Add a few slurm scripts for the cluster

experiments/README.md

@@ -10,3 +10,17 @@ jupyter-lab
 ```
 
 The `shell.nix` contains a workaround for NixOS and is not necessary for normal use.
+
+## Building NAStJA for Experiments
+
+Build it either with or without CUDA support.
+When NAStJA is built with CUDA support it will automatically switch to the GPU implementation of the dynamic ECM.
+I use the `mold` linker because it makes the code-build-test-loop slightly shorter.
+This shouldn't have any impact on the performance of the produced binary.
+If you would like to shorten the linking time even further you can add `-DNASTJA_ENABLE_IPO=OFF` to turn of Link Time Optimization (LTO).
+However, it is likely that will have an impact on performance.
+
+```
+cmake .. -DCMAKE_CXX_FLAGS="-fuse-ld=mold"
+cmake .. -DCMAKE_CXX_FLAGS="-fuse-ld=mold" -DNASTJA_ENABLE_CUDA=ON
+```

experiments/batch/build-cuda

@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+
+#SBATCH --job-name=build-cuda
+# Forschergruppe Schug
+#SBATCH --account=hkf6
+#SBATCH --partition=develbooster
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=48
+#SBATCH --time=01:00:00
+#SBATCH --output=build-cuda-%j.out
+#SBATCH --error=build-cuda-%j.err
+
+SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
+
+source "${SOURCE_DIR}/activate-nastja-modules"
+cd "${SOURCE_DIR}/nastja/build-cuda"
+
+srun make -j48

experiments/batch/build-nocuda

@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+
+#SBATCH --job-name=build-nocuda
+# Forschergruppe Schug
+#SBATCH --account=hkf6
+#SBATCH --partition=develbooster
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=48
+#SBATCH --time=01:00:00
+#SBATCH --output=build-nocuda-%j.out
+#SBATCH --error=build-nocuda-%j.err
+
+SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
+
+source "${SOURCE_DIR}/activate-nastja-modules"
+cd "${SOURCE_DIR}/nastja/build-nocuda"
+
+srun make -j48

experiments/batch/nocuda

@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+
+#SBATCH --job-name=nocuda
+# Forschergruppe Schug
+#SBATCH --account=hkf6
+# 48 Cores, 512GiB RAM, 4x NVIDIA A100 GPUs
+#SBATCH --partition=booster
+# Right now we're using a single node
+#SBATCH --nodes=1
+# Number of MPI processes
+# TODO: Change the config and set to this the maximum of 48
+#SBATCH --ntasks-per-node=16
+#SBATCH --cpus-per-task=1
+#SBATCH --time=01:00:00
+#SBATCH --output=nocuda-%j.out
+#SBATCH --error=nocuda-%j.err
+
+SOURCE_DIR=/p/project/cellsinsilico/paulslustigebude
+OUTPUT_DIR=/p/scratch/cellsinsilico/paul/nastja-out/nocuda
+
+mkdir -p "${OUTPUT_DIR}"
+source "${SOURCE_DIR}/activate-nastja-modules"
+
+srun "${SOURCE_DIR}/nastja/build-nocuda/nastja" \
+  -c "${SOURCE_DIR}/ma/experiments/configs/genesis.json" \
+  -o "${OUTPUT_DIR}"