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社区首页 >问答首页 >错误:创建用户命名空间失败:禁用用户名称空间-即使在手动禁用singularity.conf中的setuid之后

问错误:创建用户命名空间失败:禁用用户名称空间-即使在手动禁用singularity.conf中的setuid之后
EN

Stack Overflow用户
提问于 2022-09-06 07:54:50
回答 1查看 236关注 0票数 0

我必须运行一个singularity.tif文件，但是它给了我一个错误：

FATAL [U=1092,P=58809] execStarter() while extracting /net/beegfs/scratch/avanbeelen/beta-version-wgs-pipeline/cnv-tools-scripts/clinSV-0.9/clinsv.sif: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled

查看奇点文档之后，可以通过手动更改allow setuid = no文件中的etc/singularity/singularity.conf来解决此错误。但它还是给了我同样的错误。

如果您已经安装了奇异点，则可以通过在安装目录中设置“允许setuid = no in etc/singarity.conf”选项来禁用setuid流。

问题:有人能帮我解决这个错误以便我可以运行singularity.tif?吗？

重要说明：

  • 我正在研究HPC集群，在这里我没有sudo特权。
  • 我使用miniconda来安装包，包括奇异性。
  • 奇点版本= 3.8.6

我运行的代码：

代码语言：javascript
运行
复制
    export SINGULARITY_TMPDIR=/net/beegfs/scratch/avanbeelen/singularity-env
    export SINGULARITY_CACHEDIR=/net/beegfs/scratch/avanbeelen/singularity-env
    singularity -d run /net/beegfs/scratch/avanbeelen/beta-version-wgs-pipeline/cnv-tools-scripts/clinSV-0.9/clinsv.sif \
  -i "$input_path/*.bam" \
  -ref $refdata_path \
  -p $output_path

完全错误：

代码语言：javascript
运行
复制
DEBUG   [U=1092,P=58809]   persistentPreRun()            Singularity version: 3.8.6
DEBUG   [U=1092,P=58809]   persistentPreRun()            Parsing configuration file /net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/etc/singularity/singularity.conf
DEBUG   [U=1092,P=58809]   handleConfDir()               /trinity/home/avanbeelen/.singularity already exists. Not creating.
DEBUG   [U=1092,P=58809]   setValue()                    Updated flag 'tmpdir' value to: /net/beegfs/scratch/avanbeelen/singularity-env
DEBUG   [U=1092,P=58809]   execStarter()                 Saving umask 0002 for propagation into container
VERBOSE [U=1092,P=58809]   execStarter()                 Unprivileged installation: using user namespace
DEBUG   [U=1092,P=58809]   execStarter()                 Checking for encrypted system partition
DEBUG   [U=1092,P=58809]   Init()                        Image format detection
DEBUG   [U=1092,P=58809]   Init()                        Check for sandbox image format
DEBUG   [U=1092,P=58809]   Init()                        sandbox format initializer returned: not a directory image
DEBUG   [U=1092,P=58809]   Init()                        Check for sif image format
DEBUG   [U=1092,P=58809]   Init()                        sif image format detected
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_NODELIST environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_CHECKPOINT_IMAGE_DIR environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOB_NAME environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding XDG_SESSION_ID environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding HOSTNAME environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_TOPOLOGY_ADDR environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURMD_NODENAME environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_PRIO_PROCESS environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_SRUN_COMM_PORT environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding __LMOD_REF_COUNT_MODULEPATH environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding TERM environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SHELL environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LMOD_ROOT environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding HISTSIZE environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_PTY_WIN_ROW environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOB_QOS environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SSH_CLIENT environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_TOPOLOGY_ADDR_PATTERN environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding TMPDIR environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding CONDA_SHLVL environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding CONDA_PROMPT_MODIFIER environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LMOD_PKG environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_CPU_BIND_VERBOSE environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LMOD_VERSION environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SSH_TTY environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_CPU_BIND_LIST environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding USER environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_NNODES environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LS_COLORS environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding CONDA_EXE environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_STEP_NUM_NODES environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SRUN_DEBUG environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOBID environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_NTASKS environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_LAUNCH_NODE_IPADDR environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_STEP_ID environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding _CE_CONDA environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LMOD_PREPEND_BLOCK environment variable
VERBOSE [U=1092,P=58809]   SetContainerEnv()             Not forwarding SINGULARITY_TMPDIR environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding CONDA_PREFIX_1 environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding _ModuleTable001_ environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding MAIL environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_TASKS_PER_NODE environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_STEP_LAUNCHER_PORT environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_WORKING_CLUSTER environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_CPUS_PER_TASK environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOB_ID environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding CONDA_PREFIX environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LMOD_SETTARG_CMD environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding PWD environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_STEPID environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOB_USER environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_SRUN_COMM_HOST environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_CPU_BIND_TYPE environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LANG environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding MODULEPATH environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_UMASK environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_PTY_WIN_COL environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding _ModuleTable_Sz_ environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOB_UID environment variable
VERBOSE [U=1092,P=58809]   SetContainerEnv()             Not forwarding SINGULARITY_CACHEDIR environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_NODEID environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_SUBMIT_DIR environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LMOD_CMD environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_NPROCS environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_TASK_PID environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_DISTRIBUTION environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_CPUS_ON_NODE environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding _CE_M environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding HISTCONTROL environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_PROCID environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOB_NODELIST environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SHLVL environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_PTY_PORT environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_LOCALID environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_CLUSTER_NAME environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOB_CPUS_PER_NODE environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOB_GID environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_SUBMIT_HOST environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_GTIDS environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding BASH_ENV environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOB_PARTITION environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding CONDA_PYTHON_EXE environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LOGNAME environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_STEP_NUM_TASKS environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SSH_CONNECTION environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOB_ACCOUNT environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding MODULESHOME environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_JOB_NUM_NODES environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding CONDA_DEFAULT_ENV environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LMOD_SETTARG_FULL_SUPPORT environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LESSOPEN environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_STEP_TASKS_PER_NODE environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LMOD_FULL_SETTARG_SUPPORT environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_STEP_NODELIST environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding XDG_RUNTIME_DIR environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding DISPLAY environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LMOD_DIR environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding SLURM_CPU_BIND environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding LMOD_COLORIZE environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding BASH_FUNC_module() environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding BASH_FUNC_ml() environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding _ environment variable
DEBUG   [U=1092,P=58809]   SetContainerEnv()             Forwarding USER_PATH environment variable
VERBOSE [U=1092,P=58809]   SetContainerEnv()             Setting HOME=/trinity/home/avanbeelen
VERBOSE [U=1092,P=58809]   SetContainerEnv()             Setting PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
VERBOSE [U=1092,P=58809]   execStarter()                 User namespace requested, convert image /net/beegfs/scratch/avanbeelen/beta-version-wgs-pipeline/cnv-tools-scripts/clinSV-0.9/clinsv.sif to sandbox
INFO    [U=1092,P=58809]   execStarter()                 Converting SIF file to temporary sandbox...
DEBUG   [U=1092,P=58809]   Init()                        Image format detection
DEBUG   [U=1092,P=58809]   Init()                        Check for sandbox image format
DEBUG   [U=1092,P=58809]   Init()                        sandbox format initializer returned: not a directory image
DEBUG   [U=1092,P=58809]   Init()                        Check for sif image format
DEBUG   [U=1092,P=58809]   Init()                        sif image format detected
DEBUG   [U=1092,P=58809]   extract()                     Excluding /dev directory during root filesystem extraction (non root user)
DEBUG   [U=1092,P=58809]   extract()                     Trying unsquashfs options: [-no-xattrs -r]
DEBUG   [U=1092,P=58809]   unsquashfsSandboxCmd()        Calling wrapped unsquashfs: singularity [-q exec --no-home --no-nv --no-rocm -C --no-init --writable -B /net/beegfs/scratch/avanbeelen/singularity-env/rootfs-2015816184:/image -B /net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/unsquashfs:/net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/unsquashfs:ro -B /lib64/libpthread.so.0:/lib64/libpthread.so.0:ro -B /lib64/libm.so.6:/lib64/libm.so.6:ro -B /net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/../lib/libz.so.1:/net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/../lib/libz.so.1:ro -B /net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/../lib/liblzma.so.5:/net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/../lib/liblzma.so.5:ro -B /net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/../lib/liblzo2.so.2:/net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/../lib/liblzo2.so.2:ro -B /net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/../lib/liblz4.so.1:/net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/../lib/liblz4.so.1:ro -B /net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/../lib/libzstd.so.1:/net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/../lib/libzstd.so.1:ro -B /lib64/libc.so.6:/lib64/libc.so.6:ro -B /lib64/ld-linux-x86-64.so.2:/lib64/ld-linux-x86-64.so.2:ro -B /lib64/librt.so.1:/lib64/librt.so.1:ro /net/beegfs/scratch/avanbeelen/singularity-env/rootfs-2015816184/tmp-rootfs-4287831676 /lib64/ld-linux-x86-64.so.2 /net/beegfs/scratch/avanbeelen/miniconda3/envs/wgs_pipeline/bin/unsquashfs -no-xattrs -r -d /image/root /image/archive-3018451646 ^(.{0}[^d]|.{1}[^e]|.{2}[^v]|.{3}[^\x2f]).*$]
FATAL   [U=1092,P=58809]   execStarter()                 while extracting /net/beegfs/scratch/avanbeelen/beta-version-wgs-pipeline/cnv-tools-scripts/clinSV-0.9/clinsv.sif: root filesystem extraction failed: extract command failed: ERROR  : Failed to create user namespace: user namespace disabled
: exit status 1
singularity-container
linux-namespaces
linux
debugging
EN

回答 1

Stack Overflow用户

回答已采纳

发布于 2022-09-10 12:28:50

简短的回答:问你的HPC管理员安装奇点。

奇点依赖于根拥有的二进制文件，因此非特权的conda安装不太可能工作。为了使配置更改达到您想要的效果，必须使用特殊标志编译奇点，主机操作系统必须启用适当的内核设置。两者的细节都在管理设置文档中。

票数 1
EN
页面原文内容由Stack Overflow提供。腾讯云小微IT领域专用引擎提供翻译支持
原文链接：

https://stackoverflow.com/questions/73618551

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