neuronflow
commented
9 months ago did you solve it?
Open vanossj opened 3 years ago
neuronflow
commented
9 months ago did you solve it?
pyushkevich
commented
9 months ago Unless you are running an old version of the code, greedy should be built with ITK5.
Here is a dockerfile that builds greedy and other tools from our group:
https://github.com/pyushkevich/tk-docker
And the container itself is pyushkevich/tk:latest
On Wed, Dec 20, 2023 at 7:11 PM neuronflow @.***> wrote:
did you solve it?
— Reply to this email directly, view it on GitHub https://github.com/pyushkevich/greedy/issues/23#issuecomment-1865301221, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJPEW73IQMREXCRESE774DYKN5EDAVCNFSM4X5MYASKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBWGUZTAMJSGIYQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
neuronflow
commented
9 months ago Thank you. Will this work on ARM CPUs, specifically M1 Apple silicon?
pyushkevich
commented
9 months ago The Docker container won't work on M1, but I believe the script in the Dockerfile should work.
On Thu, Dec 21, 2023 at 9:26 AM neuronflow @.***> wrote:
Thank you. Will this work on ARM CPUs, specifically M1 Apple silicon?
— Reply to this email directly, view it on GitHub https://github.com/pyushkevich/greedy/issues/23#issuecomment-1866362168, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJPEW4HRVVYZAATLJK5Y63YKRBK3AVCNFSM4X5MYASKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBWGYZTMMRRGY4A . You are receiving this because you commented.Message ID: @.***>
neuronflow
commented
9 months ago we are trying to build greedy in a debian based docker running on an M1 Mac without success so far.
Here are our current efforts:
FROM python:3.10.13-bullseye
ARG BUILD_JOBS=16
# # Setup LST-AI
RUN mkdir -p /custom_apps/lst_directory
# Install prerequisites
# c.f. https://greedy.readthedocs.io/en/latest/install.html#compiling-from-source-code
RUN apt-get update && \
apt-get install -y cmake g++ git
# Install additional dependencies for VTK
RUN apt-get install -y libgl1-mesa-dev libxt-dev
# Install libpng
RUN apt-get install -y libpng-dev
# Build VTK
# Download and unpack VTK
WORKDIR /VTK
RUN git clone https://gitlab.kitware.com/vtk/vtk.git
WORKDIR /VTK/vtk
RUN git checkout v9.1.0
# Create and navigate to the build directory for VTK
RUN mkdir VTK-build
WORKDIR /VTK/vtk/VTK-build
# Run CMake to configure and build VTK
RUN cmake -DCMAKE_BUILD_TYPE=Release ..
RUN make -j ${BUILD_JOBS}
RUN make install
# Build ITK
# c.f. https://itk.org/Wiki/ITK/Getting_Started/Build/Linux
# Clone the ITK repository
RUN git clone https://github.com/InsightSoftwareConsortium/ITK.git /ITK
WORKDIR /ITK
# Checkout the specific version
RUN git checkout v5.1.2
# Create and navigate to the build directory
RUN mkdir -p /ITK/build
WORKDIR /ITK/build
# Run CMake to configure and build ITK
RUN cmake -DModule_ITKPNG=ON \
-DITK_USE_SYSTEM_PNG=ON \
-DBUILD_TESTING=OFF \
-DCMAKE_BUILD_TYPE=Release ..
# run build process
RUN make -j ${BUILD_JOBS}
RUN make install
# Clone the greedy repository
RUN git clone https://github.com/pyushkevich/greedy /greedy
WORKDIR /greedy
RUN git checkout 1eafa4c6659b7a669fb299ce98d9531fc23e332a
# Set the working directory to the build directory
WORKDIR /greedy/build
# Run ccmake from the build directory
RUN cmake -DITK_DIR=/ITK/build \
-DVTK_DIR=/VTK/vtk/VTK-build \
-DCMAKE_BUILD_TYPE=Release \
..
RUN make -j ${BUILD_JOBS}
RUN make installcurrently when we run greedy inside the container we get:
greedy: error while loading shared libraries: libvtkIOPLY-9.1.so.1: cannot open shared object file: No such file or directorySounds like LD_LIBRARY_PATH should be set in the environment to point to where the VTK build places the .so files. Or in your VTK build, make it be static.
On Thu, Dec 21, 2023 at 11:08 AM neuronflow @.***> wrote:
we are trying to build greedy in a debian based docker running on an M1 Mac without success so far.
Here are our current efforts:
FROM python:3.10.13-bullseye
ARG BUILD_JOBS=16
Setup LST-AI
RUN mkdir -p /custom_apps/lst_directory
Install prerequisites
c.f. https://greedy.readthedocs.io/en/latest/install.html#compiling-from-source-code
RUN apt-get update && \ apt-get install -y cmake g++ git
Install additional dependencies for VTK
RUN apt-get install -y libgl1-mesa-dev libxt-dev
Install libpng
RUN apt-get install -y libpng-dev
Build VTK
Download and unpack VTK
WORKDIR /VTK RUN git clone https://gitlab.kitware.com/vtk/vtk.git WORKDIR /VTK/vtk RUN git checkout v9.1.0
Create and navigate to the build directory for VTK
RUN mkdir VTK-build WORKDIR /VTK/vtk/VTK-build
Run CMake to configure and build VTK
RUN cmake -DCMAKE_BUILD_TYPE=Release .. RUN make -j ${BUILD_JOBS} RUN make install
Build ITK
c.f. https://itk.org/Wiki/ITK/Getting_Started/Build/Linux
Clone the ITK repository
RUN git clone https://github.com/InsightSoftwareConsortium/ITK.git /ITK WORKDIR /ITK
Checkout the specific version
RUN git checkout v5.1.2
Create and navigate to the build directory
RUN mkdir -p /ITK/build WORKDIR /ITK/build
Run CMake to configure and build ITK
RUN cmake -DModule_ITKPNG=ON \ -DITK_USE_SYSTEM_PNG=ON \ -DBUILD_TESTING=OFF \ -DCMAKE_BUILD_TYPE=Release ..
run build process
RUN make -j ${BUILD_JOBS} RUN make install
Clone the greedy repository
RUN git clone https://github.com/pyushkevich/greedy /greedy WORKDIR /greedy RUN git checkout 1eafa4c6659b7a669fb299ce98d9531fc23e332a
Set the working directory to the build directory
WORKDIR /greedy/build
Run ccmake from the build directory
RUN cmake -DITK_DIR=/ITK/build \ -DVTK_DIR=/VTK/vtk/VTK-build \ -DCMAKE_BUILD_TYPE=Release \ .. RUN make -j ${BUILD_JOBS} RUN make install
currently when we run greedy inside the container we get:
greedy: error while loading shared libraries: libvtkIOPLY-9.1.so.1: cannot open shared object file: No such file or directory
— Reply to this email directly, view it on GitHub https://github.com/pyushkevich/greedy/issues/23#issuecomment-1866574920, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJPEW7UVK6YUXLYFPRYBCDYKRNH7AVCNFSM4X5MYASKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBWGY2TONBZGIYA . You are receiving this because you commented.Message ID: @.***>
neuronflow
commented
9 months ago The Docker container won't work on M1, but I believe the script in the Dockerfile should work. … On Thu, Dec 21, 2023 at 9:26 AM neuronflow @.> wrote: Thank you. Will this work on ARM CPUs, specifically M1 Apple silicon? — Reply to this email directly, view it on GitHub <#23 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJPEW4HRVVYZAATLJK5Y63YKRBK3AVCNFSM4X5MYASKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBWGYZTMMRRGY4A . You are receiving this because you commented.Message ID: @.>
Thanks, I will try to find out how to implement what you suggested.
Meanwhile I used your Dockerfile to build an image on my M1 system and added our payload to it. However, when I create containers from it I get:
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Python 3.10.0
jilei-hao
commented
9 months ago @neuronflow do you need to run greedy on a M1 machine, or do you need to run it on another linux machine?
If your greedy is meant to be running on a M1 machine, try this binary instead of building from scratch.
neuronflow
commented
9 months ago @jilei-hao We need to run greedy inside a Linux-based docker container running on OSX on a M1 machine.
We managed to get it running now, thanks to the advice from @pyushkevich.
This file seems to work:
FROM python:3.10.13-bullseye
ARG BUILD_JOBS=8
# # Setup LST-AI
RUN mkdir -p /custom_apps/lst_directory
# Install prerequisites
# c.f. https://greedy.readthedocs.io/en/latest/install.html#compiling-from-source-code
RUN apt-get update && \
apt-get install -y cmake g++ git
# Install additional dependencies for VTK
RUN apt-get install -y libgl1-mesa-dev libxt-dev
# Install libpng
RUN apt-get install -y libpng-dev
# Build VTK
# Download and unpack VTK
WORKDIR /VTK
RUN git clone https://gitlab.kitware.com/vtk/vtk.git
WORKDIR /VTK/vtk
RUN git checkout v9.1.0
# Create and navigate to the build directory for VTK
RUN mkdir VTK-build
WORKDIR /VTK/vtk/VTK-build
# ENV LD_LIBRARY_PATH=/VTK/vtk/VTK-build:$LD_LIBRARY_PATH
# Run CMake to configure and build VTK
RUN cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=OFF ..
RUN make -j ${BUILD_JOBS}
RUN make install
# Build ITK
# c.f. https://itk.org/Wiki/ITK/Getting_Started/Build/Linux
# Clone the ITK repository
RUN git clone https://github.com/InsightSoftwareConsortium/ITK.git /ITK
WORKDIR /ITK
# Checkout the specific version
RUN git checkout v5.1.2
# Create and navigate to the build directory
RUN mkdir -p /ITK/build
WORKDIR /ITK/build
# Run CMake to configure and build ITK
RUN cmake -DModule_ITKPNG=ON \
-DITK_USE_SYSTEM_PNG=ON \
-DBUILD_TESTING=OFF \
-DBUILD_SHARED_LIBS=OFF \
-DCMAKE_BUILD_TYPE=Release ..
# run build process
RUN make -j ${BUILD_JOBS}
RUN make install
# Clone the greedy repository
RUN git clone https://github.com/pyushkevich/greedy /greedy
WORKDIR /greedy
RUN git checkout 1eafa4c6659b7a669fb299ce98d9531fc23e332a
# Set the working directory to the build directory
WORKDIR /greedy/build
# Run ccmake from the build directory
RUN cmake -DITK_DIR=/ITK/build \
-DVTK_DIR=/VTK/vtk/VTK-build \
-DCMAKE_BUILD_TYPE=Release \
-DBUILD_SHARED_LIBS=OFF \
..
RUN make -j ${BUILD_JOBS}
RUN make install
I've been trying to get greedy to build in a docker container but I'm running into errors with
isnanITK: 4.12.2 greedy: a9fcaac
Dockerfile
ITK builds fine but when it gets to greedy I get error messages like
full log: build.log