Merge branch 'lc-branch'

CaiLiLab · Oct 25, 2021 · 6f6847c · 6f6847c
2 parents 384d93a + f733c0c
commit 6f6847c
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Showing 5 changed files with 11 additions and 10 deletions.
diff --git a/MuRaL/run_predict.py b/MuRaL/run_predict.py
@@ -244,7 +244,7 @@ def main():
         for i in range(nvmlDeviceGetCount()):
             h = nvmlDeviceGetHandleByIndex(i)
             info = nvmlDeviceGetMemoryInfo(h)
-            if info.free > 1.5*(2**30): # Reserve 1.5GB
+            if info.free > 2.0*(2**30): # Reserve 2GB GPU memory
                 cuda_id = str(i)
                 break
 

diff --git a/MuRaL/run_train_TL_raytune.py b/MuRaL/run_train_TL_raytune.py
@@ -173,7 +173,7 @@ def parse_arguments(parser):
                           Default: 'loss'.
                           """ ).strip())
 
-    raytune_args.add_argument('--ray_ncpus', type=int, metavar='INT', default=6, 
+    raytune_args.add_argument('--ray_ncpus', type=int, metavar='INT', default=2, 
                           help=textwrap.dedent("""
                           Number of CPUs requested by Ray-Tune. Default: 6.
                           """ ).strip())
@@ -183,9 +183,9 @@ def parse_arguments(parser):
                           Number of GPUs requested by Ray-Tune. Default: 1.
                           """ ).strip())
 
-    raytune_args.add_argument('--cpu_per_trial', type=int, metavar='INT', default=3, 
+    raytune_args.add_argument('--cpu_per_trial', type=int, metavar='INT', default=2, 
                           help=textwrap.dedent("""
-                          Number of CPUs used per trial. Default: 3.
+                          Number of CPUs used per trial. Default: 2.
                           """ ).strip())
 
     raytune_args.add_argument('--gpu_per_trial', type=float, metavar='FLOAT', default=0.19, 

diff --git a/MuRaL/run_train_raytune.py b/MuRaL/run_train_raytune.py
@@ -232,19 +232,19 @@ def parse_arguments(parser):
                           Default: 'loss'.
                           """ ).strip())
 
-    raytune_args.add_argument('--ray_ncpus', type=int, metavar='INT', default=6, 
+    raytune_args.add_argument('--ray_ncpus', type=int, metavar='INT', default=4, 
                           help=textwrap.dedent("""
-                          Number of CPUs requested by Ray-Tune. Default: 6.
+                          Number of CPUs requested by Ray-Tune. Default: 4.
                           """ ).strip())
 
     raytune_args.add_argument('--ray_ngpus', type=int, metavar='INT', default=1, 
                           help=textwrap.dedent("""
                           Number of GPUs requested by Ray-Tune. Default: 1.
                           """ ).strip())
 
-    raytune_args.add_argument('--cpu_per_trial', type=int, metavar='INT', default=3, 
+    raytune_args.add_argument('--cpu_per_trial', type=int, metavar='INT', default=2, 
                           help=textwrap.dedent("""
-                          Number of CPUs used per trial. Default: 3.
+                          Number of CPUs used per trial. Default: 2.
                           """ ).strip())
 
     raytune_args.add_argument('--gpu_per_trial', type=float, metavar='FLOAT', default=0.15, 

diff --git a/examples/README b/examples/README
@@ -1,4 +1,4 @@
-This folder provides example data and command lines for run MuRaL commands.
+This folder provides example data and command lines for running MuRaL commands.
 
 The 'data/' folder contains training/validation/testing BED-formatted files and a FASTA file 'seq.fa' served as the reference genome for the BED files.
 

diff --git a/install_env_conda.sh b/install_env_conda.sh
@@ -1,7 +1,8 @@
 git clone [email protected]:CaiLiLab/MuRaL.git
 
 conda env create -n mural -f environment.yml
-'conda env update --file environment.yml --prune
+# if the installation interupted due to network, run the following:
+# conda env update -n mural -f environment.yml --prune
 
 conda activate mural