创建R应用报错 #1078
Comments
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在 auth #!/usr/bin/env bash
#echo "ABC" >> ~/b.txt
#echo $@ >> ~/b.txt
#echo ${RSTUDIO_PASSWORD} >> ~/b.txt
#echo ${PASSWORD} >> ~/b.txt
# Confirm username is supplied
#if [[ $# -ne 1 ]]; then
# echo "Usage: auth USERNAME"
# exit 1
#fi
USERNAME="${1}"
#echo "DD" >> ~/b.txt
# Confirm password environment variable exists
if [[ -z ${RSTUDIO_PASSWORD} ]]; then
echo "The environment variable RSTUDIO_PASSWORD is not set"
exit 1
fi
#echo "EE" >> ~/b.txt
# Read in the password from user
read -s -p "Password: " PASSWORD
echo ""
if [[ ${USERNAME} == ${USER} && ${PASSWORD} == ${RSTUDIO_PASSWORD} ]]; then
echo "Successful authentication"
exit 0
else
echo "Invalid authentication"
exit 1
fi
rsession.log 通过Singularity 进入镜像正常 [root@hpc-node1 rstudio-server]# singularity shell rstudio.sif
Singularity> ls /usr/lib/rstudio-server/bin/
crash-handler-proxy crashpad_handler crashpad_http_upload postback quarto r-ldpath rpostback rserver rserver-pam rserver-url rsession rstudio-server
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任何人有相关进展吗？ |
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请问问题解决了吗 |
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没有 |
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重新使用以下环境编译以后还是不行，报错404。 连接的url好像有问题？日志中没有报错，看上去正常。 |
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通过IP:port的方式能正常使用，通过已创建应用中的连接链接类使用这种 下面是rstudio.yml的配置文件。 # 这个应用的ID
id: rstudio
# 这个应用的名字
name: RStudio
# 指定应用类型为web
type: web
# Web应用的配置
web:
# 指定反向代理类型
proxyType: relative
# 准备脚本
beforeScript: |
export PORT=$(get_port)
export PASSWORD=$(get_password 12)
export SLURM_COMPUTE_NODE_HOSTNAME=$(hostname)
export APPURI="${PROXY_BASE_PATH}/${SLURM_COMPUTE_NODE_HOSTNAME}/${PORT}/"
export USER=${USER}
export SINGULARITY_VERSION="singularity/4.2.0"
# 运行任务的脚本。可以使用准备脚本定义的变量
script: |
setup_env () {
# Additional environment which could be moved into a module
export RSTUDIO_PASSWORD=${PASSWORD}
# Change these to suit
export RSTUDIO_SERVER_IMAGE="/data/software/rstudio-server/rstudio.sif"
# 容器中rstudio的路径
export RSTUDIO_HOME=/usr/lib/rstudio-server
export RSTUDIO_BIN_PATH=${RSTUDIO_HOME}/bin
export RSTUDIO_RSERVER=${RSTUDIO_BIN_PATH}/rserver
export RSTUDIO_RSESSION=${RSTUDIO_BIN_PATH}/rsession
export RSTUDIO_AUTH="/data/software/rstudio-server/auth"
export RSESSION_WRAPPER_FILE="${PWD}/rsession.sh"
export DB_CONF_FILE="${PWD}/database.conf"
export WHICHR=/data/software/R/${r_version}/bin/R
}
setup_env
module switch ${SINGULARITY_VERSION}
(
umask 077
sed 's/^ \{2\}//' > "${RSESSION_WRAPPER_FILE}" << EOL
#!/usr/bin/env bash
# Log all output from this script
export RSESSION_LOG_FILE="${PWD}/rsession.log"
exec &>>"\${RSESSION_LOG_FILE}"
# Launch the original command
echo "Launching rsession..."
set -x
exec ${RSTUDIO_RSESSION} --r-libs-user "${R_LIBS_USER}" "\${@}"
EOL
)
chmod 700 "${RSESSION_WRAPPER_FILE}"
cd "${HOME}"
export TMPDIR="$(mktemp -d)"
mkdir -p "$TMPDIR/rstudio-server"
python -c 'from uuid import uuid4; print(uuid4())' > "$TMPDIR/rstudio-server/secure-cookie-key"
chmod 0600 "$TMPDIR/rstudio-server/secure-cookie-key"
(
umask 177
cat > "${DB_CONF_FILE}" << EOL
provider=sqlite
directory=${HOME}/.local/share/rstudio/database
EOL
)
set -x
# Launch the RStudio Server
echo "Starting up rserver..."
# RStudio Server 1.4.1103之前版本不需要--database-config-file，之后版本需要增加此配置
singularity run -B "/tmp:/tmp","/data:/data" "$RSTUDIO_SERVER_IMAGE" ${RSTUDIO_RSERVER} \
--www-port "${PORT}" \
--auth-none 1 \
--auth-pam-helper-path "${RSTUDIO_AUTH}" \
--auth-encrypt-password 0 \
--rsession-path "${RSESSION_WRAPPER_FILE}" \
--server-data-dir "${TMPDIR}" \
--server-user ${USER} \
--secure-cookie-key-file "${TMPDIR}/rstudio-server/secure-cookie-key" \
--database-config-file "${DB_CONF_FILE}" \
--rsession-which-r ${WHICHR}
echo 'Singularity as exited...'
# 如何连接应用
connect:
method: POST
path: /auth-do-sign-in
formData:
password: "{{ PASSWORD }}"
username: "{{ USER }}"
appUri: "{{ APPURI }}"
# 配置HTML表单
attributes:
- type: select
name: r_version
label: 请选择R版本
select:
- value: R-4.2.3
label: 4.2.3
- type: text
name: sbatchOptions
label: 其他sbatch参数
required: false
placeholder: "比如：--gpus gres:2 --time 10" |
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按文档https://icode.pku.edu.cn/SCOW/docs/deploy/config/portal/apps/apps/rstudio 配置
RStudio Server 1.4.1103及之后版本源码方式的RStudio Server后，创建R应用报错下面是输出日志slurm-13.out
before.sh
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