From 210d2eb5cc54ecf61eb79850f53fda9b47aef6e4 Mon Sep 17 00:00:00 2001 From: Sam Friedman Date: Thu, 22 Jun 2023 12:10:18 -0400 Subject: [PATCH 01/10] update description for v23 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 03e1770..03646e4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ FROM ubuntu:16.04 -LABEL Description="Amber and Amber Tool 18" +LABEL Description="Amber and Amber Tool 23" # Mount Point RUN mkdir -p /data From e66045e35bdea79a221a70d710eaed56ed100e59 Mon Sep 17 00:00:00 2001 From: Sam Friedman Date: Thu, 22 Jun 2023 12:10:51 -0400 Subject: [PATCH 02/10] update Ubuntu LTS version for newer gcc etc --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 03646e4..64779a2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:16.04 +FROM ubuntu:18.04 LABEL Description="Amber and Amber Tool 23" From b0d2af6e9b5a4289c3d8f2e59bd8b0b5a5616a39 Mon Sep 17 00:00:00 2001 From: Sam Friedman Date: Thu, 22 Jun 2023 12:12:00 -0400 Subject: [PATCH 03/10] update to required cmake, gcc packages --- Dockerfile | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 64779a2..76f8c61 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,8 +6,14 @@ LABEL Description="Amber and Amber Tool 23" RUN mkdir -p /data VOLUME /data -# Instalol c++ Chain -RUN apt-get update && apt-get install -y cmake wget csh flex patch gfortran g++ make xorg-dev libbz2-dev zlib1g-dev libboost-dev libboost-thread-dev libboost-system-dev bash xorg lightdm +# Install c++ Chain +RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install tzdata +RUN apt-get install -y cmake wget csh flex patch gfortran gcc-6 make xorg-dev libbz2-dev zlib1g-dev libboost-dev libboost-thread-dev libboost-system-dev bash xorg lightdm +# Update cmake to minimum required for building Amber22/23 (3.8.1) +RUN apt remove cmake -y && \ + wget https://cmake.org/files/v3.8/cmake-3.8.1-Linux-x86_64.sh && \ + chmod +x cmake-3.8.1-Linux-x86_64.sh && \ + bash cmake-3.8.1-Linux-x86_64.sh --skip-license # Install OpenMPI #RUN apt-get install -y openmpi-bin libopenmpi-dev From 420151b492f412edc7e9b9a763c5c8c035564f4c Mon Sep 17 00:00:00 2001 From: Sam Friedman Date: Thu, 22 Jun 2023 12:12:25 -0400 Subject: [PATCH 04/10] update dir names for v23 --- Dockerfile | 39 ++++++++++++++++++++------------------- 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/Dockerfile b/Dockerfile index 76f8c61..2ae4f42 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,39 +11,40 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install tzdata RUN apt-get install -y cmake wget csh flex patch gfortran gcc-6 make xorg-dev libbz2-dev zlib1g-dev libboost-dev libboost-thread-dev libboost-system-dev bash xorg lightdm # Update cmake to minimum required for building Amber22/23 (3.8.1) RUN apt remove cmake -y && \ - wget https://cmake.org/files/v3.8/cmake-3.8.1-Linux-x86_64.sh && \ - chmod +x cmake-3.8.1-Linux-x86_64.sh && \ - bash cmake-3.8.1-Linux-x86_64.sh --skip-license + wget https://cmake.org/files/v3.8/cmake-3.8.1-Linux-x86_64.sh && \ + chmod +x cmake-3.8.1-Linux-x86_64.sh && \ + bash cmake-3.8.1-Linux-x86_64.sh --skip-license # Install OpenMPI #RUN apt-get install -y openmpi-bin libopenmpi-dev # Amber source code -RUN mkdir /amber_source && mkdir /amber -COPY Amber18.tar.bz2 /amber_source/ -COPY AmberTools18.tar.bz2 /amber_source/ +RUN mkdir /amber22_src && mkdir /amber +COPY Amber22.tar.bz2 /amber22_src/ +COPY AmberTools23.tar.bz2 /amber22_src/ - -WORKDIR /amber_source -RUN tar -jxvf AmberTools18.tar.bz2 && \ - tar -jxvf Amber18.tar.bz2 && \ - rm -rf AmberTools18.tar.bz2 && \ - rm -rf Amber18.tar.bz2 +WORKDIR /amber22_src + +RUN tar -jxf AmberTools23.tar.bz2 && \ + tar -jxf Amber22.tar.bz2 && \ + rm -rf AmberTools23.tar.bz2 && \ + rm -rf Amber22.tar.bz2 # CMake -RUN cd amber18 && \ - mkdir build && \ - cd build && \ - cmake .. -DAPPLY_UPDATES=TRUE -DCMAKE_INSTALL_PREFIX=/amber -DBUILD_GUI=TRUE -DBUILD_PERL=TRUE -DCOMPILER=GNU -DCUDA=FALSE -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE && \ - make && \ - make install +RUN cd amber22_src && \ + cd build && \ + ./run_cmake && \ + # cmake .. -DAPPLY_UPDATES=TRUE -DCMAKE_INSTALL_PREFIX=/amber -DBUILD_GUI=TRUE -DBUILD_PERL=TRUE -DCOMPILER=GNU -DCUDA=FALSE -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE && \ + # make && \ + make install ENV AMBERHOME=/amber ENV PATH=/amber/bin:$PATH ENV LD_LIBRARY_PATH=/amber/lib:$LD_LIBRARY_PATH -RUN rm -rf /amber_source +RUN rm -rf /amber22_src +RUN echo "source /amber/amber.sh" >> /root/.bashrc ###### VNC ####### From aec74a8c9058b916273b69dae4dfa5686a9c05db Mon Sep 17 00:00:00 2001 From: Sam Friedman Date: Tue, 27 Jun 2023 11:01:42 -0400 Subject: [PATCH 05/10] update cmake to required 3.10 --- Dockerfile | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index 2ae4f42..0e58e8a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,12 +8,12 @@ VOLUME /data # Install c++ Chain RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install tzdata -RUN apt-get install -y cmake wget csh flex patch gfortran gcc-6 make xorg-dev libbz2-dev zlib1g-dev libboost-dev libboost-thread-dev libboost-system-dev bash xorg lightdm -# Update cmake to minimum required for building Amber22/23 (3.8.1) +RUN apt-get install -y cmake wget csh libfl-dev libbison-dev patch gfortran gcc-6 make xorg-dev libbz2-dev zlib1g-dev libboost-dev libboost-thread-dev libboost-system-dev bash xorg lightdm +# Update cmake to minimum required for building Amber22/23 RUN apt remove cmake -y && \ - wget https://cmake.org/files/v3.8/cmake-3.8.1-Linux-x86_64.sh && \ - chmod +x cmake-3.8.1-Linux-x86_64.sh && \ - bash cmake-3.8.1-Linux-x86_64.sh --skip-license + wget -q https://cmake.org/files/v3.10/cmake-3.10.3-Linux-x86_64.sh && \ + chmod +x cmake-3.10.3-Linux-x86_64.sh && \ + bash cmake-3.10.3-Linux-x86_64.sh --skip-license # Install OpenMPI #RUN apt-get install -y openmpi-bin libopenmpi-dev From 0a88bf056814afa16ccbeca992969c30a7c6da3b Mon Sep 17 00:00:00 2001 From: Sam Friedman Date: Tue, 27 Jun 2023 11:01:50 -0400 Subject: [PATCH 06/10] update tigervnc download link --- src/ubuntu/install/tigervnc.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ubuntu/install/tigervnc.sh b/src/ubuntu/install/tigervnc.sh index c18e015..53536b6 100644 --- a/src/ubuntu/install/tigervnc.sh +++ b/src/ubuntu/install/tigervnc.sh @@ -2,4 +2,4 @@ set -e echo "Install TigerVNC server" -wget -qO- https://dl.bintray.com/tigervnc/stable/tigervnc-1.8.0.x86_64.tar.gz | tar xz --strip 1 -C / +wget -qO- https://sourceforge.net/projects/tigervnc/files/stable/1.13.0/tigervnc-1.13.0.x86_64.tar.gz/download | tar xz --strip 1 -C / From 558005cd5ec97d1bde530f391b1dfd96d2e1bf26 Mon Sep 17 00:00:00 2001 From: Sam Friedman Date: Tue, 27 Jun 2023 11:56:33 -0400 Subject: [PATCH 07/10] Add platform tag to fix rosetta build errors on M1 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 0e58e8a..efabc5e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:18.04 +FROM --platform=linux/amd64 ubuntu:18.04 LABEL Description="Amber and Amber Tool 23" From 9bf602f77e23cd491c3d4bfcff86b175988f800e Mon Sep 17 00:00:00 2001 From: Sam Friedman Date: Tue, 27 Jun 2023 17:12:09 -0400 Subject: [PATCH 08/10] Set tigerVNC download link to v1.8 --- src/ubuntu/install/tigervnc.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ubuntu/install/tigervnc.sh b/src/ubuntu/install/tigervnc.sh index 53536b6..e0792bc 100644 --- a/src/ubuntu/install/tigervnc.sh +++ b/src/ubuntu/install/tigervnc.sh @@ -2,4 +2,4 @@ set -e echo "Install TigerVNC server" -wget -qO- https://sourceforge.net/projects/tigervnc/files/stable/1.13.0/tigervnc-1.13.0.x86_64.tar.gz/download | tar xz --strip 1 -C / +wget -qO- https://sourceforge.net/projects/tigervnc/files/stable/1.8.0/tigervnc-1.8.0.x86_64.tar.gz/download | tar xz --strip 1 -C / From fb3483a30c4b70c42bba21e07adee181b49a9ff0 Mon Sep 17 00:00:00 2001 From: Sam Friedman Date: Tue, 27 Jun 2023 17:12:39 -0400 Subject: [PATCH 09/10] add tigervnc binaries to path --- Dockerfile | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Dockerfile b/Dockerfile index efabc5e..86ba702 100644 --- a/Dockerfile +++ b/Dockerfile @@ -81,6 +81,8 @@ ENV LANG='en_US.UTF-8' LANGUAGE='en_US:en' LC_ALL='en_US.UTF-8' ### Install xvnc-server & noVNC - HTML5 based VNC viewer RUN $INST_SCRIPTS/tigervnc.sh RUN $INST_SCRIPTS/no_vnc.sh +# tigervnc script installs vncserver binary to /usr/libexec +ENV PATH=/usr/libexec:$PATH ### Install firefox RUN $INST_SCRIPTS/firefox.sh @@ -108,6 +110,7 @@ RUN cd vmd-1.9.3 && \ cd src && \ make install RUN cd / && rm -rf /othertools +WORKDIR / USER 1000 From c47a51e768fb64cf10e17e0746a4e3e42c73742b Mon Sep 17 00:00:00 2001 From: Sam Friedman Date: Tue, 27 Jun 2023 17:12:51 -0400 Subject: [PATCH 10/10] re-enable cmake configs --- Dockerfile | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 86ba702..c20ff4e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,9 +35,8 @@ RUN tar -jxf AmberTools23.tar.bz2 && \ # CMake RUN cd amber22_src && \ cd build && \ - ./run_cmake && \ - # cmake .. -DAPPLY_UPDATES=TRUE -DCMAKE_INSTALL_PREFIX=/amber -DBUILD_GUI=TRUE -DBUILD_PERL=TRUE -DCOMPILER=GNU -DCUDA=FALSE -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE && \ - # make && \ + cmake .. -DAPPLY_UPDATES=TRUE -DCMAKE_INSTALL_PREFIX=/amber -DBUILD_GUI=TRUE -DBUILD_PERL=TRUE -DCOMPILER=GNU -DCUDA=FALSE -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE && \ + make && \ make install ENV AMBERHOME=/amber