Merge branch 'master' of https://git.ufz.de/hertelj/deepfplearn

submitTrainingGPU.noAC.sh

+#!/bin/bash
+
+#$ -N dfpl_train_gpu_noAC
+#$ -S /bin/bash
+#$ -l h_rt=10:00:00
+#$ -l h_vmem=30G	# singularity requires a fair bit of memory
+#$ -l gpu=1	# request GPUs here!
+#$ -binding linear:1
+
+# output files
+#$ -o /work/$USER/$JOB_NAME.out
+#$ -e /work/$USER/$JOB_NAME.err
+
+# Train on Sun et al data
+singularity run --nv /global/apps/deepFPlearn/deepfplearn.sif train -i /data/bioinf/projects/data/2019_IDA-chem/deepFPlearn/input/Sun_etal_dataset.csv -o /data/bioinf/projects/data/2019_IDA-chem/deepFPlearn/modeltraining/kfoldCV_GPU/noAC/ -t 'smiles' -k 'topological' -s 2048 -e 2000 -l 0.2 -K 5 -v 2
+
+# Train on BindingDB data
+singularity run --nv /global/apps/deepFPlearn/deepfplearn-sc.sif train -i /data/bioinf/projects/data/2020_deepFPlearn/dataSources/BindingDB/data/07_BindingDB.trainingSet.csv -o /data/bioinf/projects/data/2019_IDA-chem/deepFPlearn/modeltraining/kfoldCV_GPU/noAC/ -t 'smiles' -k 'topological' -s 2048 -e 2000 -l 0.2 -K 5 -v 2 -m
+
+# Train on combinded Sun-BindingDB data set
+singularity run --nv /global/apps/deepFPlearn/deepfplearn-sc.sif train -i /data/bioinf/projects/data/2020_deepFPlearn/dataSources/combinedBDBSund/01_combinedSUN-BDB.dataset.4training.csv -o /data/bioinf/projects/data/2019_IDA-chem/deepFPlearn/modeltraining/kfoldCV_GPU/noAC/combinedBDBSUN/ -t 'smiles' -k 'topological' -s 2048 -e 2000 -l 0.2 -K 5 -v 2 -m
+
+#Your job 6639483 ("dfpl_train_gpu_noAC") has been submitted
+# 09.07.2020 13:17

submitTrainingGPU.sh

 #!/bin/bash
 
-#$ -N dfpl_train_gpu
+#$ -N dfpl_train_gpu_AC
 #$ -S /bin/bash
-#$ -l h_rt=00:20:00
-#$ -l h_vmem=20G	# singularity requires a fair bit of memory
+#$ -l h_rt=10:00:00
+#$ -l h_vmem=30G	# singularity requires a fair bit of memory
 #$ -l gpu=1	# request GPUs here!
 #$ -binding linear:1
 
@@ -11,4 +11,14 @@
 #$ -o /work/$USER/$JOB_NAME.out
 #$ -e /work/$USER/$JOB_NAME.err
 
+# Train on Sun et al data
 singularity run --nv /global/apps/deepFPlearn/deepfplearn.sif train -i /data/bioinf/projects/data/2019_IDA-chem/deepFPlearn/input/Sun_etal_dataset.csv -o /data/bioinf/projects/data/2019_IDA-chem/deepFPlearn/modeltraining/kfoldCV_GPU/ -t 'smiles' -k 'topological' -s 2048 -a -d 256 -e 2000 -l 0.2 -K 5 -v 2
+
+# Train on BindingDB data
+singularity run --nv /global/apps/deepFPlearn/deepfplearn-sc.sif train -i /data/bioinf/projects/data/2020_deepFPlearn/dataSources/BindingDB/data/07_BindingDB.trainingSet.csv -o /data/bioinf/projects/data/2019_IDA-chem/deepFPlearn/modeltraining/kfoldCV_GPU/ -t 'smiles' -k 'topological' -s 2048 -a -d 256 -e 2000 -l 0.2 -K 5 -v 2 -m
+
+# Train on combinded Sun-BindingDB data set
+singularity run --nv /global/apps/deepFPlearn/deepfplearn-sc.sif train -i /data/bioinf/projects/data/2020_deepFPlearn/dataSources/combinedBDBSund/01_combinedSUN-BDB.dataset.4training.csv -o /data/bioinf/projects/data/2019_IDA-chem/deepFPlearn/modeltraining/kfoldCV_GPU/combinedBDBSUN/ -t 'smiles' -k 'topological' -s 2048 -a -d 256 -e 2000 -l 0.2 -K 5 -v 2 -m
+
+#Your job 6639482 ("dfpl_train_gpu_AC") has been submitted
+# 09.07.2020 13:16