From a10814bbefaee82d4a0b5f812b3f5053f603c732 Mon Sep 17 00:00:00 2001 From: souheil-yazji Date: Mon, 4 Dec 2023 15:55:59 +0000 Subject: [PATCH 1/3] feat(ompp-ubuntu): add ulimit soft limit --- ompp-run-ubuntu/Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/ompp-run-ubuntu/Dockerfile b/ompp-run-ubuntu/Dockerfile index 2c7a8cd..f2a2e60 100644 --- a/ompp-run-ubuntu/Dockerfile +++ b/ompp-run-ubuntu/Dockerfile @@ -1,4 +1,4 @@ -# Docker image to run openM++ models on latest Ubuntu LTS +# Docker image to run openM++ models on latest Ubuntu 22.04 # # https://github.com/openmpp/docker/blob/master/ompp-run-ubuntu/ # @@ -71,6 +71,8 @@ RUN mkdir cd ${HOME} && \ USER $OMPP_USER +RUN ulimit -s -S 65536 + SHELL ["/bin/bash", "-c"] # default command check MPIEXEC verson, when used as a kubernetes container override with custom mpiexec execution From 3a9ae53fc47c8f494383f07bf7e619d1258b761b Mon Sep 17 00:00:00 2001 From: souheil-yazji Date: Tue, 5 Dec 2023 14:45:11 +0000 Subject: [PATCH 2/3] feat(ompp-ubuntu): add ulimit soft limit --- ompp-run-ubuntu/Dockerfile | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/ompp-run-ubuntu/Dockerfile b/ompp-run-ubuntu/Dockerfile index f2a2e60..80ed2ef 100644 --- a/ompp-run-ubuntu/Dockerfile +++ b/ompp-run-ubuntu/Dockerfile @@ -35,6 +35,9 @@ FROM ubuntu:22.04 # disable debconf terminal input ARG DEBIAN_FRONTEND=noninteractive +# inject to the default bashrc as non other exist, can change later +RUN echo "ulimit -S -s 65536" >> etc/bash.bashrc + # update base image, install dependencies, cleanup RUN apt-get update && \ apt-get install -y \ @@ -71,9 +74,7 @@ RUN mkdir cd ${HOME} && \ USER $OMPP_USER -RUN ulimit -s -S 65536 - SHELL ["/bin/bash", "-c"] # default command check MPIEXEC verson, when used as a kubernetes container override with custom mpiexec execution -CMD mpiexec -V \ No newline at end of file +# CMD mpiexec -V \ No newline at end of file From 5080ea686689e5e2b8384d1fa2c2433a5d822157 Mon Sep 17 00:00:00 2001 From: souheil-yazji Date: Tue, 5 Dec 2023 15:00:30 +0000 Subject: [PATCH 3/3] chore(ompp): optimize and clean up --- ompp-run-ubuntu/Dockerfile | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/ompp-run-ubuntu/Dockerfile b/ompp-run-ubuntu/Dockerfile index 80ed2ef..d446f4e 100644 --- a/ompp-run-ubuntu/Dockerfile +++ b/ompp-run-ubuntu/Dockerfile @@ -35,11 +35,10 @@ FROM ubuntu:22.04 # disable debconf terminal input ARG DEBIAN_FRONTEND=noninteractive -# inject to the default bashrc as non other exist, can change later -RUN echo "ulimit -S -s 65536" >> etc/bash.bashrc - +# For OncoSim MPI inject to the default bashrc as non other exist, can change later +RUN echo "ulimit -S -s 65536" >> etc/bash.bashrc && \ # update base image, install dependencies, cleanup -RUN apt-get update && \ + apt-get update && \ apt-get install -y \ apt-utils \ sqlite3 \ @@ -77,4 +76,4 @@ USER $OMPP_USER SHELL ["/bin/bash", "-c"] # default command check MPIEXEC verson, when used as a kubernetes container override with custom mpiexec execution -# CMD mpiexec -V \ No newline at end of file +CMD mpiexec -V \ No newline at end of file