From f733c0cb8a3fa1007e50765e6947582d9aca8f37 Mon Sep 17 00:00:00 2001 From: cailigd Date: Mon, 25 Oct 2021 09:26:09 +0800 Subject: [PATCH] change default cpu_per_trial --- MuRaL/run_predict.py | 2 +- MuRaL/run_train_TL_raytune.py | 6 +++--- MuRaL/run_train_raytune.py | 8 ++++---- examples/README | 2 +- install_env_conda.sh | 3 ++- 5 files changed, 11 insertions(+), 10 deletions(-) diff --git a/MuRaL/run_predict.py b/MuRaL/run_predict.py index d367979..27a5fbd 100644 --- 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 index 9e30220..3ff097d 100644 --- 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 index f95294a..a3b3341 100644 --- a/MuRaL/run_train_raytune.py +++ b/MuRaL/run_train_raytune.py @@ -232,9 +232,9 @@ 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, @@ -242,9 +242,9 @@ 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=0.15, diff --git a/examples/README b/examples/README index 6aa4d9a..c45bb12 100644 --- 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 index 41c155c..35c6cae 100644 --- a/install_env_conda.sh +++ b/install_env_conda.sh @@ -1,7 +1,8 @@ git clone git@github.com: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