diff --git a/doc/src/SUMMARY.md b/doc/src/SUMMARY.md index ce966d3..05d2eb9 100644 --- a/doc/src/SUMMARY.md +++ b/doc/src/SUMMARY.md @@ -3,7 +3,6 @@ [Introduction](index.md) - [Conda packages](conda.md) - - [Glotzer lab members](glotzer.md) - [Building packages](build.md) - [Installing packages](install.md) - [License](license.md) diff --git a/doc/src/build.md b/doc/src/build.md index ca3cf4b..7e7232e 100644 --- a/doc/src/build.md +++ b/doc/src/build.md @@ -1,8 +1,5 @@ # Building packages -If you are not a Glotzer Lab member, or you would like to build these packages on a new -resource: - > Note: Replace `{{ package-manager }}` with the name of your preferred conda compatible > package manager executable. diff --git a/doc/src/conda.md b/doc/src/conda.md index 4d04d78..78a85d3 100644 --- a/doc/src/conda.md +++ b/doc/src/conda.md @@ -2,7 +2,7 @@ **glotzerlab-software** provides [conda] formatted packages built with cluster-specific *MPI* and *CUDA* libraries. Use it to add *MPI-* and *GPU-enabled* builds of the -following software packages to your conda compatible environments on HPC resources: +following software packages to your conda-compatible environments on HPC resources: - hoomd - mpi4py @@ -13,7 +13,7 @@ following software packages to your conda compatible environments on HPC resourc > **conda-forge** channel. Ensure that you have **no** packages installed > from the **default** channel before proceeding. -[miniforge] provides a conda compatible environment pre-configured to install packages +[miniforge] provides a conda-compatible environment pre-configured to install packages only from **conda-forge**. When you install [miniforge] with default options, replace: - `{{ package-manager }}` with `mamba` @@ -21,7 +21,7 @@ only from **conda-forge**. When you install [miniforge] with default options, re [miniforge]: https://github.com/conda-forge/miniforge -If you are using a different conda compatible package manager, use the appropriate +If you are using a different conda-compatible package manager, use the appropriate `{{ package-manager }}` and `{{ environment-path }}`.
diff --git a/doc/src/glotzer.md b/doc/src/glotzer.md deleted file mode 100644 index 15c694b..0000000 --- a/doc/src/glotzer.md +++ /dev/null @@ -1,59 +0,0 @@ -# Glotzer lab members - -Members of the **Glotzer lab** can install *precompiled* packages. Follow the -instructions in [on the installation page](install.md) to install the latest stable -release using the following channel paths and module versions: - -| HPC resource | Channel location | Module versions | -|--------------------|-----------------------|-----------------------| -| UMich Great Lakes | `file://nfs/turbo/glotzer/software/conda` | `module load gcc/10.3.0 openmpi/4.1.6 cuda/12.3.0` | -| Purdue ANVIL | `file://anvil/projects/x-dmr140129/software/conda` | `module load gcc/11.2.0 openmpi/4.1.6` | -| NCSA Delta | `file://projects/bbgw/software/conda` | `module load openmpi/4.1.6 cuda/12.3.0` | -| OLCF Frontier | `file://ccs/proj/mat110/software/frontier/conda` | `module load PrgEnv-gnu rocm/5.4.3; module unload darshan-runtime` | -| OLCF Andes | `file://ccs/proj/mat110/software/andes/conda` | `module load gcc/10.3.0 openmpi/4.1.2` | - -## Frontier - -Individual users should install conda compatible environments in their **home -directory** on Frontier. Importing Python packages from this environment will be *very* -slow with large node count jobs. To improve performance, generate a **tar** file from -the environment and store it on Orion. - -```shell -$ tar --directory {{ environment-path }} -cf ${MEMBERWORK}/mat110/conda-env.tar . -``` - -> Important: Repeat this step after you install or update packages with -> `{{ package-manager }}`. - - -> Note: Collaborative projects may maintain a single copy of the software in the -> shared project directory: -> `/ccs/proj/mat110/software/frontier/{{ subproject-name }}`. -> -> Collaborative projects may also utilize a single cached `conda-env.tar`: -> -> $ tar --directory /ccs/proj/mat110/software/frontier/{{ subproject-name }} \ -> -cf ${PROJWORK}/mat110/software/{{ subproject-name} }/conda-env.tar . - -Use the following lines in your job scripts (or interactively with `salloc`) to load the -environment into NVME and execute software from there: - - #SBATCH -C nvme - - module load PrgEnv-gnu rocm/5.4.3 - module unload darshan-runtime - - export CONDA_ENV_ROOT=/mnt/bb/${USER}/conda-env - srun --nodes=$SLURM_JOB_NUM_NODES --ntasks-per-node 1 mkdir ${CONDA_ENV_ROOT} - srun --nodes=$SLURM_JOB_NUM_NODES --ntasks-per-node 1 tar --directory ${CONDA_ENV_ROOT} -xpf \ - ${MEMBERWORK}/mat110/conda-env.tar - # ${PROJWORK}/mat110/software/{{ subproject-name }}/conda-env.tar # For use with shared projects. - - export PATH=${CONDA_ENV_ROOT}/bin:$PATH - - srun {srun options} command arguments - -> Note: The above script has been tested on environments with all packages installed -> into *base*. You may need to set additional environment variables or source activation -> scripts to activate conda environments within this directory.