added Bebop files

ANL/Bebop/README.md

+Bebop
+=====
+
+
+Programming environment
+-----------------------
+
+The Bebop machine has many compilers and MPI implementations, not all
+of which work correctly with Mochi. We have found `gcc@8.2.0` with
+the `intel-mpi` package to be the most reliable way of working with
+Mochi on this platform. You can work with these packages by typping:
+
+```
+$ module load gcc/8.2.0-g7hppkz
+```
+
+This command will automatically change the compiler to `gcc@8.2.0`
+and change the `intel-mpi` package to the appropriate one.
+
+
+Networking
+----------
+
+Bebop uses an Intel Omnipath fabric. The corresponding transport in
+Mercury is `ofi+psm2`, using the `+psm2` variant in `libfabric`.
+
+
+Job management
+--------------
+
+Bebop uses the Slurm workload manager. `job.sbatch` is an example
+of job file. Please modify the header (lines starting with `#SBATCH`)
+to use your project allocation and set relevant parameters. You can
+refer to [the documentation here](https://www.lcrc.anl.gov/systems/resources/bebop/)
+for more information on how to configure such a job script.
+
+Once modified, the job script may be submitted as follows.
+
+```
+$ sbatch ./job.sbatch
+```

ANL/Bebop/job.sbatch

+#!/bin/bash
+#SBATCH -N 4
+#SBATCH -p bdwall
+#SBATCH -A MY_PROJECT
+#SBATCH --time=30:00
+#SBATCH --export=ALL
+
+set -eu
+
+export PSM2_MULTI_EP=1 # prevents conflict with MPI using PSM2
+export FI_PSM2_DISCONNECT=1 # enables reconnection
+
+echo "Activating env"
+. $HOME/spack/share/spack/setup-env.sh
+module load gcc/8.2.0-g7hppkz
+spack env activate myenv
+
+echo "Starting application"
+srun -N 2 -n 4 ...

ANL/Bebop/spack.yaml

+spack:
+  specs:
+  - mochi-margo%gcc@8.2.0
+  concretization: together
+  compilers:
+  - compiler:
+      paths:
+        cc: /blues/gpfs/software/centos7/spack/opt/spack/linux-centos7-x86_64/gcc-8.1.0/gcc-8.2.0-g7hppkz/bin/gcc
+        cxx: /blues/gpfs/software/centos7/spack/opt/spack/linux-centos7-x86_64/gcc-8.1.0/gcc-8.2.0-g7hppkz/bin/g++
+        f77: /blues/gpfs/software/centos7/spack/opt/spack/linux-centos7-x86_64/gcc-8.1.0/gcc-8.2.0-g7hppkz/bin/gfortran
+        fc: /blues/gpfs/software/centos7/spack/opt/spack/linux-centos7-x86_64/gcc-8.1.0/gcc-8.2.0-g7hppkz/bin/gfortran
+      operating_system: centos7
+      target: x86_64
+      modules:
+      - gcc/8.2.0-g7hppkz
+      - intel-mpi/2018.4.274-ozfo327
+      environment: {}
+      extra_rpaths: []
+      flags: {}
+      spec: gcc@8.2.0
+  repos:
+  - path/to/sds-repo
+  packages:
+    all:
+      providers:
+        mpi: [ intel-mpi ]
+      compiler: [ gcc@8.2.0 ]
+    autoconf:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: autoconf@2.69 arch=linux-centos7-x86_64
+        prefix: /usr
+    automake:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: automake@1.13.4 arch=linux-centos7-x86_64
+        prefix: /usr
+    binutils:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: binutils@2.27 arch=linux-centos7-x86_64
+        prefix: /usr
+    bison:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: bison@3.0.4 arch=linux-centos7-x86_64
+        prefix: /usr
+    bzip2:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: bzip2@1.0.6 arch=linux-centos7-x86_64
+        prefix: /usr
+    cmake:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: cmake@3.14.2 arch=linux-centos7-x86_64
+        modules:
+        - cmake/3.14.2-gvwazz3
+    coreutils:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: coreutils@8.25 arch=linux-centos7-x86_64
+        prefix: /usr
+    findutils:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: findutils@4.5.11 arch=linux-centos7-x86_64
+        prefix: /usr
+    flex:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: flex@2.5.37 arch=linux-centos7-x86_64
+        prefix: /usr
+    gettext:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: gettext@0.19.8.1 arch=linux-centos7-x86_64
+        prefix: /usr
+    git:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: git@1.8.3.1 arch=linux-centos7-x86_64
+        prefix: /usr
+    hdf5:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: hdf5@1.10.5 arch=linux-centos7-x86_64
+        modules:
+        - hdf5/1.10.5-vozfsah
+    intel-mpi:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: intel-mpi@2018.4.274 arch=linux-centos7-x86_64
+        modules:
+        - intel-mpi/2018.4.274-ozfo327
+    libfabric:
+      variants: fabrics=psm2,sockets
+      version: []
+      target: []
+      compiler: []
+      buildable: true
+      providers: {}
+    libtool:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: libtool@2.4.2 arch=linux-centos7-x86_64
+        prefix: /usr
+    m4:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: m4@1.4.16 arch=linux-centos7-x86_64
+        prefix: /usr
+    mercury:
+      variants: ~boostsys
+      version: []
+      target: []
+      compiler: []
+      buildable: true
+      providers: {}
+    numactl:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: numactl@2.0.12 arch=linux-centos7-x86_64
+        modules:
+        - numactl/2.0.12-355ef36
+    openssl:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: openssl@1.0.2k arch=linux-centos7-x86_64
+        prefix: /usr
+    perl:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: perl@5.16.3 arch=linux-centos7-x86_64
+        prefix: /usr
+    pkg-config:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: pkg-config@0.27.1 arch=linux-centos7-x86_64
+        prefix: /usr
+    tar:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: tar@1.16 arch=linux-centos7-x86_64
+        prefix: /usr
+    texinfo:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: texinfo@5.1 arch=linux-centos7-x86_64
+        prefix: /usr
+    xz:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: xz@5.2.2 arch=linux-centos7-x86_64
+        prefix: /usr
+    zlib:
+      buildable: false
+      version: []
+      target: []
+      compiler: []
+      providers: {}
+      externals:
+      - spec: zlib@1.2.7 arch=linux-centos7-x86_64
+        prefix: /usr
+  view: true

README.md

@@ -3,4 +3,116 @@ Platform configurations for Mochi
 
 This repository provides Spack configuration files, example job scripts, and
 notes about building and running Mochi-based codes on various platforms.
-Please refer to your platform of interest for more information.
\ No newline at end of file
+Please refer to your platform of interest for more information.
+
+
+Using spack.yaml files
+----------------------
+
+Each platform subdirectory in this repository provides a `spack.yaml` file.
+Such a file is meant to fully describe a Spack environment, including some system-provided
+packages and compilers. It does so independently of any `compilers.yaml` or `packages.yaml`
+files installed in `~/.spack`, hence preventing as much as possible the possible interference
+with user-specific spack configurations.
+
+You may use `spack.yaml` files to create a
+[Spack environment](https://spack.readthedocs.io/en/latest/environments.html) in
+which Mochi packages will be installed.
+
+If you don't have Spack installed on your platform, clone it and set it up as follows.
+
+```
+$ git clone https://github.com/spack/spack.git
+$ . spack/share/spack/setup-env.sh
+```
+
+You may want to put the second line in your `.bashrc` file so that it
+gets executed when opening a terminal.
+
+You will then need to clone `sds-repo`, which contains the Mochi packages.
+
+```
+$ git clone https://xgitlab.cels.anl.gov/sds/sds-repo.git
+$ spack repo add sds-repo
+```
+
+Now clone the present repository and `cd` into the subdirectory relevant
+to your platform. For example:
+
+```
+$ git clone https://xgitlab.cels.anl.gov/sds/experiments/platform-configurations.git
+$ cd platform-configurations/ANL/Bebop
+```
+
+Edit the path to `sds-repo` in the `repos` field of the `spack.yaml` file to
+match your installation.
+
+Then, execute the following command
+(changing _myenv_ into an appropriate name for your environment).
+
+```
+$ spack env create myenv spack.yaml
+```
+
+Change to a directory outside the `platform-configurations` folders
+and activate the environment as follows.
+
+```
+$ spack env activate myenv
+```
+
+You may now add specs to your environment. For instance if you want
+to install Margo, execute the following command.
+
+```
+$ spack add mochi-margo
+```
+
+If the `spack.yaml` file provides multiple compilers and you want
+to use another than the default one, specify the compiler explicitely,
+for example:
+
+```
+$ spack add mochi-margo %gcc@8.2.0
+```
+
+Note that the `spack.yaml` file you used may already have a spec
+added as an example (usually `mochi-margo`). You can remove it as
+follows.
+
+```
+$ spack rm mochi-margo
+```
+
+Once you have added the specs you need in your environment, install
+everything by executing the following command.
+
+```
+$ spack install
+```
+
+You may add more specs later on. For more information on how to manage
+Spack environments, please refer to the Spack documentation.
+
+
+Contributing to this repository
+-------------------------------
+
+Should you want to contribute a `spack.yaml` for a particular machine,
+please submit a merge request with it, and ensure the following.
+
+*  The `spack.yaml` file should contain the compiler(s) that have been tested
+   to be working with Mochi packages.
+*  The `spack.yaml` file should try to list system-provided packages,
+   in particular packages used for building (`cmake`, `autoconf`, etc.),
+   and relevant system-provided MPI implementations.
+*  The `spack.yaml` file should contain the relevant variants for packages,
+   in particular the transport methods to use with `libfabric`.
+*  The path to the `spack.yaml` file should be of the form
+   `<institution>/<platform>/spack.yaml`.
+*  Please make sure that your `spack.yaml` is a reliable way to work with
+   Mochi on the target platform, other people will rely on it!
+
+You can also contribute changes to existing `spack.yaml` files, in particular
+to add working compilers, system packages, etc. As always, please test that
+new setups work before creating a merge request.