio3 libcfitsio3-dev libboost-all-dev
autoconf autoconf-archive autogen automake binutils-dev cmake cmake-curses-gui
cvs doxygen flex gfortran git guile-1.8-dev ipython libblas-dev libblitz0-dev
libboost-all-dev libboost-dev libfftw3-dev libfftw3-doc libgfortran3
libglib2.0-dev libgsl0-dev liblapack-dev liblog4cxx10 liblog4cxx10-dev
libopenmpi-dev libpqxx3-dev libx11-dev mgdiff mpi-default-dev patch pgplot5
python-dev python-numeric python-numpy python-scipy scons subversion-tools
swig bison libbison-dev
tcl tcl-dev tk tk-dev tk8.5-dev tcl8.5-dev
libhdf5-dev (oder: libhdf5-serial-1.8.4 libhdf5-serial-dev)
### "libhdf5-serial" is needed for DAL, it doesn't work with "libhdf5-openmpi"
wcslib-dev liblog4cplus-dev liblog4cplus-1.0-4 cython
###for parmdbplot:
python-sip python-qt4
########## LOFAR software:
Download packages:
##################
mkdir Downloads
cd Downloads
wget ftp://ftp.atnf.csiro.au/pub/software/asap/data/asap_data.tar.bz2
Download and Build Casacore:
############################
tar -xjvf ../Downloads/asap_data.tar.bz2
(This creates the "data" subdirectory)
mkdir BuildDir/casacore
cd BuildDir/casacore
svn co http://casacore.googlecode.com/svn/trunk source
mkdir -p build/opt
cd build/opt
cmake -DBUILD_TESTING=NO -DCMAKE_INSTALL_PREFIX=/opt/lofar-stuff -DUSE_FFTW3=Yes -DUSE_THREADS=YES -DUSE_HDF5=YES -DUSE_OPENMP=YES -DDATA_DIR=/opt/lofar-stuff/data ../../source
make -j12
make install
Install Casacore data:
############################
cd BuildDir/..
tar -xjvf Download/asap_data.tar.bz2
Download and Build pyrap
############################
mkdir /cluster/lofar/BuildDir/pyrap
cd /cluster/lofar/BuildDir/pyrap
svn co http://pyrap.googlecode.com/svn/trunk dev-source
export LOFAR_STUFF_ROOT="/opt/lofar-stuff"
export PATH="${PATH}:${LOFAR_STUFF_ROOT}/bin/"
export LD_LIBRARY_PATH="${LOFAR_STUFF_ROOT}/lib/"
export PYTHONPATH="${LOFAR_STUFF_ROOT}/lib/python/"
ln -s /opt/soft/lofar-stuff/lib/ /opt/soft/lofar-stuff/lib64
cd dev-source/
./batchbuild-trunk.py --casacore-root=/opt/lofar-stuff --prefix=/opt/lofar-stuff --python-prefix=/opt/lofar-stuff/lib/python
Download and Build casarest
###########################
mkdir /cluster/lofar/BuildDir/casarest
cd /cluster/lofar/BuildDir/casarest
svn co https://svn.astron.nl/casarest/trunk/casarest source
mkdir build
cd build
cmake -DCASACORE_ROOT_DIR=/opt/lofar-stuff -DBUILD_ALL=1 -DCMAKE_INSTALL_PREFIX:PATH=/opt/lofar-stuff ../source
make -j12
make install
Download and Build the LOFAR Software
#####################################
Download latest copy of LOFAR software
mkdir -p build/gnu_opt
cd build/gnu_opt
cmake -DCASACORE_ROOT_DIR=/opt/lofar-stuff/ -DBUILD_SHARED_LIBS=ON -DUSE_OPENMP=ON -DBUILD_PACKAGES="ParmDB Calibration DP3 Pipeline MSLofar LofarFT GSM" -DCMAKE_INSTALL_PREFIX:PATH=/opt/lofar-stuff ../../LOFAR/
make -j12
make install
Note: I found that the above instructions installed the pyrap python libraries in a separate folder to where LOFAR was looking, so I just found them in lofar-software/lib/python and manually pasted them into the right directory (the one LOFAR regards as PYTHONPATH)
These are some notes on how I installed some LOFAR software on Ubuntu 12.04. They are based on some notes I found on the LOFAR wiki at http://www.lofar.org/operations/doku.php?id=engineering:user_software:ubuntu_12_4.
Install main LOFAR suite
===============================================
N.B. Notes below install to strange directory. Build in one directory, and install everything else into the CASACORE directory (binary)
Dependencies:
libgtkmm-2.4-dev python-matplotlib python-pyfits libatlas-base-dev
mpi-default-bin mpi-default-dev libfreetype6-dev python-setuptools
libxml2-dev libpng12-dev libcfitsio3 libcfitsio3-dev libboost-all-dev
autoconf autoconf-archive autogen automake binutils-dev cmake cmake-curses-gui
cvs doxygen flex gfortran git guile-1.8-dev ipython libblas-dev libblitz0-dev
libboost-all-dev libboost-dev libfftw3-dev libfftw3-doc libgfortran3
libglib2.0-dev libgsl0-dev liblapack-dev liblog4cxx10 liblog4cxx10-dev
libopenmpi-dev libpqxx3-dev libx11-dev mgdiff mpi-default-dev patch pgplot5
python-dev python-numeric python-numpy python-scipy scons subversion-tools
swig bison libbison-dev
tcl tcl-dev tk tk-dev tk8.5-dev tcl8.5-dev
libhdf5-dev (oder: libhdf5-serial-1.8.4 libhdf5-serial-dev)
### "libhdf5-serial" is needed for DAL, it doesn't work with "libhdf5-openmpi"
wcslib-dev liblog4cplus-dev liblog4cplus-1.0-4 cython
###for parmdbplot:
python-sip python-qt4
########## LOFAR software:
Download packages:
##################
mkdir Downloads
cd Downloads
wget ftp://ftp.atnf.csiro.au/pub/software/asap/data/asap_data.tar.bz2
Download and Build Casacore:
############################
tar -xjvf ../Downloads/asap_data.tar.bz2
(This creates the "data" subdirectory)
mkdir BuildDir/casacore
cd BuildDir/casacore
svn co http://casacore.googlecode.com/svn/trunk source
mkdir -p build/opt
cd build/opt
cmake -DBUILD_TESTING=NO -DCMAKE_INSTALL_PREFIX=/opt/lofar-stuff -DUSE_FFTW3=Yes -DUSE_THREADS=YES -DUSE_HDF5=YES -DUSE_OPENMP=YES -DDATA_DIR=/opt/lofar-stuff/data ../../source
make -j12
make install
Install Casacore data:
############################
cd BuildDir/..
tar -xjvf Download/asap_data.tar.bz2
Download and Build pyrap
############################
mkdir /cluster/lofar/BuildDir/pyrap
cd /cluster/lofar/BuildDir/pyrap
svn co http://pyrap.googlecode.com/svn/trunk dev-source
export LOFAR_STUFF_ROOT="/opt/lofar-stuff"
export PATH="${PATH}:${LOFAR_STUFF_ROOT}/bin/"
export LD_LIBRARY_PATH="${LOFAR_STUFF_ROOT}/lib/"
export PYTHONPATH="${LOFAR_STUFF_ROOT}/lib/python/"
ln -s /opt/soft/lofar-stuff/lib/ /opt/soft/lofar-stuff/lib64
cd dev-source/
./batchbuild-trunk.py --casacore-root=/opt/lofar-stuff --prefix=/opt/lofar-stuff --python-prefix=/opt/lofar-stuff/lib/python
Download and Build casarest
###########################
mkdir /cluster/lofar/BuildDir/casarest
cd /cluster/lofar/BuildDir/casarest
svn co https://svn.astron.nl/casarest/trunk/casarest source
mkdir build
cd build
cmake -DCASACORE_ROOT_DIR=/opt/lofar-stuff -DBUILD_ALL=1 -DCMAKE_INSTALL_PREFIX:PATH=/opt/lofar-stuff ../source
make -j12
make install
Download and Build the LOFAR Software
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Download latest copy of LOFAR software
mkdir -p build/gnu_opt
cd build/gnu_opt
cmake -DCASACORE_ROOT_DIR=/opt/lofar-stuff/ -DBUILD_SHARED_LIBS=ON -DUSE_OPENMP=ON -DBUILD_PACKAGES="ParmDB Calibration DP3 Pipeline MSLofar LofarFT GSM" -DCMAKE_INSTALL_PREFIX:PATH=/opt/lofar-stuff ../../LOFAR/
make -j12
make install
Note: I found that the above instructions installed the pyrap python libraries in a separate folder to where LOFAR was looking, so I just found them in lofar-software/lib/python and manually pasted them into the right directory (the one LOFAR regards as PYTHONPATH)
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