Manage Packages with Spack
Using Installed Packages
The Research Computing Cluster uses Spack <https://spack.io> to install and manage packages, including compilers, MPI builds, and other packages. When you log into the cluster the system provided compilers and the AOMP compilers are in your default path. You can use spack commands to install new packages, create custom environments within your own user space, and load/unload packages provided in the RCC.
Listing Packages
To show what packages are currently available on the cluster, you can use the :code: spack find.
$ spack find
Loading and Unloading Packages
To load packages that have been previously installed by spack, you can use the spack load command.
For example, to load OpenMPI compiled with the gcc@10.2.0 compiler, you can use the command
spack load gcc@10.2.0 openmpi@4.0.2 % gcc@10.2.0
If you want to remove a package from your path, you can use spack unload command.
For example, to unload OpenMPI, you can use the command
spack unload openmpi@4.0.2 % gcc@10.2.0
Install packages with spack
On the RCC, spack is installed in a directory is not NFS mounted across the cluster (/opt). Because of this, running spack install commands will only install packages on the instance that you run the command on. Because of this, it is best practice to Install packages using spack environments. However, you may find it helpful to test package installations. Use the checklist below to help guide package installation with spack.
First check that the desired package can be built with spack using the
spack listcommand. Alternatively, you can visit the spack packages list page to see if the desired package is supported.Use the
spack infocommand to familiarize yourself with the packages dependencies, available versions, and available build specs.Preview what packages will be installed by using
spack spec. Keep in mind that you can specify the package version and the compiler to build with. Additionally, you can concretize the package variants to customize the installation. For example, some packages like hdf5 can be built with or without mpi support.Consider the target architecture that you want to run on. On Google Cloud, you have access to haswell/broadwell (n1 & e2 instances), cascadelake (a2, c2, & n2 instances), zen3 (n2d), and zen4 (c2d) instances. For many applications, specifying the target architecture instructs the compiler to leverage architecture specific optimizations. Often, this can improve application performance and consequently reduce runtime costs.
Install the package using the
spack installcommand. Since packages are installed from source, some packages may take a while to build.
Install packages using spack environments
Since spack’s install directory is not NFS mounted across the cluster (/opt), we highly recommend using a Spack environment. Creating a Spack environment in your home directory, which is NFS mounted, will allow those packages to be exposed to other instances in your cluster.
You can create a new environment in your home directory using
$ mkdir ${HOME}/env
$ spack env create -d ${HOME}/env
==> Updating view at /home/joe/env/.spack-env/view
==> Created environment in /home/joe/env
==> You can activate this environment with:
==> spack env activate /home/joe/env
Once created, you can active the environment
$ spack env activate ${HOME}/env
Once activated, you can install packages into your environment while using packages included with the RCC images as dependencies.
Packages are installed using spack install commands. You can read more about installing packages with Spack in the basic usage documentation.
To learn more about Spack environments, we highly recommend you walk through the Spack Environments Tutorial.
For the RCC, we highly recommend following a “build,test,deploy” model for operations. This process involves baking a VM image that has your desired applications installed, using one of the RCC images as a base. As part of the build process, you can test a deployment with your applications installed using fluid-run. Upon passing tests, you can then deploy using the RCC-tf module. Occasionally, too, you may find yourself in a situation where you want to install packages on-the-fly on your cluster. For either scenario, Spack supports the installation of a large number of packages from source, which gives you the ability to control compilation flags and the types of features to include with each packages build.
If you are an administrator of an RCC, or you are self-administrating, you can also build packages on top of the RCC images. With this approach, packages are installed under the /opt directory on VM images and you deploy the cluster using this new image.
For more information on baking images for your applications,see the RCC Apps documentation.
Spack can be used to bring packages into your search path.
To list packages that are currently available, you can run spack find
$ spack find
==> 153 installed packages
-- linux-centos7-broadwell / gcc@9.4.0 --------------------------
berkeley-db@18.1.40 json-c@0.15 libunistring@0.9.10 readline@8.1
bzip2@1.0.8 libaio@0.3.110 libxml2@2.9.12 shadow@4.8.1
cryptsetup@2.3.5 libbsd@0.11.3 lvm2@2.03.05 singularity@3.7.4
curl@7.78.0 libedit@3.1-20210216 ncurses@6.2 squashfs@4.4
expat@2.4.1 libgpg-error@1.42 openssh@8.7p1 tar@1.26
gdbm@1.19 libiconv@1.16 openssl@1.1.1l util-linux@2.37.2
gettext@0.21 libidn2@2.3.0 pcre2@10.36 util-linux-uuid@2.36.2
git@2.31.1 libmd@1.0.3 perl@5.34.0 xz@5.2.5
go@1.16.6 libseccomp@2.3.3 popt@1.16 zlib@1.2.11
-- linux-centos7-x86_64 / clang@13.0.0 --------------------------
hpcc@1.5.0 libpciaccess@0.16 openmpi@4.0.5 valgrind@3.15.0
hwloc@2.5.0 libxml2@2.9.12 openssh@8.7p1 xz@5.2.5
libedit@3.1-20210216 ncurses@6.2 openssl@1.1.1l zlib@1.2.11
libevent@2.0.21 numactl@2.0.14 osu-micro-benchmarks@5.7.1
libiconv@1.16 openblas@0.3.17 slurm@20-11
-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
dmtcp@2.6.0 gmp@6.2.1 lua-luaposix@35.0 mpfr@4.1.0 unzip@6.0
gcc@9.4.0 lmod@8.5.6 mpc@1.1.0 ncurses@6.2 zlib@1.2.11
gcc@10.3.0 lua@5.3.5 mpc@1.1.0 readline@8.1 zstd@1.5.0
gcc@11.2.0 lua-luafilesystem@1_7_0_2 mpfr@3.1.6 tcl@8.6.11
-- linux-centos7-x86_64 / gcc@9.4.0 -----------------------------
hpcc@1.5.0 libiconv@1.16 openblas@0.3.17 slurm@20-11
hpcg@3.1 libpciaccess@0.16 openmpi@4.0.5 valgrind@3.15.0
hwloc@2.5.0 libxml2@2.9.12 openssh@8.7p1 xz@5.2.5
libedit@3.1-20210216 ncurses@6.2 openssl@1.1.1l zlib@1.2.11
libevent@2.0.21 numactl@2.0.14 osu-micro-benchmarks@5.7.1
-- linux-centos7-x86_64 / gcc@10.3.0 ----------------------------
binutils@2.37 hpctoolkit@2021.05.15 libunwind@1.5.0 osu-micro-benchmarks@5.7.1
boost@1.76.0 hwloc@2.5.0 libxml2@2.9.12 papi@6.0.0.1
bzip2@1.0.8 intel-tbb@2020.3 libxml2@2.9.12 slurm@20-11
cuda@11.2.152 intel-xed@12.0.1 mbedtls@3.0.0 tar@1.26
curl@7.78.0 libdwarf@20180129 memkind@1.10.1 valgrind@3.15.0
dyninst@11.0.1 libedit@3.1-20210216 ncurses@6.2 xerces-c@3.2.3
elfutils@0.185 libevent@2.0.21 numactl@2.0.14 xz@5.2.5
gettext@0.21 libiberty@2.33.1 openblas@0.3.17 xz@5.2.5
gotcha@1.0.3 libiconv@1.16 openmpi@4.0.5 zlib@1.2.11
hpcc@1.5.0 libmonitor@2021.04.27 openssh@8.7p1
hpcg@3.1 libpciaccess@0.16 openssl@1.1.1l
-- linux-centos7-x86_64 / gcc@11.2.0 ----------------------------
hpcc@1.5.0 libiconv@1.16 openblas@0.3.17 slurm@20-11
hpcg@3.1 libpciaccess@0.16 openmpi@4.0.5 valgrind@3.15.0
hwloc@2.5.0 libxml2@2.9.12 openssh@8.7p1 xz@5.2.5
libedit@3.1-20210216 ncurses@6.2 openssl@1.1.1l zlib@1.2.11
libevent@2.0.21 numactl@2.0.14 osu-micro-benchmarks@5.7.1
You can load a package, and all of its dependencies into your path using spack load.
$ spack load openmpi % gcc@11.2.0
Since most packages are provided with builds associated with multiple compilers, you must specify the compiler using the % compiler specifier after the package name.
To list packages that are currently loaded in your environment, use spack find --loaded
$ spack find --loaded
-- linux-centos7-x86_64 / gcc@11.2.0 ----------------------------
hwloc@2.5.0 libevent@2.0.21 libpciaccess@0.16 ncurses@6.2 openmpi@4.0.5 openssl@1.1.1l valgrind@3.15.0 zlib@1.2.11
libedit@3.1-20210216 libiconv@1.16 libxml2@2.9.12 numactl@2.0.14 openssh@8.7p1 slurm@20-11 xz@5.2.5
To unload a package from your path, use spack unload
$ spack unload openmpi % gcc@11.2.0