André Offringa's MWA pre-processing pipeline.
Once installed, simply run cotter to see the list of available options.
This is simple to compile from source, but Debian-based distros provide this library in the liberfa-dev package.
An open-source replacement for LIBSLA. This depends only on ERFA and is also simple to compile from source, but because it is a little different, instructions are listed below.
- Ensure ERFA is installed.
- Navigate to the LIBPAL releases page and download the latest version of the software in a tarball. It seems that trying to install from git requires a "Starlink-patched version of automake", which is best avoided.
- Run the usual configure-make-make install commands:
# PREFIX is where you want to install LIBPAL; a sensible choice is /usr/local
# ERFA_ROOT is where ERFA is installed; this is probably /usr
./configure --prefix="$PREFIX" --without-starlink --with-erfa="$ERFA_ROOT"
make
make install
- Note that header files are installed into an unusual place; the following command might be helpful:
ln -s "$PREFIX"/include/star/* "$PREFIX"/include
As with ERFA, this can be installed in Debian-based distros with the package aoflagger-dev. Otherwise, installation instructions can be found here.
Once you've cloned cotter and installed the dependencies, the rest is easy:
cd cotter
mkdir build
cd build
# Specifying LIBPAL_INCLUDE_DIR is necessary if LIBPAL header files are in a non-standard place.
cmake ../ -DLIBPAL_INCLUDE_DIR=/usr/local/include
make -j8
make install
If you have many libraries in non-standard places, then the following example of a cmake command might be helpful:
cmake ../ \
-DCMAKE_INSTALL_PREFIX="$PREFIX" \
-DAOFLAGGER_INCLUDE_DIR="$AOFLAGGER_INCLUDE_DIR" \
-DAOFLAGGER_LIB="$AOFLAGGER_LIB"/libaoflagger.so \
-DCASA_CASA_LIB="$CASACORE_ROOT"/lib/libcasa_casa.so \
-DCASA_INCLUDE_DIR:STRING="$CASACORE_ROOT/include/;$CASACORE_ROOT/include/casacore" \
-DCASA_MEASURES_LIB="$CASACORE_ROOT"/lib/libcasa_measures.so \
-DCASA_MS_LIB="$CASACORE_ROOT"/lib/libcasa_ms.so \
-DCASA_TABLES_LIB="$CASACORE_ROOT"/lib/libcasa_tables.so \
-DCFITSIO_LIB="$CFITSIO_ROOT"/lib/libcfitsio.so \
-DFITSIO_INCLUDE_DIR="$CFITSIO_ROOT"/include \
-DFFTW3_LIB="$FFTW_DIR"/libfftw3.so \
-DLIBPAL_INCLUDE_DIR="$LIBPAL_ROOT"/include \
-DLIBPAL_LIB="$LIBPAL_LIB"/libpal.so \
-DBLAS_LIBRARIES="$MAALI_LAPACK_HOME"/lib64/libblas.so \
-DLAPACK_LIBRARIES="$MAALI_LAPACK_HOME"/lib64/liblapack.so
An appropriate Dockerfile for creating a cotter container is provided in Dockerfile in the repo. To build the image, run the following, it will create an image called cotter:latest.
docker build -t cotter:latest .
Alternatively you can pull the latest cotter from the mwatelescope DockerHub repository:
docker pull mwatelescope/cotter:latest
One way to launch the container is to use docker run, for example:
docker run --name my_cotter --volume=/path/to/host/data:/data --rm=true cotter:latest /bin/bash -c "cotter -allowmissing -initflag 4 -m /data/OBSID_metafits.fits -flagfiles /data/OBSID_%%.mwaf -o /path/inside/container/data/OBSID.ms /data/*gpubox*.fits"
notes:
- This will perform RFI flagging and create .mwaf files for each coarse channel. See cotter -help for other ways to use cotter.
- This assumes /path/to/host/data is a directory on the machine running docker (host) containing the gpubox files and metafits for an observation. Inside the container this is exposed as /data
- --rm=true means the container will be deleted once it exits (you may or may not want this)
- OBSID is an MWA observation ID
If you find that cotter terminates unexpectedly or with "illegal instruction", you may be able to resolve this by:
- Building your own AOFlagger image (gitlab repository is here: aoflagger.
- Modify cotter's Dockerfile first line from
FROM mwatelescope/aoflagger:3.0toFROM your_aoflagger_image, then rebuild the cotter image.
- You can find premade Cotter docker images at the MWATelescope dockerhub.
- These can be used instead of building images. For example, use:
docker pull mwatelescope/cotter:4.5instead of building it yourself.