Docker上的QIIME2 :设备上没有剩余空间(尽管有)

Question

我想用QIIME2在Docker容器上分析数据。请注意，这是我第一次使用Docker。我创建了图像，然后创建了容器，并成功地开始分析一小部分数据。但是，管道的一个步骤会系统性地失败，并显示以下错误消息，抱怨剩余空间：

Plugin error from feature-classifier:
  [Errno 28] No space left on device
Debug info has been saved to /tmp_mount/qiime2-q2cli-err-8hbv6l2e.log

日志文件对我来说并没有更多的信息：

Traceback (most recent call last):
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __call__
    results = action(**arguments)
  File "<decorator-gen-326>", line 2, in classify_sklearn
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
    output_types, provenance)
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_feature_classifier/classifier.py", line 215, in classify_sklearn
    confidence=confidence)
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_feature_classifier/_skl.py", line 45, in predict
    for chunk in _chunks(reads, chunk_size)) for m in c)
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py", line 789, in __call__
    self.retrieve()
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/parallel.py", line 699, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/multiprocessing/pool.py", line 644, in get
    raise self._value
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/multiprocessing/pool.py", line 424, in _handle_tasks
    put(task)
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/pool.py", line 371, in send
    CustomizablePickler(buffer, self._reducers).dump(obj)
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/pool.py", line 240, in __call__
    for dumped_filename in dump(a, filename):
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/numpy_pickle.py", line 484, in dump
    NumpyPickler(f, protocol=protocol).dump(value)
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/pickle.py", line 408, in dump
    self.save(obj)
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/numpy_pickle.py", line 278, in save
    wrapper.write_array(obj, self)
  File "/opt/conda/envs/qiime2-2018.8/lib/python3.5/site-packages/sklearn/externals/joblib/numpy_pickle.py", line 93, in write_array
    pickler.file_handle.write(chunk.tostring('C'))
OSError: [Errno 28] No space left on device

但是还有很大的空间。

我的图像不大(6G)，inode也可以。我想要分析的输入文件很小，它只是一个测试。

我已经找到了一些具有相同问题的其他主题，但我所能尝试的都失败了。

我试过了：

-remove所有已退出的容器和悬空图像

-upgrade Docker

将TMPDIR环境变量-set到a /custom_tmp/我在容器中创建了自己。我尝试了几种方法:在QIIME2环境中，在容器中，但不在QIIME2环境中，在Dockerfile中添加ENV TMPDIR="/cutom_tmp"/，然后重新构建镜像。

将TMPDIR环境变量挂载到主机服务器上创建的/tmp_ -set /，然后将容器挂载为卷

每种情况下都会出现相同的问题。我的猜测是，也许Docker想要写入自己的tmp目录，也许是那些只剩下64M的"tmpfs“之一(参见下面的命令结果)，也许我无法用TMPDIR变量解决这个问题，但我被困在那里了……

非常感谢您的关注和建议。

操作系统:Ubuntu 14.04。

df -h

Filesystem      Size  Used Avail Use% Mounted on
none            197G   57G  131G  31% /
tmpfs            64M     0   64M   0% /dev
tmpfs            32G     0   32G   0% /sys/fs/cgroup
/dev/sda1       939G  772G  120G  87% /tmp_mount
/dev/dm-0       197G   57G  131G  31% /data
shm              64M     0   64M   0% /dev/shm
tmpfs            32G     0   32G   0% /proc/acpi
tmpfs            32G     0   32G   0% /proc/scsi
tmpfs            32G     0   32G   0% /sys/firmware

docker版本

Client:
 Version:           18.06.1-ce
 API version:       1.38
 Go version:        go1.10.3
 Git commit:        e68fc7a
 Built:             Tue Aug 21 17:24:58 2018
 OS/Arch:           linux/amd64
 Experimental:      false

Server:
 Engine:
  Version:          18.06.1-ce
  API version:      1.38 (minimum version 1.12)
  Go version:       go1.10.3
  Git commit:       e68fc7a
  Built:            Tue Aug 21 17:23:24 2018
  OS/Arch:          linux/amd64
  Experimental:     false

环境

CONDA_SHLVL=1
LC_ALL=C.UTF-8
CONDA_EXE=/opt/conda/bin/conda
XDG_CONFIG_HOME=/home/qiime2
LANG=C.UTF-8
CONDA_PREFIX=/opt/conda/envs/qiime2-2018.8
R_LIBS_USER=/opt/conda/envs/qiime2-2018.8/lib/R/library/
TINI_VERSION=v0.16.1
PYTHONNOUSERSITE=/opt/conda/envs/qiime2-2018.8/lib/python*/site-packages/
PWD=/
HOME=/home/qiime2
CONDA_PYTHON_EXE=/opt/conda/bin/python
DEBIAN_FRONTEND=noninteractive
TMPDIR=/tmp_mount/
CONDA_PROMPT_MODIFIER=(qiime2-2018.8)
TERM=xterm
MPLBACKEND=Agg
SHLVL=1
PATH=/opt/conda/envs/qiime2-2018.8/bin:~/miniconda3/bin:/opt/conda/envs/qiime2-2018.8/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
CONDA_DEFAULT_ENV=qiime2-2018.8
_=/usr/bin/env
OLDPWD=/data

Answer 1

我在那里找到了解释: forum.qiime2.org/t/error-no-28-out-of-memory/5758/16。多线程这个任务对内存来说太大了，所以我试着用一个线程，它起作用了…希望有一天它能帮助到某个人。