未找到奇点容器-B
我更改了我正在运行以下代码：
#!/bin/sh
#
#SBATCH --job-name psy-bkeeser_fmriprep
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --output /projects/core-psy/logs/nako/stephan/slurm-%j.log
#SBATCH --error /projects/core-psy/logs/nako/stephan/slurm-%j.err
singularity run --pwd /tmp3 \
--home /projects/core-psy/tmp3:/home/fmriprep \
--cleanenv \
-B /projects/core-psy/data/nako/swunderl/pa/BIDS_DATA/:/input \
-B /projects/core-psy/data/nako/bkeeser/test:/output \
-B /projects/core-psy/data/nako/bkeeser/freesurfer:/freesurfer \
-B /projects/core-psy/tmp:/opt/templateflow \
/projects/core-psy/images/nipreps-fmriprep-21.0.1.simg /input /output participant \
--fs-license-file /freesurfer/license.txt \
--skip-bids-validation \
--fs-no-reconall \
这给了我一个错误：
回溯（最近一次调用最后一次）： 文件“/opt/conda/lib/python3.8/pathlib.py”，第 1288 行，位于 mkdir 中 self._accessor.mkdir（自我，模式） FileNotFoundError：[Errno 2]没有这样的文件或目录：'/tmp/work/20220312-010716_89e666a8-3458-4f82-9ff2-b13ef397a3b4/bids_db' 在处理上述异常的过程中，又出现了一个异常： 回溯（最近一次调用最后一次）： 文件“/opt/conda/bin/fmriprep”，第 8 行，在中 系统退出（主（）） 文件“/opt/conda/lib/python3.8/site-packages/fmriprep/cli/run.py”，第 38 行， 在主要部分 解析参数（） 文件“/opt/conda/lib/python3.8/site-packages/fmriprep/cli/parser.py”，行 679，在 parse_args 中 config.from_dict(vars(opts)) 文件“/opt/conda/lib/python3.8/site-packages/fmriprep/config.py”，第 666 行， 在 from_dict 中 执行.加载（设置） 文件“/opt/conda/lib/python3.8/site-packages/fmriprep/config.py”，第 238 行， 负载中 cls.init() 文件“/opt/conda/lib/python3.8/site-packages/fmriprep/config.py”，第 465 行， 在初始化中 _db_path.mkdir(exist_ok=True, 父母=True) 文件“/opt/conda/lib/python3.8/pathlib.py”，第 1292 行，位于 mkdir 中 self.parent.mkdir（父母= True，exist_ok = True） 文件“/opt/conda/lib/python3.8/pathlib.py”，第 1288 行，位于 mkdir 中 self._accessor.mkdir（自我，模式） PermissionError：[Errno 13]权限被拒绝：'/tmp/work/20220312-010716_89e666a8-3458-4f82-9ff2-b13ef397a3b4'
……tmp文件夹似乎有问题？
I changed the I am running the following code:
#!/bin/sh
#
#SBATCH --job-name psy-bkeeser_fmriprep
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=32GB
#SBATCH --output /projects/core-psy/logs/nako/stephan/slurm-%j.log
#SBATCH --error /projects/core-psy/logs/nako/stephan/slurm-%j.err
singularity run --pwd /tmp3 \
--home /projects/core-psy/tmp3:/home/fmriprep \
--cleanenv \
-B /projects/core-psy/data/nako/swunderl/pa/BIDS_DATA/:/input \
-B /projects/core-psy/data/nako/bkeeser/test:/output \
-B /projects/core-psy/data/nako/bkeeser/freesurfer:/freesurfer \
-B /projects/core-psy/tmp:/opt/templateflow \
/projects/core-psy/images/nipreps-fmriprep-21.0.1.simg /input /output participant \
--fs-license-file /freesurfer/license.txt \
--skip-bids-validation \
--fs-no-reconall \
This gives me an error:
Traceback (most recent call last): File "/opt/conda/lib/python3.8/pathlib.py", line 1288, in mkdir self._accessor.mkdir(self, mode) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/work/20220312-010716_89e666a8-3458-4f82-9ff2-b13ef397a3b4/bids_db' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/opt/conda/bin/fmriprep", line 8, in <module> sys.exit(main()) File "/opt/conda/lib/python3.8/site-packages/fmriprep/cli/run.py", line 38,in main
parse_args()
File "/opt/conda/lib/python3.8/site-packages/fmriprep/cli/parser.py", line
679, in parse_args
config.from_dict(vars(opts))
File "/opt/conda/lib/python3.8/site-packages/fmriprep/config.py", line 666,
in from_dict
execution.load(settings)
File "/opt/conda/lib/python3.8/site-packages/fmriprep/config.py", line 238,
in load
cls.init()
File "/opt/conda/lib/python3.8/site-packages/fmriprep/config.py", line 465,
in init
_db_path.mkdir(exist_ok=True, parents=True)
File "/opt/conda/lib/python3.8/pathlib.py", line 1292, in mkdir
self.parent.mkdir(parents=True, exist_ok=True)
File "/opt/conda/lib/python3.8/pathlib.py", line 1288, in mkdir
self._accessor.mkdir(self, mode)
PermissionError: [Errno 13] Permission denied: '/tmp/work/20220312-010716_89e666a8-3458-4f82-9ff2-b13ef397a3b4'
sth seems to be wrong with the tmp folder?
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将命令拆分为多行时，不能使用这样的注释。 shell 将
-B解释为另一个命令，而不是作为singularity的参数。一种解决方案是完全删除注释行。您可以将它们放在命令上方或下方，但不能放在命令内部。
You cannot use comments like this when splitting a command across multiple lines. The shell is interpreting
-Bas a another command, not as an argument tosingularity.One solution is to remove the commented lines altogher. You can put them above or below the command, but not inside the command.
--pwd /tmp3 参数指向的目录在运行命令的上下文中似乎不存在。如果删除它，您可能会成功绑定其他目录。
如果这不能解决错误，您可能需要尝试从 --home 切换到将可写文件夹安装到 /opt/templateflow 并按照此处的建议在运行命令中设置 TEMPLATEFLOW_HOME 变量：https://www.nipreps.org/apps/singularity/#templateflow-and-singularity
The --pwd /tmp3 argument points to a directory that does not seem to exist from the context of your run command. If you remove this, you may have success binding the other directories.
If this does not resolve the error, you might want to try switching from --home to mounting a writeable folder to /opt/templateflow and setting the TEMPLATEFLOW_HOME variable in your run command as suggested here: https://www.nipreps.org/apps/singularity/#templateflow-and-singularity