fix(mutagenesis): use lustre dir paths for more universal access #136

Also fixed issue with huggingface caching

SBATCH/run_mutagenesis.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-#SBATCH -t 10:00
+#SBATCH -t 30:00
 #SBATCH --job-name=run_mutagenesis_davis_esm
 #SBATCH --mem=10G
 

SBATCH/run_platinum.sh

@@ -14,8 +14,8 @@
 
 # Then to get most accurate mutagenesis you can average these matrices
 # and visualize them with src.analysis.mutagenesis_plot.plot_sequence
-
-cd /home/jyaacoub/projects/def-sushant/jyaacoub/MutDTA
+ROOT_DIR="/lustre06/project/6069023"
+cd ${ROOT_DIR}/jyaacoub/MutDTA
 source .venv/bin/activate
 
 python -u run_platinum.py \

SBATCH/test.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+ROOT_DIR="/lustre06/project/6069023"
+SCRATCH_DIR="/lustre07/scratch/jyaacoub/" # this is used for outputs on narval
+BIN_DIR="${ROOT_DIR}/jyaacoub/bin" # for modeller
+
+# Modeller is needed for this to run... (see: Generic install - https://salilab.org/modeller/10.5/release.html#unix)
+export PYTHONPATH="${PYTHONPATH}:${BIN_DIR}/modeller10.5/lib/x86_64-intel8/python3.3:${BIN_DIR}/modeller10.5/lib/x86_64-intel8:${BIN_DIR}/modeller10.5/modlib"
+export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BIN_DIR}/modeller10.5/lib/x86_64-intel8"
+
+cd ${ROOT_DIR}/jyaacoub/MutDTA
+source .venv/bin/activate
+
+# export TRANSFORMERS_CACHE="${ROOT_DIR}/jyaacoub/hf_models/"
+# export HF_HOME=${TRANSFORMERS_CACHE}
+# export HF_HUB_OFFLINE=1
+
+python -u playground.py

playground.py

@@ -1,13 +1,20 @@
 #%%
+import os
+print("os.env.TRANSFORMERS_CACHE - ", os.environ.get('TRANSFORMERS_CACHE'))
+print("           os.env.HF_HOME - ", os.environ.get('HF_HOME'))
+print("    os.env.HF_HUB_OFFLINE - ", os.environ.get('HF_HUB_OFFLINE'))
+
 import torch
 from tqdm import tqdm
-import os
 from src import cfg
 
 from src.utils.loader import Loader
 DEVICE = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
 
-print("os.env - ", os.environ['HF_HOME'])
+print("\n############### After imports: #############")
+print("os.env.TRANSFORMERS_CACHE - ", os.environ['TRANSFORMERS_CACHE'])
+print("           os.env.HF_HOME - ", os.environ['HF_HOME'])
+print("    os.env.HF_HUB_OFFLINE - ", os.environ['HF_HUB_OFFLINE'])
 m, _ = Loader.load_tuned_model('davis_esm', fold=0, device=DEVICE)
 m.eval()