Installing the Cooperative Computing Tools

The CCTools software runs on Linux and Mac computers, whether laptops, desktops, or large high performance clusters. There are several ways to install:

Install From Conda

Installing via the Conda package manager will give you a personal installation of the software in your home directory. You may already have Conda installed. To check:

$ conda list

If it fails, then you should install Miniconda. Miniconda is a light version of Anaconda, and we recommend it as it is much faster to install. We also recommend installing the version for Python 3.9

Once Conda is installed, then install CCTools with:

# run this command once
$ conda create -n cctools-env -y -c conda-forge --strict-channel-priority python ndcctools

# run this command every time you want to use cctools
$ conda activate cctools-env

# run this command every time you want to update your version of cctools (after `activate` as above).
$ conda update -y -c conda-forge ndcctools

Note

You could simply run the command conda install -y -c conda-forge ndcctools without creating a new environment. However, sometimes conda takes a long time to resolve all dependencies when adding new packages to an already existing environment.

And that's it! You can test your setup following the instructions here.

Warning

On Mac, the available from conda CCTools does not work with Python 2.7 or with perl. For such case, please compile CCTools from source.

Install From Spack

Alternatively, you can install CCTools using the spack.io package manager. Spack will compile CCTools for you, and it is recommended for HPC sites for which a conda installation is not available, or which have special software stack requirements (such as specially compiled python versions).

First you need to check that the spack command is available. In a terminal type:

$ spack help

If this command fails, then please install spack following the instructions here.

Once spack is installed, install CCTools with:

$ spack install cctools

To use CCTools, you need to load it into the spack environment with:

$ spack load cctools

You only need to do spack install once, but you will need spack load cctools everytime you want to use CCTools.

Once this command finished, you can test your installation following the instructions here.

Install From Github

If you wish to install the latest version of CCTools to try a new feature or develop new code then you can install from github. This requires that you first install the necessary software dependencies, and the easiest way to do this is to create a new cctools-dev environment via Conda:

unset PYTHONPATH
conda create -y -n cctools-dev -c conda-forge --strict-channel-priority python=3 gcc_linux-64 gxx_linux-64 gdb m4 perl swig make zlib libopenssl-static openssl conda-pack
conda activate cctools-dev

Now that you are inside the cctools-dev environment, you can check out the software repository and build it:

git clone git://github.com/cooperative-computing-lab/cctools.git cctools-src
cd cctools-src
./configure --with-base-dir $CONDA_PREFIX --prefix $HOME/cctools
make
make install

The next time you log in, be sure to activate the environment again:

unset PYTHONPATH
conda activate cctools-dev

Note

To use the installed software you will need to set the environment variables PATH, PYTHONPATH, and PERL5LIB as explained here.

Install From Source Tarball

In a similar way, you can download a source package from the download page. Then unpack the tarball and compile:

$ tar zxf cctools-*-source.tar.gz
$ cd cctools-src
$ ./configure --prefix $HOME/cctools
$ make
$ make install

Note

To use the installed software you will need to set the environment variables PATH, PYTHONPATH, and PERL5LIB as explained here.

Install From Binary Tarball

The CCTools software is pre-built for a small number of platforms. Download a source package from the download page. And follow this recipe while logged in as any ordinary user:

$ tar zxf cctools-*-source.tar.gz
$ cd cctools-*-source
$ ./configure --prefix $HOME/cctools
$ make
$ make install

Note

To use the installed software you will need to set the environment variables PATH, PYTHONPATH, and PERL5LIB as explained here.

Setting Your Environment

If you installed CCTools from github, source tarball, or from a binary tarball, you will need to set some environment variables.

First determine the python and perl versions you are using:

# Note: your output may vary according to your python version.
$ python -c 'from sys import version_info; print("{}.{}".format(version_info.major, version_info.minor))'
3.7

# Note: your output may vary according to your perl version.
$ perl -e 'print("$^V\n")'
5.16.3

Now update your environment variables with those versions:

$ export PATH=$HOME/cctools/bin:$PATH

# Change 3.7 to the python version you found above.
$ export PYTHONPATH=$HOME/cctools/lib/python3.7/site-packages:${PYTHONPATH}

# Change 5.16.3 to the perl version you found above.
$ export PERL5LIB=$HOME/cctools/lib/perl5/site_perl/5.16.3:${PERL5LIB}

Testing Your Installation

You can test that the key programs are available with:

$ work_queue_worker --version
work_queue_worker version 7.4.3 FINAL (released 2022-02-03 16:26:52 +0000)

$ makeflow --version
makeflow version 7.4.3 FINAL (released 2022-02-03 16:26:52 +0000)
...

You can test that the python and perl modules are available with:

$ python -c 'import work_queue; print(work_queue.WORK_QUEUE_DEFAULT_PORT)'
9123

$ perl -MWork_Queue -e 'print("$Work_Queue::WORK_QUEUE_DEFAULT_PORT\n")'
9123

If the above commands fail, please make sure that you follow one (and only one!) of the methods above. For example, if you are using a conda installation, make sure that your PYTHONPATH is unset.

Warning

Remember that for installations from source you need swig at compile time, and to set the environment variables PATH, PYTHONPATH and PERL5LIB appropriately, as explained here.

For conda and spack installation you should not need to manually set any of these variables, and in fact setting them may produce errors.

Special Cases

The software will happily build and run without installing any external packages. Optionally, the CCTools will interoperate with a variety of external packages for security, data access, and novel research methods. To use these, you must download and install them separately:

Once the desired packages are correctly installed, unpack the CCTools and then issue a configure command that points to all of the other installations. Then, make and install as before. For example:

$ ./configure --with-globus-path /usr/local/globus
$ make && make install

SWIG

CCTools needs SWIG during compilation to provide python and perl support. SWIG is available through conda, or as a package of many linux distributions. Once SWIG is installed, the configure script should automatically find it if the executable swig is somewhere in your PATH.

Note

If ./configure cannot find your SWIG installation, you can use a command line option as follows: ./configure --with-swig-path /path/to/swig

iRODS

Building Parrot with support for the iRODS service requires some custom build instructions, since Parrot requires access to some internals of iRODS that are not usually available. To do this, first make a source build of iRODS in your home directory:

cd $HOME
git clone https://github.com/irods/irods-source
cd irods-source
git checkout 4.0.3
$ packaging/build.sh --run-in-place icommands
cd ..

Then, configure and build CCTools relative to that installation:

$ git clone https://github.com/cooperative-computing-lab/cctools cctools-source
$ cd cctools-source
$ ./configure --with-irods-path ../irods-src
$ make && make install

MPI

Building with MPI requires a valid MPI installation to be in your path. Generally CCTools compiles with both intel-ompi and MPICH. If you do not have mpi installed already, we suggest downloading the latest MPICH from the MPICH website. The latest known supporting version of MPICH with CCTools is MPICH-3.2.1. Simply build MPICH as is best for your site/system, and then place the binaries in your path. We also suggest configuring MPICH to use gcc as the compiling software. For example:

$ tar -xvf MPICH-3.2.1.tar.gz
$ cd MPICH-3.2.1 CC=gcc CXX=g++
$ ./configure
$ make && make install

Once MPI is in your path, configure CCTools to use MPI and then install. For example:

$ cd ~/cctools
$ ./configure --with-mpi-path=`which mpicc`
$ make && install `

Now, our tools will be MPI enabled, allowing you to run Makeflow as an MPI job, as well as using both WorkQueue as MPI jobs, and submitting Makeflow and WorkQueue together as a single MPI job.

Build on Mac OSX

In order to build CCTools on Mac OS X you must first have the Xcode Command Line Tools installed. For OS X 10.9 and later this can be done using the following command:

xcode-select --install

Then, click "Install" in the window that appears on the screen. If the command line tools are already installed, you will get an error and can proceed with the instructions in the "Installing From Source" section above. For OS X versions before 10.9, you will need to first install Xcode. Xcode can be found in the App Store or on the installation disk.

License

The Cooperative Computing Tools are Copyright (C) 2003-2004 Douglas Thain and Copyright (C) 2005- The University of Notre Dame. All rights reserved. This software is distributed under the GNU General Public License.