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ComparativeGenomicsToolkit
cactus
Commits
433bf9db
Commit
433bf9db
authored
Jun 14, 2022
by
Glenn Hickey
Browse files
try to use cuda/driver combo terra actually supports
parent
e52e91b2
Pipeline
#1763
passed with stage
in 72 minutes and 28 seconds
Changes
2
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2
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Dockerfile.segalign
View file @
433bf9db
FROM nvidia/cuda:11.7.0-devel-ubuntu22.04 as builder
FROM nvidia/cuda:11.4.3-devel-ubuntu20.04 as builder
# Prevent dpkg from trying to ask any questions, ever
ENV DEBIAN_FRONTEND noninteractive
# system dependencies are installed by ./installUbuntu.sh below, but we need sudo first
RUN apt-get -qq -y update && \
...
...
@@ -16,7 +19,7 @@ RUN git clone https://github.com/ComparativeGenomicsToolkit/SegAlign.git /WGA_GP
RUN cd /WGA_GPU && rm -rf build && ./scripts/installUbuntu.sh -c && git rev-parse HEAD > /Segalign.commit
# Create a thinner final Docker image with only runtime dependencies
FROM nvidia/cuda:11.
7.0
-runtime-ubuntu2
2
.04
FROM nvidia/cuda:11.
4.3
-runtime-ubuntu2
0
.04
# Install runtime dependencies
RUN apt-get -qq -y update && \
...
...
src/cactus/progressive/cactus_prepare.py
View file @
433bf9db
...
...
@@ -80,7 +80,7 @@ def main(toil_mode=False):
parser
.
add_argument
(
"--gpu"
,
action
=
"store_true"
,
help
=
"use gpu-enabled lastz in cactus-blast and cactus-preprocess"
)
parser
.
add_argument
(
"--gpuType"
,
default
=
"nvidia-tesla-v100"
,
help
=
"GPU type (to set in WDL runtime parameters, use only with --wdl)"
)
parser
.
add_argument
(
"--gpuCount"
,
type
=
int
,
default
=
1
,
help
=
"GPU count (to set in WDL runtime parametersm, use only with --wdl)"
)
parser
.
add_argument
(
"--nvidiaDriver"
,
default
=
"4
4
0.
64
.0
0
"
,
help
=
"Nvidia driver version"
)
parser
.
add_argument
(
"--nvidiaDriver"
,
default
=
"4
7
0.
82
.0
1
"
,
help
=
"Nvidia driver version"
)
parser
.
add_argument
(
"--gpuZone"
,
default
=
"us-central1-a"
,
help
=
"zone used for gpu task"
)
parser
.
add_argument
(
"--zone"
,
default
=
"us-west2-a"
,
help
=
"zone used for all but gpu tasks"
)
...
...
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