创建R应用报错 - Githubissues

zhengkang2020 commented 7 months ago

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

+ echo 'Starting up rserver...'
Starting up rserver...
+ singularity run -B /tmp:/tmp,/data:/data /data/software/rstudio-server/rstudio.sif /usr/lib/rstudio-server/bin/rserver --www-port 37943 --auth-none 1 --auth-pam-helper-path /data/software/rstudio-server/auth --auth-encrypt-password 0 --rsession-path /data/home/zhengkangzhang/scow/appData/RStudio-20240123-101708/rsession.sh --server-data-dir /tmp/tmp.aai6St5wgV --server-user zhengkangzhang --secure-cookie-key-file /tmp/tmp.aai6St5wgV/rstudio-server/secure-cookie-key --database-config-file /data/home/zhengkangzhang/scow/appData/RStudio-20240123-101708/database.conf --rsession-which-r /data/software/R/R-4.2.3/bin/R

before.sh

export PROXY_BASE_PATH=/api/proxy/hpc01/relative
export r_version=R-4.2.3
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=${USER}
export SINGULARITY_VERSION="singularity/3.9.2"
echo -e "{\"HOST\":\"$HOST\",\"PORT\":$PORT,\"PASSWORD\":\"$PASSWORD\",\"USER\":\"$USER\",\"APPURI\":\"$APPURI\"}" >$SERVER_SESSION_INFO

zhengkang2020 commented 7 months ago

在/data/software/rstudio-server目录新建auth文件后，报错改变

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

Launching rsession...
+ exec /usr/lib/rstudio-server/bin/rsession --r-libs-user '' -u XXXX --session-use-secure-cookies 0 --session-root-path / --session-same-site 0 --session-use-file-storage 1 --launcher-token 57050296 --r-restore-workspace 2 --r-run-rprofile 2
/usr/lib/rstudio-server/bin/rsession: error while loading shared libraries: libgfortran.so.5: cannot open shared object file: No such file or directory
Launching rsession...

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

zhengkang2020 commented 5 months ago

任何人有相关进展吗？

wyzhh commented 2 months ago

请问问题解决了吗

zhengkang2020 commented 2 months ago

没有，暂时放弃了。期待解决！

PKUHPC / SCOW

创建R应用报错 #1078