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e29a775
auto-detect arm platform in build.sh
tijszwinkels Jul 5, 2024
0f68b03
Add exp branch
pgleeson Aug 15, 2024
259750b
Merge pull request #355 from tijszwinkels/detect-arm
pgleeson Aug 15, 2024
c11c5b1
Add the jupyterlab for compatibility with binder
Sep 21, 2024
dc7afef
Merge pull request #358 from tomichec/287-mybinder
pgleeson Oct 4, 2024
42d80bc
Merge branch 'development' into test_jupyterlab2
pgleeson Oct 4, 2024
e878e3d
Merge branch 'patch-1' of github.com:pikid/OpenWorm into pikid-patch-1
pgleeson Oct 4, 2024
9516673
Merge branch 'pikid-patch-1' into test_jupyterlab2
pgleeson Oct 4, 2024
1abda59
Merge branch 'experimental' into test_jupyterlab2
pgleeson Oct 4, 2024
d36a9fe
Arch check in rebuild also
pgleeson Oct 5, 2024
4e6e757
Initial jupyterlab run script
pgleeson Oct 5, 2024
b6ffffe
Copy out positions buffer also
pgleeson Oct 10, 2024
36a80c3
Merge branch 'master' into experimental
pgleeson Jun 6, 2025
724761f
Merge branch 'development' into experimental
pgleeson Jul 31, 2025
5a569e2
Better jupyterlab install
pgleeson Jul 31, 2025
715de9f
Tidying up image
pgleeson Jul 31, 2025
3a9e7a2
Improves the master_openworm script - makes it more realsitic about w…
pgleeson Aug 8, 2025
2b19881
Improve options o run.sh, able to pass a configuration, e.g. ./run.sh…
pgleeson Aug 8, 2025
551d12c
Use default worm_crawl_half_resolution
pgleeson Aug 8, 2025
cd45918
Improved test
pgleeson Aug 8, 2025
1adf562
Merge branch 'development' into experimental
pgleeson Nov 14, 2025
2cf0ac4
Allow no c302 option to be passed with: -n
pgleeson Dec 1, 2025
b753a5a
Merge branch 'test_all' into experimental
pgleeson Dec 1, 2025
9e97618
Tweak to test runs
pgleeson Dec 4, 2025
06e3b82
Merge branch 'test_all' into experimental
pgleeson Dec 4, 2025
70bfcc3
Merge branch 'experimental' of github.com:openworm/OpenWorm into expe…
pgleeson Dec 4, 2025
e924670
Merge branch 'test_all' into experimental
pgleeson Dec 8, 2025
57a640a
Merge branch 'test_all' into experimental
pgleeson Dec 8, 2025
1a09dfe
Merge branch 'master' into experimental
pgleeson Mar 19, 2026
a31148a
Merge branch 'development' into experimental
pgleeson Mar 19, 2026
2bb5cb2
Merge branch 'test_all' into experimental
pgleeson Mar 24, 2026
0feafd6
Merge branch 'master' into experimental
pgleeson Mar 30, 2026
0745402
Fix the uid conflict by removing ubuntu user
Apr 14, 2026
3126205
Merge branch 'development' into experimental
pgleeson Apr 21, 2026
1e8a647
Merge pull request #384 from Ahiknsr/uid_conflict
pgleeson Apr 21, 2026
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22 changes: 10 additions & 12 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -5,18 +5,16 @@ LABEL maintainer="David Lung (lungdm@gmail.com); Padraig Gleeson (p.gleeson@gmai
ARG USR=ow
ENV USER=$USR

RUN touch /var/mail/ubuntu && chown ubuntu /var/mail/ubuntu && userdel -r ubuntu

RUN apt-get update && \
apt-get upgrade -y && \
apt-get dist-upgrade -y

RUN mkdir -p /etc/sudoers.d && \
export uid=1000 gid=1000 && \
mkdir -p /home/$USER && \
echo "$USER:x:${uid}:${gid}:$USER,,,:/home/$USER:/bin/bash" >> /etc/passwd && \
echo "$USER:x:${uid}:" >> /etc/group && \
echo "$USER ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/$USER && \
chmod 0440 /etc/sudoers.d/$USER && \
chown ${uid}:${gid} -R /home/$USER
RUN apt-get update && apt-get install -y sudo && \
useradd -m -s /bin/bash -u 1000 $USER && \
echo "$USER ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/$USER && \
chmod 0440 /etc/sudoers.d/$USER

ENV DEBIAN_FRONTEND=noninteractive

Expand All @@ -29,12 +27,11 @@ RUN apt-get install -y --no-install-recommends apt-utils \
wget nano htop build-essential make git automake autoconf \
g++ rpm libtool libncurses5-dev zlib1g-dev bison flex \
sudo xorg openbox x11-xserver-utils \
libxext-dev libncurses-dev mercurial \
libxext-dev libncurses-dev \
freeglut3-dev libglu1-mesa-dev libglew-dev python3-dev python3-pip \
kmod dkms linux-source linux-headers-generic \
maven openjdk-8-jdk \
openjdk-21-jdk \
libnuma1 \
openmpi-bin libopenmpi-dev \
libgl1 libglx-mesa0 libgl1-mesa-dri libfreetype6-dev \
libxft-dev unzip ffmpeg xvfb tmux

Expand Down Expand Up @@ -96,7 +93,8 @@ ENV NEURON_MODULE_OPTIONS=-nogui
RUN wget https://master.dl.sourceforge.net/project/nicehashsgminerv5viptools/APP%20SDK%20A%20Complete%20Development%20Platform/AMD%20APP%20SDK%203.0%20for%2064-bit%20Linux/AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2 && \
tar -xf AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2 && \
printf 'Y\n\n' | sudo ./AMD-APP-SDK-v3.0.130.136-GA-linux64.sh && \
rm AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2
rm AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2 && \
rm AMD-APP-SDK-v3.0.130.136-GA-linux64.sh

RUN sudo ln -s /opt/AMDAPPSDK-3.0/lib/x86_64/sdk/libOpenCL.so.1 /usr/lib/libOpenCL.so.1
RUN sudo ln -s /opt/AMDAPPSDK-3.0/lib/x86_64/sdk/libamdocl64.so /usr/lib/libamdocl64.so
Expand Down