Install Wire-Cell Toolkit

# Install Wire-Cell Toolkit  There are several ways to install Wire-Cell Toolkit on your local computer (see, e.g. [here](https://wirecell.github.io/manual.html#outline-container-orga7919bf)). To avoid choice overloading and get you started as quickly as possible, we describe an **officially recommended** way of installation: using the [cvmfs](https://cernvm.cern.ch/) network file system and the [singularity](https://singularity.lbl.gov/) container. This way allows you to both develop Wire-Cell by itself and integrate it with other software frameworks such as LArSoft. ## Install CVMFS [CVMFS](https://cernvm.cern.ch/) (CernVM File System) is a utility that mounts remote directories over HTTP. CVMFS provides a simple way to distribute software binaries. Follow [Brett's instruction](https://github.com/WireCell/wire-cell-singularity/blob/master/cvmfs.org) for details of installation. For the lazy ubuntu'ers: ```bash sudo apt-get install lsb-release wget https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest_all.deb sudo dpkg -i cvmfs-release-latest_all.deb sudo apt-get update sudo apt-get install cvmfs cvmfs-config-default sudo cvmfs_config setup ``` Create a configuration file at `/etc/cvmfs/default.local` as follows: ```bash # required, add more if needed. CVMFS_REPOSITORIES=larsoft.opensciencegrid.org,uboone.opensciencegrid.org,dune.opensciencegrid.org,icarus.opensciencegrid.org # requires, replace with actual proxy, or just "DIRECT" if none CVMFS_HTTP_PROXY="DIRECT" # BNL Physics department users may use # CVMFS_HTTP_PROXY="http://batch3.phy.bnl.gov:3128;DIRECT" CVMFS_QUOTA_LIMIT=25000 CVMFS_CACHE_BASE=/mnt/ssd/cvmfs ``` Now test with ```bash cvmfs_config probe ``` , and you should see **three** `Probing ... OK` messages. (**Optional**) If you also want access to the data in `dune.osgstorage.org`, for example, the photon library in the protoDUNE-SP simulation as will be introduced shortly, it is required to append `dune.osgstorage.org` to `CVMFS_REPOSITORIES` in `/etc/cvmfs/default.local`. Check that the other repositories work: ``` cvmfs_config chksetup cvmfs_config probe ``` The second command may fail on dune.osgstorage.org, we fix that next. ``` cp /cvmfs/config-osg.opensciencegrid.org/etc/cvmfs/domain.d/osgstorage.org.conf /etc/cvmfs/domain.d/ cvmfs_config chksetup cvmfs_config probe ``` Now, `dune.osgstorage.org` should be "OK" and the directory should be accessible: `/cvmfs/dune.osgstorage.org/`  ## Install Singularity [Singularity](https://singularity.lbl.gov/) is a lightweight container that provides an operating-system level virtualization. It is popular in the world of scientific high-performance computing (HPC). For Wire-Cell development, we use singularity to provide a virtual [scientific linux](https://www.scientificlinux.org/) environment. Follow [here](https://sylabs.io/guides/3.0/user-guide/installation.html) for detailed installation instructions. For the lazy ubuntu'ers, first, install the `go` language: ```bash sudo apt-get update && sudo apt-get install -y \ build-essential libssl-dev uuid-dev \ libgpgme11-dev squashfs-tools libseccomp-dev pkg-config sudo wget https://dl.google.com/go/go1.11.5.linux-amd64.tar.gz # or other versions sudo tar -C /usr/local -xf go1.11.5.linux-amd64.tar.gz echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \ echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \ source ~/.bashrc go get -u github.com/golang/dep/cmd/dep ``` Then, install `singularity` from source ```bash go get -d github.com/sylabs/singularity cd $GOPATH/src/github.com/sylabs/singularity git checkout -b v3.0.3 v3.0.3 # or other tags ./mconfig && \ make -C ./builddir && \ sudo make -C ./builddir install ``` ### Troubleshooting Depending on the filesystem, `singularity` might not be able to mount certain drives and will abort with an error message similar to: ``` error: can't mount image /proc/self/fd/3: failed to mount squashfs filesystem: invalid argument ``` This has been patched from `v3.5.3` onwards, but to force it to work on `v3.0.3`, one can modify the source code by opening: ```bash $EDITOR ${GOPATH}/src/github.com/sylabs/singularity/internal/pkg/util/fs/mount/mount.go ``` and replacing the codeblock: ```bash options = fmt.Sprintf("loop,offset=%d,sizelimit=%d,errors=remount-ro", offset, sizelimit) ``` with ```bash options = fmt.Sprintf("loop,offset=%d,sizelimit=%d", offset, sizelimit) if fstype == "ext3" { options += ",errors=remount-ro" } ``` and rebuilding with the `mconfig` command as before. This is because `remount-ro` is an invalid argument to provide while mounting squashfs drives, as squashfs doesn't recognize it. More context is given [here](https://stackoverflow.com/questions/63061424/squashfs-error-when-running-singularity-after-ubuntu-upgrade) ## Use wcdo `wcdo` is a command line tool that provides convenient methods to do stuff with Wire-Cell in a Singularity container. Follow [Brett's instruction](https://github.com/WireCell/wire-cell-singularity/blob/master/wcdo.org) to get started, or see the [next section](/f0u9JweCTxizBfufKZzvVg) for example workflows.