| # $1 is the name of the scripts folder | |
| # $2 are the tasks to run, seperated by comma | |
| # $3 is the gpu ids that used for training, seperated by comma | |
| # $4 is an optional argument that, if present, skips the check for finished tasks | |
| IFS=',' read -ra arr <<< $2 | |
| CUDA_VISIBLE_DEVICES=$3 | |
| echo "CUDA_VISIBLE_DEVICES="$CUDA_VISIBLE_DEVICES | |
| if [ -z "$4" ]; then | |
| echo "Check if tasks have finished" | |
| fi | |
| for fold in {0..4} | |
| do | |
| for gene in ${arr[@]} | |
| do | |
| # use original yaml as template | |
| if [[ $gene == "Itan.CKB.Cancer" || $gene == "ICC" ]]; then | |
| for task in $(cat scripts/gene.txt); do | |
| echo "Begin "$task | |
| # check if task has finished, unless the skip argument is present | |
| if [ -z "$4" ]; then | |
| logdir=$(cat $1/$task.5fold/$task.fold.$fold.yaml | grep log_dir | sed 's/.*: //') | |
| num_epochs=$(cat $1/$task.5fold/$task.fold.$fold.yaml | grep num_epochs | sed 's/.*: //') | |
| if [ -f $logdir/model.epoch.$num_epochs.pt ]; then | |
| echo "Skip "$task | |
| continue | |
| fi | |
| fi | |
| python -W ignore::UserWarning:torch_geometric.data.collate:147 train.py --conf $1/$task.5fold/$task.fold.$fold.yaml --mode train_4_fold | |
| done | |
| else | |
| echo "Begin "$gene | |
| # check if task has finished, unless the skip argument is present | |
| if [ -z "$4" ]; then | |
| logdir=$(cat $1/$gene.5fold/$gene.fold.$fold.yaml | grep log_dir | sed 's/.*: //') | |
| num_epochs=$(cat $1/$gene.5fold/$gene.fold.$fold.yaml | grep num_epochs | sed 's/.*: //') | |
| if [ -f $logdir/model.epoch.$num_epochs.pt ]; then | |
| echo "Skip "$gene | |
| continue | |
| fi | |
| fi | |
| python -W ignore::UserWarning:torch_geometric.data.collate:147 train.py --conf $1/$gene.5fold/$gene.fold.$fold.yaml --mode train_4_fold | |
| fi | |
| done | |
| done | |