I used singularity to pull stream container, then I Run singularity shell to spawn a new shell within stream container and interact with it as though it were a small VM. it looks like this:
(base) [chenx@sumner030 software]$ singularity shell stream_latest.sif
Singularity stream_latest.sif:~/li-lab/chenx/software>
then,I run python, and import steam, however, i met the following issue:
Singularity stream_latest.sif:~/li-lab/chenx/software> python
Python 3.7.6 | packaged by conda-forge | (default, Mar 23 2020, 23:03:20)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import stream as st
Traceback (most recent call last):
File "", line 1, in
File "/opt/conda/lib/python3.7/site-packages/stream/init.py", line 1, in
from .core import *
File "/opt/conda/lib/python3.7/site-packages/stream/core.py", line 24, in
import umap
File "/opt/conda/lib/python3.7/site-packages/umap/init.py", line 1, in
from .umap import UMAP
File "/opt/conda/lib/python3.7/site-packages/umap/umap.py", line 53, in
from umap.layouts import (
File "/opt/conda/lib/python3.7/site-packages/umap/layouts.py", line 36, in
"dim": numba.types.int32,
File "/opt/conda/lib/python3.7/site-packages/numba/core/decorators.py", line 191, in wrapper
disp.enable_caching()
File "/opt/conda/lib/python3.7/site-packages/numba/core/dispatcher.py", line 705, in enable_caching
self._cache = FunctionCache(self.py_func)
File "/opt/conda/lib/python3.7/site-packages/numba/core/caching.py", line 613, in init
self._impl = self._impl_class(py_func)
File "/opt/conda/lib/python3.7/site-packages/numba/core/caching.py", line 348, in init
"for file %r" % (qualname, source_path))
RuntimeError: cannot cach function 'rdist': no locator available for file '/opt/conda/lib/python3.7/site-packages/umap/layouts.py'
Could you give me some suggestions? I supposed container should not have some issue, since we have build all the environment stream need.
I used singularity to pull stream container, then I Run singularity shell to spawn a new shell within stream container and interact with it as though it were a small VM. it looks like this: (base) [chenx@sumner030 software]$ singularity shell stream_latest.sif Singularity stream_latest.sif:~/li-lab/chenx/software>
then,I run python, and import steam, however, i met the following issue: Singularity stream_latest.sif:~/li-lab/chenx/software> python Python 3.7.6 | packaged by conda-forge | (default, Mar 23 2020, 23:03:20) [GCC 7.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import stream as st Traceback (most recent call last): File "", line 1, in
File "/opt/conda/lib/python3.7/site-packages/stream/init.py", line 1, in
from .core import *
File "/opt/conda/lib/python3.7/site-packages/stream/core.py", line 24, in
import umap
File "/opt/conda/lib/python3.7/site-packages/umap/init.py", line 1, in
from .umap import UMAP
File "/opt/conda/lib/python3.7/site-packages/umap/umap.py", line 53, in
from umap.layouts import (
File "/opt/conda/lib/python3.7/site-packages/umap/layouts.py", line 36, in
"dim": numba.types.int32,
File "/opt/conda/lib/python3.7/site-packages/numba/core/decorators.py", line 191, in wrapper
disp.enable_caching()
File "/opt/conda/lib/python3.7/site-packages/numba/core/dispatcher.py", line 705, in enable_caching
self._cache = FunctionCache(self.py_func)
File "/opt/conda/lib/python3.7/site-packages/numba/core/caching.py", line 613, in init
self._impl = self._impl_class(py_func)
File "/opt/conda/lib/python3.7/site-packages/numba/core/caching.py", line 348, in init
"for file %r" % (qualname, source_path))
RuntimeError: cannot cach function 'rdist': no locator available for file '/opt/conda/lib/python3.7/site-packages/umap/layouts.py'
Could you give me some suggestions? I supposed container should not have some issue, since we have build all the environment stream need.
Thank you.