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Commit 037fceb8 authored by Patrick James Pascual's avatar Patrick James Pascual
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feat: upgraded to version CryoSPARC 4.5.3.

parent 4f4b88b7
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.secret/*
*license_id*
......@@ -6,10 +6,10 @@ ENV DEBIAN_FRONTEND noninteractive
COPY mozilla.pin /etc/apt/preferences.d/mozilla
RUN curl -fsSL https://www.mongodb.org/static/pgp/server-6.0.asc | gpg --dearmor -o /usr/share/keyrings/mongodb-6.0-keyring.gpg \
&& echo "deb [ arch=amd64,arch64 signed-by=/usr/share/keyrings/mongodb-6.0-keyring.gpg ] https://repo.mongodb.org/apt/ubuntu jammy/mongodb-org/6.0 multiverse" | tee /etc/apt/sources.list.d/mongodb-org-6.0.list \
&& apt-get update \
&& apt-get update -y \
&& wget -q https://packages.mozilla.org/apt/repo-signing-key.gpg -O /usr/share/keyrings/packages.mozilla.org.asc \
&& echo "deb [ arch=amd64 signed-by=/usr/share/keyrings/packages.mozilla.org.asc ] https://packages.mozilla.org/apt mozilla main" > /etc/apt/sources.list.d/mozilla.list \
&& apt-get update \
&& apt-get update -y \
&& apt-get install -y --no-install-recommends \
firefox \
zip unzip \
......@@ -76,8 +76,9 @@ RUN ${CRYOSPARC_MASTER_DIR}/deps/anaconda/envs/cryosparc_master_env/bin/python3
ARG MOTIONCOR2_VERSION=1.4.5
ENV MOTIONCOR2_VERSION=${MOTIONCOR2_VERSION}
ENV CUDA_TOOLKIT_VERSION="Cuda100-10-22-2021"
RUN cd /usr/local/bin \
&& curl -L 'https://drive.google.com/uc?export=download&id=1-Ub5lBBmel8U8U0uibORiH6wfxp9I1kn' > MotionCor2_${MOTIONCOR2_VERSION}.zip \
RUN --mount=type=secret,id=motioncor2_license_id \
&& cd /usr/local/bin \
&& curl -L 'https://drive.google.com/uc?export=download&id=$(cat /run/secrets/motioncor2_license_id)' > MotionCor2_${MOTIONCOR2_VERSION}.zip \
&& unzip MotionCor2_${MOTIONCOR2_VERSION}.zip \
&& rm -f MotionCor2_${MOTIONCOR2_VERSION}.zip \
&& ln -sf MotionCor2_${MOTIONCOR2_VERSION}-${CUDA_TOOLKIT_VERSION} MotionCor2
......@@ -88,7 +89,9 @@ RUN cd /usr/local/bin \
ARG TOPAZ_VERSION=0.2.5
ENV TOPAZ_VERSION=${TOPAZ_VERSION}
ENV TOPAZ_CUDA_TOOLKIT_VERSION=12.2.0
RUN /app/cryosparc_worker/deps/anaconda/bin/conda install topaz=${TOPAZ_VERSION} cuda-libraries-dev cuda-nvcc cuda-nvtx cuda-cupti -c nvidia/label/cuda-${TOPAZ_CUDA_TOOLKIT_VERSION} -c tbepler -c pytorch
RUN ${CRYOSPARC_WORKER_DIR}/deps/anaconda/bin/conda install topaz=${TOPAZ_VERSION} cuda-libraries-dev cuda-nvcc cuda-nvtx cuda-cupti -c nvidia/label/cuda-${TOPAZ_CUDA_TOOLKIT_VERSION} -c tbepler -c pytorch
RUN ${CRYOSPARC_WORKER_DIR}/deps/anaconda/bin/conda create -n topaz python=3.6
COPY topaz.sh ${CRYOSPARC_WORKER_DIR}/deps/anaconda/bin/topaz.sh
###
#
......
CRYOSPARC_VERSION ?= 4.4.1
CRYOSPARC_PATCH ?= 240110
CRYOSPARC_RELEASE ?= 3
CRYOSPARC_VERSION ?= 4.5.3
CRYOSPARC_PATCH ?=
CRYOSPARC_RELEASE ?= 0
CONTAINER_RUNTIME ?= docker
IMAGE ?= slaclab/cryosparc-desktop
......@@ -11,22 +11,29 @@ CRYOSPARC_FULL_VERSION = $(CRYOSPARC_VERSION)
else
CRYOSPARC_FULL_VERSION = $(CRYOSPARC_VERSION)+$(CRYOSPARC_PATCH)
endif
ifeq ($(CRYOSPARC_RELEASE),)
TAG = $(subst +,-,$(CRYOSPARC_FULL_VERSION))
else
TAG = $(subst +,-,$(CRYOSPARC_FULL_VERSION)-$(CRYOSPARC_RELEASE))
endif
CRYOSPARC_IMAGE_INSTALL_DIR = /sdf/group/cryoem/sw/images/cryosparc/$(CRYOSPARC_FULL_VERSION)-desktop
echo_tag: tag
echo "TAG=$(TAG)"
license:
mkdir .secret
echo ${CRYOSPARC_LICENSE_ID} > .secret/license_id.txt
mkdir -p etc/.secrets
echo ${CRYOSPARC_LICENSE_ID} > etc/.secrets/cryosparc_license_id.txt
echo ${MOTIONCOR2_LICENSE_ID} > etc/.secrets/motioncor2_license_id.txt
build: tag
COMPOSE_DOCKER_CLI_BUILD=1 DOCKER_BUILDKIT=1 $(CONTAINER_RUNTIME) build \
--build-arg CRYOSPARC_VERSION=${CRYOSPARC_VERSION} \
--build-arg CRYOSPARC_PATCH=${CRYOSPARC_PATCH} \
--platform linux/amd64 \
--progress=plain \
--secret id=cryosparc_license_id,src=.secret/license_id.txt \
--secret id=cryosparc_license_id,src=etc/.secrets/cryosparc_license_id.txt \
--secret id=motioncor2_license_id,src=etc/.secrets/motioncor2_license_id.txt \
. -f Dockerfile.desktop \
-t $(IMAGE):${TAG}
......
[Desktop Entry]
Type=Application
Exec=sh ./cryosparc_launcher.sh
Exec=bash cryosparc_launcher.sh
Hidden=false
X-GNOME-Autostart-enabled=true
Name=CryoSPARC Web App
......@@ -54,12 +54,16 @@ THIS_USER=$(whoami)
THIS_USER_SUFFIX=${USER_SUFFIX:-'slac.stanford.edu'}
ACCOUNT="${THIS_USER}@${THIS_USER_SUFFIX}"
rm -f "${SOCK_FILE}" || true
cryosparcm start database
cryosparcm fixdbport
cryosparcm restart
# ensure that the mongo replset is correct
MONGO_PORT=$(( $CRYOSPARC_BASE_PORT + 1 ))
export CRYOSPARC_MONGO_EXTRA_FLAGS=" --unixSocketPrefix ${LSCRATCH}"
${CRYOSPARC_MASTER_DIR}/bin/cryosparcm start database
${CRYOSPARC_MASTER_DIR}/bin/cryosparcm fixdbport
${CRYOSPARC_MASTER_DIR}/bin/cryosparcm restart
# creat cryosparc local accounts
create_account() {
......@@ -78,6 +82,8 @@ if [ -e "/init.d/accounts" ]; then
fi
# need to restart to get login prompt
cryosparcm start database
cryosparcm fixdbport
cryosparcm restart
echo "Success starting cryosparc master!"
......
topaz.sh 0 → 100644
#!/bin/bash --login
if command -v conda > /dev/null 2>&1; then
conda deactivate > /dev/null 2>&1 || true # ignore any errors
conda deactivate > /dev/null 2>&1 || true # ignore any errors
fi
unset _CE_CONDA
unset CONDA_DEFAULT_ENV
unset CONDA_EXE
unset CONDA_PREFIX
unset CONDA_PROMPT_MODIFIER
unset CONDA_PYTHON_EXE
unset CONDA_SHLVL
unset PYTHONPATH
unset LD_PRELOAD
unset LD_LIBRARY_PATH
set -euo pipefail
set +euo pipefail
export BIN_PATH=/app/cryosparc_worker/deps/anaconda/bin
${BIN_PATH}/activate topaz_env
set -euo pipefail
exec ${BIN_PATH}/topaz $@
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