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2 changes: 2 additions & 0 deletions Gemfile
Original file line number Diff line number Diff line change
Expand Up @@ -5,3 +5,5 @@ gem "jekyll", "~> 4.3.3"
gem "html-proofer", "~> 5.0"

gem "just-the-docs", "~> 0.8.2"

gem "jekyll-relative-links", "~> 0.7.0"
3 changes: 3 additions & 0 deletions _config.yml
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Expand Up @@ -13,3 +13,6 @@ ga_tracking: G-X2LPWRLJ7X
includes:
head:
- head_custom.html

plugins:
- jekyll-relative-links
8 changes: 4 additions & 4 deletions about/hardware.md
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Expand Up @@ -26,10 +26,10 @@ math: mathjax2
| Largemem | 3 | AMD 9654 | | 768 GB | 1.9TB | 13,989 |
| CPU | 25 | AMD 9654 | | 368 GB | 1.9TB | 12,998 |

| CPU | Cores | Threads | Base | Boost | L3 Cache |
| ---------------------------------------------------------------------- | ----- | ------- | ------ | ------------------ | -------- |
| [AMD Epyc 9654 CPU](https://www.amd.com/en/products/cpu/amd-epyc-9654) | 96 | 192 | 2.6GHz | 3.55GHz (All Core) | 384MB |
| [AMD Epyc 7513 CPU](https://www.amd.com/en/products/cpu/amd-epyc-7513) | 32 | 64 | 2.6GHz | 3.65GHz (Max) | 128MB |
| CPU | μArch | Cores | Threads | Base | Boost | L3 Cache |
| ---------------------------------------------------------------------------------------------------------------------------------- | ----- | ----- | ------- | ------ | ------------------ | -------- |
| [AMD Epyc 9654 CPU](https://www.amd.com/en/products/processors/server/epyc/4th-generation-9004-and-8004-series/amd-epyc-9654.html) | Zen4 | 96 | 192 | 2.6GHz | 3.55GHz (All Core) | 384MB |
| [AMD Epyc 7513 CPU](https://www.amd.com/en/products/processors/server/epyc/7003-series/amd-epyc-7513.html) | Zen3 | 32 | 64 | 2.6GHz | 3.65GHz (Max) | 128MB |

> Nodes are partitioned by *threads*, not *cores*. Picking 1 or a multiple of 2 is advisable; see [sbatch's](https://slurm.schedmd.com/sbatch.html) `--distribution` flag

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50 changes: 50 additions & 0 deletions about/user_software.md
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Expand Up @@ -147,3 +147,53 @@ packages:
scalapack: [amdsclapack, netlib-scalapack]

```

## Julia

## Minimizing Redundant Precompilation

As Artemis is a [heterogeneous cluster](./hardware.md#cluster-architecture), switching between different partitions can trigger frequent precompilation, as Julia attempts to recompile for the current microarchitecture. To avoid this set [`JULIA_CPU_TARGET`](https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_CPU_TARGET) to an appropriate setting.

For example, within your `~/.bashrc` or equivalent, put:

```shell
export JULIA_CPU_TARGET="generic;znver4,clone_all;znver3,clone_all;haswell"
```

This will instruct Julia to compile for Zen4 (Most Worker Nodes), Zen3 (A100 Nodes) and haswell (Head node), with a generic CPU target as a fallback. This will increase the size of `~/.julia/compiled` as 3 sets of system and package images will now need to be stored. For more information see the [Julia docs](https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_CPU_TARGET).


### Example Precompile Job Script
```shell
#!/bin/bash
#SBATCH -p venkvis-cpu
#SBATCH --cpus-per-task 4
#SBATCH --mem-per-cpu 1800M
#SBATCH --time=0:20:00
set -x
my_job_header

# Configure Julia
export JULIA_CPU_TARGET="generic;znver4,clone_all;znver3,clone_all;haswell"
export JULIA_PKG_PRECOMPILE_AUTO=0 # Disable automatic precompilation so we control when it happens (Mainly for MPI)
export JULIA_NUM_PRECOMPILE_TASKS=$SLURM_CPUS_ON_NODE # Limit precompilation tasks to the number of CPUs

# Uncomment if using MPI.jl
# module --ignore_cache load openmpi/4.1.6
# julia --color=no --startup-file=no --project -e 'using MPIPreferences; MPIPreferences.use_system_binary()'

# Precompile the Project
julia --color=no --startup-file=no --project -e 'using Pkg; Pkg.resolve(); Pkg.instantiate(); Pkg.precompile(timing=true)'
```

The job script would then look like:

```shell
# [Job Header Goes Here]

export JULIA_CPU_TARGET="generic;znver4,clone_all;znver3,clone_all;haswell"

julia --startup-file=no --project ...
```

> Note: `--startup-file=no` is needed to avoid loading packages from your base environment (i.e. Revise) and
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