Gene Embedding | Euler Submission & HPO

.gitignore

@@ -189,4 +189,7 @@ tensorboard/
 *.parquet
 
 perturbench_data/
-assets/
+assets/
+
+# anything containing "tmp"
+*tmp*

cluster/note.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+#SBATCH --output=logs/log_files/info_%j.out
+#SBATCH --error=logs/log_files/info_%j.err
+#SBATCH --time=02:00:00
+#SBATCH --ntasks=1
+#SBATCH --mem-per-cpu=16G
+#SBATCH --gpus=1
+#SBATCH --gres=gpumem:20g
+
+
+module load stack/2024-06 cuda/12.8.0
+eval "$(micromamba shell hook -s bash)"
+micromamba activate causalcell
+python src/perturbench/modelcore/train.py experiment=neurips2024/frangieh21/cpa_best_params_frangieh21

cluster/submit_hpo_job.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+#SBATCH --output=/cluster/scratch/fluebeck/perturbench_logs/log_files/hpo_%j.out
+#SBATCH --error=/cluster/scratch/fluebeck/perturbench_logs/log_files/hpo_%j.err
+#SBATCH --time=48:00:00
+#SBATCH --ntasks=1
+#SBATCH --job-name=latent_hpo_norman19_scgpt
+
+export HYDRA_FULL_ERROR=1
+module load stack/2024-06 cuda/12.8.0
+eval "$(micromamba shell hook -s bash)"
+micromamba activate causalcell
+
+# Submit HPO job
+python src/perturbench/modelcore/train.py hpo=latent_additive_hpo experiment=neurips2024/norman19/latent_scgpt_best_params_norman19

cluster/submit_job_euler.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+#SBATCH --output=/cluster/scratch/fluebeck/perturbench_logs/log_files/info_%j.out
+#SBATCH --error=/cluster/scratch/fluebeck/perturbench_logs/log_files/info_%j.err
+#SBATCH --time=06:00:00
+#SBATCH --ntasks=1
+#SBATCH --mem-per-cpu=64G
+#SBATCH --gpus=1
+#SBATCH --gres=gpumem:40g
+
+
+export HYDRA_FULL_ERROR=1
+module load stack/2024-06 cuda/12.8.0
+eval "$(micromamba shell hook -s bash)"
+micromamba activate causalcell
+python te.py #src/perturbench/modelcore/train.py experiment=neurips2024/frangieh21/latent_embedding_best_params_frangieh21

environment.yaml

@@ -0,0 +1,14 @@
+name: causalcell
+channels:
+  - nvidia
+  - pytorch
+  - conda-forge
+# channel_priority: strict
+dependencies:
+  - python=3.11
+  - ipykernel
+  - pandas
+  - numpy
+  - matplotlib
+  - seaborn
+  - pip