Pilot repository

Pilot software stack (2021.12)¶

Caveats¶

The current EESSI pilot software stack (version 2021.12) is the 7th iteration, and there are some known issues and limitations, please take these into account:

First of all: the EESSI pilot software stack is NOT READY FOR PRODUCTION!

Do not use it for production work, and be careful when testing it on production systems!

Reporting problems¶

If you notice any problems, please report them via https://github.com/EESSI/software-layer/issues.

Accessing the EESSI pilot repository through Singularity¶

The easiest way to access the EESSI pilot repository is by using Singularity. If Singularity is installed already, no admin privileges are required. No other software is needed either on the host.

A container image is available in the GitHub Container Registry (see https://github.com/EESSI/filesystem-layer/pkgs/container/client-pilot). It only contains a minimal operating system + the necessary packages to access the EESSI pilot repository through CernVM-FS, and it is suitable for aarch64, ppc64le, and x86_64.

The container image can be used directly by Singularity (no prior download required), as follows:

First, create some local directories in /tmp/$USER which will be bind mounted in the container:
```
mkdir -p /tmp/$USER/{var-lib-cvmfs,var-run-cvmfs,home}
```
These provides space for the CernVM-FS cache, and an empty home directory to use in the container.

Set the $SINGULARITY_BIND and $SINGULARITY_HOME environment variables to configure Singularity:

export SINGULARITY_BIND="/tmp/$USER/var-run-cvmfs:/var/run/cvmfs,/tmp/$USER/var-lib-cvmfs:/var/lib/cvmfs"
export SINGULARITY_HOME="/tmp/$USER/home:/home/$USER"

Start the container using singularity shell, using --fusemount to mount the EESSI pilot repository (using the cvmfs2 command that is included in the container image):

export EESSI_PILOT="container:cvmfs2 pilot.eessi-hpc.org /cvmfs/pilot.eessi-hpc.org"
singularity shell --fusemount "$EESSI_PILOT" docker://ghcr.io/eessi/client-pilot:centos7

This should give you a shell in the container, where the EESSI pilot repository is mounted:

$ singularity shell --fusemount "$EESSI_PILOT" docker://ghcr.io/eessi/client-pilot:centos7
INFO:    Using cached SIF image
CernVM-FS: pre-mounted on file descriptor 3
CernVM-FS: loading Fuse module... done
Singularity>

It is possible that you see some scary looking warnings, but those can be ignored for now.

To verify that things are working, check the contents of the /cvmfs/pilot.eessi-hpc.org/versions/2021.12 directory:

Singularity> ls /cvmfs/pilot.eessi-hpc.org/versions/2021.12
compat  init  software

Standard installation¶

For those with privileges on their system, there are a number of example installation scripts for different architectures and operating systems available in the EESSI demo repository.

Here we prefer the Singularity approach as we can guarantee that the container image is up to date.

Setting up the EESSI environment¶

Once you have the EESSI pilot repository mounted, you can set up the environment by sourcing the provided init script:

source /cvmfs/pilot.eessi-hpc.org/versions/2021.12/init/bash

If all goes well, you should see output like this:

Found EESSI pilot repo @ /cvmfs/pilot.eessi-hpc.org/versions/2021.12!
Using x86_64/intel/haswell as software subdirectory.
Using /cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/modules/all as the directory to be added to MODULEPATH.
Found Lmod configuration file at /cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/.lmod/lmodrc.lua
Initializing Lmod...
Prepending /cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/modules/all to $MODULEPATH...
Environment set up to use EESSI pilot software stack, have fun!
[EESSI pilot 2021.12] $

Now you're all set up! Go ahead and explore the software stack using "module avail", and go wild with testing the available software installations!

Testing the EESSI pilot software stack¶

Please test the EESSI pilot software stack as you see fit: running simple commands, performing small calculations or running small benchmarks, etc.

Test scripts that have been verified to work correctly using the pilot software stack are available at https://github.com/EESSI/software-layer/tree/main/tests .

Giving feedback or reporting problems¶

Any feedback is welcome, and questions or problems reports are welcome as well, through one of the EESSI communication channels:

(preferred!) EESSI software-layer GitHub repository: https://github.com/EESSI/software-layer/issues
EESSI mailing list (eessi@list.rug.nl)
EESSI Slack: https://eessi-hpc.slack.com (get an invite via https://www.eessi-hpc.org/join)
monthly EESSI meetings (first Thursday of the month at 2pm CEST)

Available software¶

(last update: Mar 21st 2022)

EESSI currently supports the following HPC applications as well as all their dependencies:

GROMACS (2020.1 and 2020.4)
OpenFOAM (v2006 and 8)
R (4.0.0) + R-bundle-Bioconductor (3.11) + RStudio Server (1.3.1093)
TensorFlow (2.3.1) and Horovod (0.21.3)
OSU-Micro-Benchmarks (5.6.3)
ReFrame (3.9.1)
Spark (3.1.1)
IPython (7.15.0)
QuantumESPRESSO (6.6) (currently not available on ppc64le)
WRF (3.9.1.1)

[EESSI pilot 2021.12] $ module --nx avail

--------------------------- /cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/modules/all ----------------------------
   ant/1.10.8-Java-11                                              LMDB/0.9.24-GCCcore-9.3.0
   Arrow/0.17.1-foss-2020a-Python-3.8.2                            lz4/1.9.2-GCCcore-9.3.0
   Bazel/3.6.0-GCCcore-9.3.0                                       Mako/1.1.2-GCCcore-9.3.0
   Bison/3.5.3-GCCcore-9.3.0                                       MariaDB-connector-c/3.1.7-GCCcore-9.3.0
   Boost/1.72.0-gompi-2020a                                        matplotlib/3.2.1-foss-2020a-Python-3.8.2
   cairo/1.16.0-GCCcore-9.3.0                                      Mesa/20.0.2-GCCcore-9.3.0
   CGAL/4.14.3-gompi-2020a-Python-3.8.2                            Meson/0.55.1-GCCcore-9.3.0-Python-3.8.2
   CMake/3.16.4-GCCcore-9.3.0                                      METIS/5.1.0-GCCcore-9.3.0
   CMake/3.20.1-GCCcore-10.3.0                                     MPFR/4.0.2-GCCcore-9.3.0
   code-server/3.7.3                                               NASM/2.14.02-GCCcore-9.3.0
   DB/18.1.32-GCCcore-9.3.0                                        ncdf4/1.17-foss-2020a-R-4.0.0
   DB/18.1.40-GCCcore-10.3.0                                       netCDF-Fortran/4.5.2-gompi-2020a
   double-conversion/3.1.5-GCCcore-9.3.0                           netCDF/4.7.4-gompi-2020a
   Doxygen/1.8.17-GCCcore-9.3.0                                    nettle/3.6-GCCcore-9.3.0
   EasyBuild/4.5.0                                                 networkx/2.4-foss-2020a-Python-3.8.2
   EasyBuild/4.5.1                                         (D)     Ninja/1.10.0-GCCcore-9.3.0
   Eigen/3.3.7-GCCcore-9.3.0                                       NLopt/2.6.1-GCCcore-9.3.0
   Eigen/3.3.9-GCCcore-10.3.0                                      NSPR/4.25-GCCcore-9.3.0
   ELPA/2019.11.001-foss-2020a                                     NSS/3.51-GCCcore-9.3.0
   expat/2.2.9-GCCcore-9.3.0                                       nsync/1.24.0-GCCcore-9.3.0
   expat/2.2.9-GCCcore-10.3.0                                      numactl/2.0.13-GCCcore-9.3.0
   FFmpeg/4.2.2-GCCcore-9.3.0                                      numactl/2.0.14-GCCcore-10.3.0
   FFTW/3.3.8-gompi-2020a                                          OpenBLAS/0.3.9-GCC-9.3.0
   FFTW/3.3.9-gompi-2021a                                          OpenBLAS/0.3.15-GCC-10.3.0
   flatbuffers/1.12.0-GCCcore-9.3.0                                OpenFOAM/v2006-foss-2020a
   FlexiBLAS/3.0.4-GCC-10.3.0                                      OpenFOAM/8-foss-2020a                              (D)
   fontconfig/2.13.92-GCCcore-9.3.0                                OpenMPI/4.0.3-GCC-9.3.0
   foss/2020a                                                      OpenMPI/4.1.1-GCC-10.3.0
   foss/2021a                                                      OpenPGM/5.2.122-GCCcore-9.3.0
   freetype/2.10.1-GCCcore-9.3.0                                   OpenSSL/1.1                                        (D)
   FriBidi/1.0.9-GCCcore-9.3.0                                     OSU-Micro-Benchmarks/5.6.3-gompi-2020a
   GCC/9.3.0                                                       Pango/1.44.7-GCCcore-9.3.0
   GCC/10.3.0                                                      ParaView/5.8.0-foss-2020a-Python-3.8.2-mpi
   GCCcore/9.3.0                                                   PCRE/8.44-GCCcore-9.3.0
   GCCcore/10.3.0                                                  PCRE2/10.34-GCCcore-9.3.0
   Ghostscript/9.52-GCCcore-9.3.0                                  Perl/5.30.2-GCCcore-9.3.0
   giflib/5.2.1-GCCcore-9.3.0                                      Perl/5.32.1-GCCcore-10.3.0
   git/2.23.0-GCCcore-9.3.0-nodocs                                 pixman/0.38.4-GCCcore-9.3.0
   git/2.32.0-GCCcore-10.3.0-nodocs                        (D)     pkg-config/0.29.2-GCCcore-9.3.0
   GLib/2.64.1-GCCcore-9.3.0                                       pkg-config/0.29.2-GCCcore-10.3.0
   GLPK/4.65-GCCcore-9.3.0                                         pkg-config/0.29.2                                  (D)
   GMP/6.2.0-GCCcore-9.3.0                                         pkgconfig/1.5.1-GCCcore-9.3.0-Python-3.8.2
   GMP/6.2.1-GCCcore-10.3.0                                        PMIx/3.1.5-GCCcore-9.3.0
   gnuplot/5.2.8-GCCcore-9.3.0                                     PMIx/3.2.3-GCCcore-10.3.0
   GObject-Introspection/1.64.0-GCCcore-9.3.0-Python-3.8.2         poetry/1.0.9-GCCcore-9.3.0-Python-3.8.2
   gompi/2020a                                                     protobuf-python/3.13.0-foss-2020a-Python-3.8.2
   gompi/2021a                                                     protobuf/3.13.0-GCCcore-9.3.0
   groff/1.22.4-GCCcore-9.3.0                                      pybind11/2.4.3-GCCcore-9.3.0-Python-3.8.2
   groff/1.22.4-GCCcore-10.3.0                                     pybind11/2.6.2-GCCcore-10.3.0
   GROMACS/2020.1-foss-2020a-Python-3.8.2                          Python/2.7.18-GCCcore-9.3.0
   GROMACS/2020.4-foss-2020a-Python-3.8.2                  (D)     Python/3.8.2-GCCcore-9.3.0
   GSL/2.6-GCC-9.3.0                                               Python/3.9.5-GCCcore-10.3.0-bare
   gzip/1.10-GCCcore-9.3.0                                         Python/3.9.5-GCCcore-10.3.0
   h5py/2.10.0-foss-2020a-Python-3.8.2                             PyYAML/5.3-GCCcore-9.3.0
   HarfBuzz/2.6.4-GCCcore-9.3.0                                    Qt5/5.14.1-GCCcore-9.3.0
   HDF5/1.10.6-gompi-2020a                                         QuantumESPRESSO/6.6-foss-2020a
   Horovod/0.21.3-foss-2020a-TensorFlow-2.3.1-Python-3.8.2         R-bundle-Bioconductor/3.11-foss-2020a-R-4.0.0
   hwloc/2.2.0-GCCcore-9.3.0                                       R/4.0.0-foss-2020a
   hwloc/2.4.1-GCCcore-10.3.0                                      re2c/1.3-GCCcore-9.3.0
   hypothesis/6.13.1-GCCcore-10.3.0                                RStudio-Server/1.3.1093-foss-2020a-Java-11-R-4.0.0
   ICU/66.1-GCCcore-9.3.0                                          Rust/1.52.1-GCCcore-10.3.0
   ImageMagick/7.0.10-1-GCCcore-9.3.0                              ScaLAPACK/2.1.0-gompi-2020a
   IPython/7.15.0-foss-2020a-Python-3.8.2                          ScaLAPACK/2.1.0-gompi-2021a-fb
   JasPer/2.0.14-GCCcore-9.3.0                                     scikit-build/0.10.0-foss-2020a-Python-3.8.2
   Java/11.0.2                                             (11)    SciPy-bundle/2020.03-foss-2020a-Python-3.8.2
   jbigkit/2.1-GCCcore-9.3.0                                       SciPy-bundle/2021.05-foss-2021a
   JsonCpp/1.9.4-GCCcore-9.3.0                                     SCOTCH/6.0.9-gompi-2020a
   LAME/3.100-GCCcore-9.3.0                                        snappy/1.1.8-GCCcore-9.3.0
   libarchive/3.5.1-GCCcore-10.3.0                                 Spark/3.1.1-foss-2020a-Python-3.8.2
   libcerf/1.13-GCCcore-9.3.0                                      SQLite/3.31.1-GCCcore-9.3.0
   libdrm/2.4.100-GCCcore-9.3.0                                    SQLite/3.35.4-GCCcore-10.3.0
   libevent/2.1.11-GCCcore-9.3.0                                   SWIG/4.0.1-GCCcore-9.3.0
   libevent/2.1.12-GCCcore-10.3.0                                  Szip/2.1.1-GCCcore-9.3.0
   libfabric/1.11.0-GCCcore-9.3.0                                  Tcl/8.6.10-GCCcore-9.3.0
   libfabric/1.12.1-GCCcore-10.3.0                                 Tcl/8.6.11-GCCcore-10.3.0
   libffi/3.3-GCCcore-9.3.0                                        tcsh/6.22.02-GCCcore-9.3.0
   libffi/3.3-GCCcore-10.3.0                                       TensorFlow/2.3.1-foss-2020a-Python-3.8.2
   libgd/2.3.0-GCCcore-9.3.0                                       time/1.9-GCCcore-9.3.0
   libGLU/9.0.1-GCCcore-9.3.0                                      Tk/8.6.10-GCCcore-9.3.0
   libglvnd/1.2.0-GCCcore-9.3.0                                    Tkinter/3.8.2-GCCcore-9.3.0
   libiconv/1.16-GCCcore-9.3.0                                     UCX/1.8.0-GCCcore-9.3.0
   libjpeg-turbo/2.0.4-GCCcore-9.3.0                               UCX/1.10.0-GCCcore-10.3.0
   libpciaccess/0.16-GCCcore-9.3.0                                 UDUNITS/2.2.26-foss-2020a
   libpciaccess/0.16-GCCcore-10.3.0                                UnZip/6.0-GCCcore-9.3.0
   libpng/1.6.37-GCCcore-9.3.0                                     UnZip/6.0-GCCcore-10.3.0
   libsndfile/1.0.28-GCCcore-9.3.0                                 WRF/3.9.1.1-foss-2020a-dmpar
   libsodium/1.0.18-GCCcore-9.3.0                                  X11/20200222-GCCcore-9.3.0
   LibTIFF/4.1.0-GCCcore-9.3.0                                     x264/20191217-GCCcore-9.3.0
   libtirpc/1.2.6-GCCcore-9.3.0                                    x265/3.3-GCCcore-9.3.0
   libunwind/1.3.1-GCCcore-9.3.0                                   xorg-macros/1.19.2-GCCcore-9.3.0
   libxc/4.3.4-GCC-9.3.0                                           xorg-macros/1.19.3-GCCcore-10.3.0
   libxml2/2.9.10-GCCcore-9.3.0                                    Xvfb/1.20.9-GCCcore-9.3.0
   libxml2/2.9.10-GCCcore-10.3.0                                   Yasm/1.3.0-GCCcore-9.3.0
   libyaml/0.2.2-GCCcore-9.3.0                                     ZeroMQ/4.3.2-GCCcore-9.3.0
   LittleCMS/2.9-GCCcore-9.3.0                                     Zip/3.0-GCCcore-9.3.0
   LLVM/9.0.1-GCCcore-9.3.0                                        zstd/1.4.4-GCCcore-9.3.0

Architecture and micro-architecture support¶

x86_64¶

generic (currently implies march=x86-64 and -mtune=generic)
AMD
- zen2 (Rome)
- zen3 (Milan)
Intel
- haswell
- skylake_avx512

aarch64/arm64¶

generic (currently implies -march=armv8-a and -mtune=generic)
AWS Graviton2

ppc64le¶

generic
power9le

EasyBuild configuration¶

EasyBuild v4.5.1 was used to install the software in the 2021.12 version of the pilot repository. For some installations pull requests with changes that will be included in later EasyBuild versions were leveraged, see the build script that was used.

An example configuration of the build environment based on https://github.com/EESSI/software-layer can be seen here:

$ eb --show-config
#
# Current EasyBuild configuration
# (C: command line argument, D: default value, E: environment variable, F: configuration file)
#
buildpath         (E) = /tmp/eessi-build/easybuild/build
containerpath     (E) = /tmp/eessi-build/easybuild/containers
debug             (E) = True
filter-deps       (E) = Autoconf, Automake, Autotools, binutils, bzip2, cURL, DBus, flex, gettext, gperf, help2man, intltool, libreadline, libtool, Lua, M4, makeinfo, ncurses, util-linux, XZ, zlib
filter-env-vars   (E) = LD_LIBRARY_PATH
hooks             (E) = /home/eessi-build/software-layer/eb_hooks.py
ignore-osdeps     (E) = True
installpath       (E) = /cvmfs/pilot.eessi-hpc.org/2021.06/software/linux/x86_64/intel/haswell
module-extensions (E) = True
packagepath       (E) = /tmp/eessi-build/easybuild/packages
prefix            (E) = /tmp/eessi-build/easybuild
repositorypath    (E) = /tmp/eessi-build/easybuild/ebfiles_repo
robot-paths       (D) = /cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/software/EasyBuild/4.5.1/easybuild/easyconfigs
rpath             (E) = True
sourcepath        (E) = /tmp/eessi-build/easybuild/sources:
sysroot           (E) = /cvmfs/pilot.eessi-hpc.org/versions/2021.12/compat/linux/x86_64
trace             (E) = True
zip-logs          (E) = bzip2

Last update: March 21, 2022