High Performance Computing and Emerging Technologies Group

OBBA/230

https://www.psi.ch/en/awi/high-performance-computing-and-emerging-technologies-group

Repositories

5

Projects Packages Code

cryosparc_docker (latest)

Published 2025-04-22 14:45:14 +02:00 by viessm_h

Installation

Pull the image from the command line:

docker pull gitea.psi.ch/hpce/cryosparc_docker:latest

Digest

sha256:a7a550e8453416550fde4376e915fb2af323bc88c59a12258f6f600d2b13938a

For more information on the Container registry, see the documentation.

Image Layers

ARG RELEASE

ARG LAUNCHPAD_BUILD_ARCH

LABEL org.opencontainers.image.ref.name=ubuntu

LABEL org.opencontainers.image.version=20.04

ADD file:655d373cb551d0dd5d7867f88a4f98908dc3f16190986f693e88c423e6f21b8d in /

CMD ["/bin/bash"]

ENV NVARCH=x86_64

ENV NVIDIA_REQUIRE_CUDA=cuda>=11.8 brand=tesla,driver>=450,driver<451 brand=tesla,driver>=470,driver<471 brand=unknown,driver>=470,driver<471 brand=nvidia,driver>=470,driver<471 brand=nvidiartx,driver>=470,driver<471 brand=geforce,driver>=470,driver<471 brand=geforcertx,driver>=470,driver<471 brand=quadro,driver>=470,driver<471 brand=quadrortx,driver>=470,driver<471 brand=titan,driver>=470,driver<471 brand=titanrtx,driver>=470,driver<471 brand=tesla,driver>=510,driver<511 brand=unknown,driver>=510,driver<511 brand=nvidia,driver>=510,driver<511 brand=nvidiartx,driver>=510,driver<511 brand=geforce,driver>=510,driver<511 brand=geforcertx,driver>=510,driver<511 brand=quadro,driver>=510,driver<511 brand=quadrortx,driver>=510,driver<511 brand=titan,driver>=510,driver<511 brand=titanrtx,driver>=510,driver<511 brand=tesla,driver>=515,driver<516 brand=unknown,driver>=515,driver<516 brand=nvidia,driver>=515,driver<516 brand=nvidiartx,driver>=515,driver<516 brand=geforce,driver>=515,driver<516 brand=geforcertx,driver>=515,driver<516 brand=quadro,driver>=515,driver<516 brand=quadrortx,driver>=515,driver<516 brand=titan,driver>=515,driver<516 brand=titanrtx,driver>=515,driver<516

ENV NV_CUDA_CUDART_VERSION=11.8.89-1

ENV NV_CUDA_COMPAT_PACKAGE=cuda-compat-11-8

ARG TARGETARCH

LABEL maintainer=NVIDIA CORPORATION <cudatools@nvidia.com>

RUN |1 TARGETARCH=amd64 /bin/sh -c apt-get update && apt-get install -y --no-install-recommends gnupg2 curl ca-certificates && curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/${NVARCH}/3bf863cc.pub | apt-key add - && echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/${NVARCH} /" > /etc/apt/sources.list.d/cuda.list && apt-get purge --autoremove -y curl && rm -rf /var/lib/apt/lists/* # buildkit

ENV CUDA_VERSION=11.8.0

RUN |1 TARGETARCH=amd64 /bin/sh -c apt-get update && apt-get install -y --no-install-recommends cuda-cudart-11-8=${NV_CUDA_CUDART_VERSION} ${NV_CUDA_COMPAT_PACKAGE} && rm -rf /var/lib/apt/lists/* # buildkit

RUN |1 TARGETARCH=amd64 /bin/sh -c echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf && echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf # buildkit

ENV PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

ENV LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64

COPY NGC-DL-CONTAINER-LICENSE / # buildkit

ENV NVIDIA_VISIBLE_DEVICES=all

ENV NVIDIA_DRIVER_CAPABILITIES=compute,utility

ENV NV_CUDA_LIB_VERSION=11.8.0-1

ENV NV_NVTX_VERSION=11.8.86-1

ENV NV_LIBNPP_VERSION=11.8.0.86-1

ENV NV_LIBNPP_PACKAGE=libnpp-11-8=11.8.0.86-1

ENV NV_LIBCUSPARSE_VERSION=11.7.5.86-1

ENV NV_LIBCUBLAS_PACKAGE_NAME=libcublas-11-8

ENV NV_LIBCUBLAS_VERSION=11.11.3.6-1

ENV NV_LIBCUBLAS_PACKAGE=libcublas-11-8=11.11.3.6-1

ENV NV_LIBNCCL_PACKAGE_NAME=libnccl2

ENV NV_LIBNCCL_PACKAGE_VERSION=2.16.2-1

ENV NCCL_VERSION=2.16.2-1

ENV NV_LIBNCCL_PACKAGE=libnccl2=2.16.2-1+cuda11.8

ARG TARGETARCH

LABEL maintainer=NVIDIA CORPORATION <cudatools@nvidia.com>

RUN |1 TARGETARCH=amd64 /bin/sh -c apt-get update && apt-get install -y --no-install-recommends cuda-libraries-11-8=${NV_CUDA_LIB_VERSION} ${NV_LIBNPP_PACKAGE} cuda-nvtx-11-8=${NV_NVTX_VERSION} libcusparse-11-8=${NV_LIBCUSPARSE_VERSION} ${NV_LIBCUBLAS_PACKAGE} ${NV_LIBNCCL_PACKAGE} && rm -rf /var/lib/apt/lists/* # buildkit

RUN |1 TARGETARCH=amd64 /bin/sh -c apt-mark hold ${NV_LIBCUBLAS_PACKAGE_NAME} ${NV_LIBNCCL_PACKAGE_NAME} # buildkit

COPY entrypoint.d/ /opt/nvidia/entrypoint.d/ # buildkit

COPY nvidia_entrypoint.sh /opt/nvidia/ # buildkit

ENV NVIDIA_PRODUCT_NAME=CUDA

ENTRYPOINT ["/opt/nvidia/nvidia_entrypoint.sh"]

ENV NV_CUDA_LIB_VERSION=11.8.0-1

ENV NV_CUDA_CUDART_DEV_VERSION=11.8.89-1

ENV NV_NVML_DEV_VERSION=11.8.86-1

ENV NV_LIBCUSPARSE_DEV_VERSION=11.7.5.86-1

ENV NV_LIBNPP_DEV_VERSION=11.8.0.86-1

ENV NV_LIBNPP_DEV_PACKAGE=libnpp-dev-11-8=11.8.0.86-1

ENV NV_LIBCUBLAS_DEV_VERSION=11.11.3.6-1

ENV NV_LIBCUBLAS_DEV_PACKAGE_NAME=libcublas-dev-11-8

ENV NV_LIBCUBLAS_DEV_PACKAGE=libcublas-dev-11-8=11.11.3.6-1

ENV NV_CUDA_NSIGHT_COMPUTE_VERSION=11.8.0-1

ENV NV_CUDA_NSIGHT_COMPUTE_DEV_PACKAGE=cuda-nsight-compute-11-8=11.8.0-1

ENV NV_NVPROF_VERSION=11.8.87-1

ENV NV_NVPROF_DEV_PACKAGE=cuda-nvprof-11-8=11.8.87-1

ENV NV_LIBNCCL_DEV_PACKAGE_NAME=libnccl-dev

ENV NV_LIBNCCL_DEV_PACKAGE_VERSION=2.16.2-1

ENV NCCL_VERSION=2.16.2-1

ENV NV_LIBNCCL_DEV_PACKAGE=libnccl-dev=2.16.2-1+cuda11.8

ARG TARGETARCH

LABEL maintainer=NVIDIA CORPORATION <cudatools@nvidia.com>

RUN |1 TARGETARCH=amd64 /bin/sh -c apt-get update && apt-get install -y --no-install-recommends libtinfo5 libncursesw5 cuda-cudart-dev-11-8=${NV_CUDA_CUDART_DEV_VERSION} cuda-command-line-tools-11-8=${NV_CUDA_LIB_VERSION} cuda-minimal-build-11-8=${NV_CUDA_LIB_VERSION} cuda-libraries-dev-11-8=${NV_CUDA_LIB_VERSION} cuda-nvml-dev-11-8=${NV_NVML_DEV_VERSION} ${NV_NVPROF_DEV_PACKAGE} ${NV_LIBNPP_DEV_PACKAGE} libcusparse-dev-11-8=${NV_LIBCUSPARSE_DEV_VERSION} ${NV_LIBCUBLAS_DEV_PACKAGE} ${NV_LIBNCCL_DEV_PACKAGE} ${NV_CUDA_NSIGHT_COMPUTE_DEV_PACKAGE} && rm -rf /var/lib/apt/lists/* # buildkit

RUN |1 TARGETARCH=amd64 /bin/sh -c apt-mark hold ${NV_LIBCUBLAS_DEV_PACKAGE_NAME} ${NV_LIBNCCL_DEV_PACKAGE_NAME} # buildkit

ENV LIBRARY_PATH=/usr/local/cuda/lib64/stubs

STOPSIGNAL SIGRTMIN+3

ENV DEBIAN_FRONTEND=noninteractive

ENV container=docker

ARG MUNGEUSER=983

ARG MUNGEGROUP=983

ARG SLURMUSER=120

ARG SLURMGROUP=120

RUN |4 MUNGEUSER=983 MUNGEGROUP=983 SLURMUSER=120 SLURMGROUP=120 /bin/sh -c groupadd -f -g $SLURMGROUP slurm && useradd -m -c "SLURM workload manager" -d /var/lib/slurm -u $SLURMUSER -g slurm -s /bin/bash slurm # buildkit

RUN |4 MUNGEUSER=983 MUNGEGROUP=983 SLURMUSER=120 SLURMGROUP=120 /bin/sh -c apt-get update && apt-get install -y --no-install-recommends zip unzip python python3 python3-dev python3-setuptools python3-pip libtiff5 netbase ed curl iputils-ping sudo net-tools openssh-server jq slurmd nodejs systemd && rm -rf /var/lib/apt/lists/* # buildkit

RUN |4 MUNGEUSER=983 MUNGEGROUP=983 SLURMUSER=120 SLURMGROUP=120 /bin/sh -c curl -fsSL https://pgp.mongodb.com/server-6.0.asc | gpg -o /usr/share/keyrings/mongodb-server-6.0.gpg --dearmor && echo "deb [ arch=amd64,arm64 signed-by=/usr/share/keyrings/mongodb-server-6.0.gpg ] https://repo.mongodb.org/apt/ubuntu focal/mongodb-org/6.0 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-6.0.list # buildkit

RUN |4 MUNGEUSER=983 MUNGEGROUP=983 SLURMUSER=120 SLURMGROUP=120 /bin/sh -c groupmod -o -g $MUNGEGROUP munge && usermod -c "MUNGE Uid 'N' Gid Emporium" -d /var/lib/munge -u $MUNGEUSER -g munge -s /sbin/nologin munge && chown -R munge:$MUNGEGROUP /etc/munge # buildkit

ENV CRYOSPARC_ROOT_DIR=/app

RUN |4 MUNGEUSER=983 MUNGEGROUP=983 SLURMUSER=120 SLURMGROUP=120 /bin/sh -c mkdir -p ${CRYOSPARC_ROOT_DIR} # buildkit

WORKDIR /app

ARG CRYOSPARC_VERSION=4.2.1

ENV CRYOSPARC_VERSION=4.2.1

ENV CRYOSPARC_MASTER_DIR=/app/cryosparc_master

COPY cryosparc_master /app/cryosparc_master # buildkit

RUN |5 MUNGEUSER=983 MUNGEGROUP=983 SLURMUSER=120 SLURMGROUP=120 CRYOSPARC_VERSION=4.2.1 /bin/sh -c cd ${CRYOSPARC_MASTER_DIR} && bash ./install.sh --license "$(cat /run/secrets/cryosparc_license_id)" --yes --allowroot && sed -i 's/^export CRYOSPARC_LICENSE_ID=.*$/export CRYOSPARC_LICENSE_ID=TBD/g' ${CRYOSPARC_MASTER_DIR}/config.sh # buildkit

RUN |5 MUNGEUSER=983 MUNGEGROUP=983 SLURMUSER=120 SLURMGROUP=120 CRYOSPARC_VERSION=4.2.1 /bin/sh -c sed -i 's: disk_has_space=.*: disk_has_space="true":g' ${CRYOSPARC_MASTER_DIR}/bin/cryosparcm # buildkit

ENV CRYOSPARC_WORKER_DIR=/app/cryosparc_worker

COPY cryosparc_worker /app/cryosparc_worker # buildkit

RUN |5 MUNGEUSER=983 MUNGEGROUP=983 SLURMUSER=120 SLURMGROUP=120 CRYOSPARC_VERSION=4.2.1 /bin/sh -c cd ${CRYOSPARC_WORKER_DIR} && bash ./install.sh --license "$(cat /run/secrets/cryosparc_license_id)" --yes --cudapath /usr/local/cuda && sed -i 's/^export CRYOSPARC_LICENSE_ID=.*$/export CRYOSPARC_LICENSE_ID=TBD/g' ${CRYOSPARC_WORKER_DIR}/config.sh # buildkit

ARG MOTIONCOR2_VERSION=1.6.4

ENV MOTIONCOR2_VERSION=1.6.4

RUN |6 MUNGEUSER=983 MUNGEGROUP=983 SLURMUSER=120 SLURMGROUP=120 CRYOSPARC_VERSION=4.2.1 MOTIONCOR2_VERSION=1.6.4 /bin/sh -c cd /usr/local/bin && curl -L 'https://drive.google.com/uc?export=download&id=1hskY_AbXVgrl_BUIjWokDNLZK0c1FLxF' > MotionCor2_${MOTIONCOR2_VERSION}.zip && unzip MotionCor2_${MOTIONCOR2_VERSION}.zip && rm -f MotionCor2_${MOTIONCOR2_VERSION}.zip && ln -sf MotionCor2_${MOTIONCOR2_VERSION}-Cuda100 MotionCor2 # buildkit

RUN |6 MUNGEUSER=983 MUNGEGROUP=983 SLURMUSER=120 SLURMGROUP=120 CRYOSPARC_VERSION=4.2.1 MOTIONCOR2_VERSION=1.6.4 /bin/sh -c systemctl enable munge.service && systemctl enable slurmd.service # buildkit

RUN |6 MUNGEUSER=983 MUNGEGROUP=983 SLURMUSER=120 SLURMGROUP=120 CRYOSPARC_VERSION=4.2.1 MOTIONCOR2_VERSION=1.6.4 /bin/sh -c systemctl set-default multi-user.target # buildkit

CMD ["/usr/lib/systemd/systemd" "--system"]

Labels

Key	Value
maintainer	NVIDIA CORPORATION <cudatools@nvidia.com>
org.opencontainers.image.ref.name	ubuntu
org.opencontainers.image.version	20.04

Details

Container

2025-04-22 14:45:14 +02:00

0

OCI / Docker

linux/amd64

8.2 GiB

Versions (2) View all

latest 2025-04-22

2302-20231220tt160713 2025-04-22