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nrdg / cloudknot

A python library to run your existing code on AWS Batch
https://nrdg.github.io/cloudknot/
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BuildError 2.0 #266

Closed 36000 closed 1 year ago

36000 commented 3 years ago

When trying to run pyafq with cloudknot I get this error:

BuildError: The command '/bin/sh -c pip install --no-cache-dir -r /tmp/requirements.txt     && pip install --no-cache-dir git+https://github.com/bloomdt-uw/pyAFQ.git@enh-callosum-rois' returned a non-zero code: 1

I looked at requirements.txt, and tried to pip install it in a temporary docker container based on python:3.8 . It gets this error:

ERROR: Cannot install boto3==1.16.30 and s3fs because these package versions have conflicting dependencies.

The contents of requirements.txt are:

cloudpickle==1.6.0
s3fs==0.5.1
numpy==1.19.4
boto3==1.16.30

My guess is the latest boto3 and s3fs are conflicting, and that's causing the problem. But I could be wrong. Also, if I am right, then I am not sure why the error just started happening today, because I think boto3 would have to go all the way back to 1.14 to start playing nice with s3fs.

The imports in the function I am passing into the knot look like this:

    import logging
    import s3fs

    from AFQ.data import fetch_hcp
    import AFQ.api as api
    import AFQ.mask as afm
    import numpy as np
    import os.path as op
arokem commented 3 years ago

I realize that you mentioned that you were building off of a Python 3.8 image. Is there any chance that this has to do with the recent release of Python 3.9? I ran into some gnarly dependency issues because of that last week (not on CK, just using conda locally).

36000 commented 3 years ago

It's possible. Numpy also recently upgraded to not support 3.6 anymore. I have tried using 3.7, 3.8, and 3.9 as base images, all with the same result.

36000 commented 3 years ago

Here is the full error:

---------------------------------------------------------------------------
BuildError                                Traceback (most recent call last)
<ipython-input-13-6130c613b3e8> in <module>
      8     volume_size=64,
      9     max_vcpus=256,
---> 10     memory=128000)

~/cloudknot/cloudknot/cloudknot.py in __init__(self, name, pars, pars_policies, docker_image, base_image, func, image_script_path, image_work_dir, image_github_installs, username, repo_name, image_tags, job_definition_name, job_def_vcpus, memory, retries, compute_environment_name, instance_types, min_vcpus, max_vcpus, desired_vcpus, volume_size, image_id, ec2_key_pair, bid_percentage, job_queue_name, priority, aws_resource_tags)
   1484 
   1485             self._docker_image, self._docker_repo, repo_cleanup = futures[
-> 1486                 "docker-image"
   1487             ].result()
   1488 

~/miniconda3/envs/afq/lib/python3.7/concurrent/futures/_base.py in result(self, timeout)
    433                 raise CancelledError()
    434             elif self._state == FINISHED:
--> 435                 return self.__get_result()
    436             else:
    437                 raise TimeoutError()

~/miniconda3/envs/afq/lib/python3.7/concurrent/futures/_base.py in __get_result(self)
    382     def __get_result(self):
    383         if self._exception:
--> 384             raise self._exception
    385         else:
    386             return self._result

~/miniconda3/envs/afq/lib/python3.7/concurrent/futures/thread.py in run(self)
     55 
     56         try:
---> 57             result = self.fn(*self.args, **self.kwargs)
     58         except BaseException as exc:
     59             self.future.set_exception(exc)

~/cloudknot/cloudknot/cloudknot.py in set_dockerimage(knot_name, input_docker_image, func_, script_path, work_dir, base_image_, github_installs, username_, tags, repo_name_)
   1411 
   1412                 if not di.images:
-> 1413                     di.build(tags=tags)
   1414                     mod_logger.info(
   1415                         "knot {name:s} built docker image {i!s}"

~/cloudknot/cloudknot/dockerimage.py in build(self, tags, image_name)
    640                 path=self.build_path,
    641                 dockerfile=self.docker_path,
--> 642                 tag=im["name"] + ":" + im["tag"],
    643             )
    644 

~/miniconda3/envs/afq/lib/python3.7/site-packages/docker/models/images.py in build(self, **kwargs)
    285         for chunk in internal_stream:
    286             if 'error' in chunk:
--> 287                 raise BuildError(chunk['error'], result_stream)
    288             if 'stream' in chunk:
    289                 match = re.search(

BuildError: The command '/bin/sh -c pip install --no-cache-dir -r /tmp/requirements.txt     && pip install --no-cache-dir git+https://github.com/bloomdt-uw/pyAFQ.git@enh-callosum-rois' returned a non-zero code: 1
36000 commented 3 years ago

Here is the docker trace:

Sending build context to Docker daemon  10.24kB
Step 1/8 : FROM python:3.8
 ---> ffb0799a2ad9
Step 2/8 : COPY requirements.txt /tmp/
 ---> 6e87d1f39e7c
Step 3/8 : RUN pip install --no-cache-dir -r /tmp/requirements.txt     && pip install --no-cache-dir git+https://github.com/bloomdt-uw/pyAFQ.git@enh-callosum-rois
 ---> Running in 301bfe3958da
Collecting boto3==1.16.30
  Downloading boto3-1.16.30-py2.py3-none-any.whl (129 kB)
Collecting cloudpickle==1.6.0
  Downloading cloudpickle-1.6.0-py3-none-any.whl (23 kB)
Collecting numpy==1.19.4
  Downloading numpy-1.19.4-cp38-cp38-manylinux2010_x86_64.whl (14.5 MB)
Collecting s3fs==0.5.1
  Downloading s3fs-0.5.1-py3-none-any.whl (21 kB)
Collecting aiobotocore>=1.0.1
  Downloading aiobotocore-1.1.2-py3-none-any.whl (45 kB)
  Downloading aiobotocore-1.1.1-py3-none-any.whl (45 kB)
  Downloading aiobotocore-1.1.0-py3-none-any.whl (43 kB)
  Downloading aiobotocore-1.0.7-py3-none-any.whl (42 kB)
  Downloading aiobotocore-1.0.6-py3-none-any.whl (42 kB)
  Downloading aiobotocore-1.0.5-py3-none-any.whl (42 kB)
  Downloading aiobotocore-1.0.4-py3-none-any.whl (41 kB)
  Downloading aiobotocore-1.0.3-py3-none-any.whl (40 kB)
  Downloading aiobotocore-1.0.2-py3-none-any.whl (40 kB)
  Downloading aiobotocore-1.0.1-py3-none-any.whl (40 kB)
INFO: pip is looking at multiple versions of <Python from Requires-Python> to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of s3fs to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of numpy to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of cloudpickle to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of boto3 to determine which version is compatible with other requirements. This could take a while.
ERROR: Cannot install -r /tmp/requirements.txt (line 3) and s3fs because these package versions have conflicting dependencies.

The conflict is caused by:
    boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30
    aiobotocore 1.1.2 depends on botocore<1.17.45 and >=1.17.44
    boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30
    aiobotocore 1.1.1 depends on botocore<1.17.45 and >=1.17.44
    boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30
    aiobotocore 1.1.0 depends on botocore<1.17.45 and >=1.17.44
    boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30
    aiobotocore 1.0.7 depends on botocore<1.15.33 and >=1.15.32
    boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30
    aiobotocore 1.0.6 depends on botocore<1.15.33 and >=1.15.32
    boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30
    aiobotocore 1.0.5 depends on botocore<1.15.33 and >=1.15.32
    boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30
    aiobotocore 1.0.4 depends on botocore<1.15.33 and >=1.15.32
    boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30
    aiobotocore 1.0.3 depends on botocore<1.15.33 and >=1.15.32
    boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30
    aiobotocore 1.0.2 depends on botocore<1.15.33 and >=1.15.32
    boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30
    aiobotocore 1.0.1 depends on botocore<1.15.33 and >=1.15.32

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies
The command '/bin/sh -c pip install --no-cache-dir -r /tmp/requirements.txt     && pip install --no-cache-dir git+https://github.com/bloomdt-uw/pyAFQ.git@enh-callosum-rois' returned a non-zero code: 1
arokem commented 3 years ago

Did you manage to sort this one out with GitHub installs?

On Mon, Dec 7, 2020 at 12:55 PM John Kruper notifications@github.com wrote:

Here is the docker trace:

Sending build context to Docker daemon 10.24kB Step 1/8 : FROM python:3.8 ---> ffb0799a2ad9 Step 2/8 : COPY requirements.txt /tmp/ ---> 6e87d1f39e7c Step 3/8 : RUN pip install --no-cache-dir -r /tmp/requirements.txt && pip install --no-cache-dir git+https://github.com/bloomdt-uw/pyAFQ.git@enh-callosum-rois ---> Running in 301bfe3958da Collecting boto3==1.16.30 Downloading boto3-1.16.30-py2.py3-none-any.whl (129 kB) Collecting cloudpickle==1.6.0 Downloading cloudpickle-1.6.0-py3-none-any.whl (23 kB) Collecting numpy==1.19.4 Downloading numpy-1.19.4-cp38-cp38-manylinux2010_x86_64.whl (14.5 MB) Collecting s3fs==0.5.1 Downloading s3fs-0.5.1-py3-none-any.whl (21 kB) Collecting aiobotocore>=1.0.1 Downloading aiobotocore-1.1.2-py3-none-any.whl (45 kB) Downloading aiobotocore-1.1.1-py3-none-any.whl (45 kB) Downloading aiobotocore-1.1.0-py3-none-any.whl (43 kB) Downloading aiobotocore-1.0.7-py3-none-any.whl (42 kB) Downloading aiobotocore-1.0.6-py3-none-any.whl (42 kB) Downloading aiobotocore-1.0.5-py3-none-any.whl (42 kB) Downloading aiobotocore-1.0.4-py3-none-any.whl (41 kB) Downloading aiobotocore-1.0.3-py3-none-any.whl (40 kB) Downloading aiobotocore-1.0.2-py3-none-any.whl (40 kB) Downloading aiobotocore-1.0.1-py3-none-any.whl (40 kB) INFO: pip is looking at multiple versions of to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of s3fs to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of numpy to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of cloudpickle to determine which version is compatible with other requirements. This could take a while. INFO: pip is looking at multiple versions of boto3 to determine which version is compatible with other requirements. This could take a while. ERROR: Cannot install -r /tmp/requirements.txt (line 3) and s3fs because these package versions have conflicting dependencies.

The conflict is caused by: boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30 aiobotocore 1.1.2 depends on botocore<1.17.45 and >=1.17.44 boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30 aiobotocore 1.1.1 depends on botocore<1.17.45 and >=1.17.44 boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30 aiobotocore 1.1.0 depends on botocore<1.17.45 and >=1.17.44 boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30 aiobotocore 1.0.7 depends on botocore<1.15.33 and >=1.15.32 boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30 aiobotocore 1.0.6 depends on botocore<1.15.33 and >=1.15.32 boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30 aiobotocore 1.0.5 depends on botocore<1.15.33 and >=1.15.32 boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30 aiobotocore 1.0.4 depends on botocore<1.15.33 and >=1.15.32 boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30 aiobotocore 1.0.3 depends on botocore<1.15.33 and >=1.15.32 boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30 aiobotocore 1.0.2 depends on botocore<1.15.33 and >=1.15.32 boto3 1.16.30 depends on botocore<1.20.0 and >=1.19.30 aiobotocore 1.0.1 depends on botocore<1.15.33 and >=1.15.32

To fix this you could try to:

  1. loosen the range of package versions you've specified
  2. remove package versions to allow pip attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies The command '/bin/sh -c pip install --no-cache-dir -r /tmp/requirements.txt && pip install --no-cache-dir git+https://github.com/bloomdt-uw/pyAFQ.git@enh-callosum-rois' returned a non-zero code: 1

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