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Posted to dev@singa.apache.org by GitBox <gi...@apache.org> on 2020/03/19 06:06:07 UTC
[GitHub] [singa] chrishkchris opened a new issue #631: Is there any runtime
problem of onnx in Travis CPU version related to libprotobuf.so.20?
chrishkchris opened a new issue #631: Is there any runtime problem of onnx in Travis CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631
In the log of travis CI CPU version build, it displays the error in test_onnx that cannot import libprotobuf.so.20
```
======================================================================
3966
ERROR: test_onnx (unittest.loader._FailedTest)
3967
----------------------------------------------------------------------
3968
ImportError: Failed to import test module: test_onnx
3969
Traceback (most recent call last):
3970
File "/home/travis/conda-bld-1971.5/singa_1584596418932/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.7/unittest/loader.py", line 436, in _find_test_path
3971
module = self._get_module_from_name(name)
3972
File "/home/travis/conda-bld-1971.5/singa_1584596418932/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name
3973
__import__(name)
3974
File "/home/travis/conda-bld-1971.5/singa_1584596418932/test_tmp/test/python/test_onnx.py", line 24, in <module>
3975
from singa import sonnx
3976
File "/home/travis/conda-bld-1971.5/singa_1584596418932/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.7/site-packages/singa/sonnx.py", line 23, in <module>
3977
import onnx.utils
3978
File "/home/travis/conda-bld-1971.5/singa_1584596418932/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/python3.7/site-packages/onnx/__init__.py", line 8, in <module>
3979
from .onnx_cpp2py_export import ONNX_ML
3980
ImportError: libprotobuf.so.20: cannot open shared object file: No such file or directory
```
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[GitHub] [singa] nudles commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
nudles commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601051020
you can try. I got many troubles when I was trying to upgrade protobuf..
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[GitHub] [singa] chrishkchris edited a comment on issue #631: Is there any
runtime problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris edited a comment on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601523589
After quite a exhaustive search of conda package versions' combinations, I found that this seems to be working for both onnx and singa:
```
host:
- swig 3.0.12
- openblas 0.3.9
- protobuf 3.9.2
- glog 0.3.5
- numpy 1.11.3
- cudnn {{ cudnn }} # ['cudnn' in str(build_str)]
- dnnl {{ dnnl }}
- python {{ python }}
run:
- {{ pin_compatible('glog', max_pin='x.x') }}
- {{ pin_compatible('numpy', max_pin='x.x') }}
- {{ pin_compatible('dnnl', max_pin='x.x') }}
- cudnn {{ cudnn }} # ['cudnn' in str(build_str)]
- python {{ python }}
- libprotobuf 3.9.2
- libopenblas 0.3.9
- pillow
- future
- tqdm
- onnx 1.6.0
- deprecated 1.2.7
```
onnx 1.5 fails one more test case due to numerical error, so I choose onnx 1.6
However, now there are still two errors in the test case I am investigating why:
```
+ python run.py
..............................................................................................................................EE...................................................F............................................................................................................................................................................................................................
======================================================================
ERROR: test_clip (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1896, in test_clip
name='test_clip_example')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 55, in expect
outputs_dict = sonnx.run_node(onnx_node, input_tensors, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1300, in run_node
return cls._run_node(onnx_node, inputs, handle, forward, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1324, in _run_node
outputs = forward(*inputs) if handle is None else forward(
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 499, in clip
return Clip(min, max)(x)[0]
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 245, in __call__
return self._do_forward(*xs)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 295, in _do_forward
ys = self.forward(*xs)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 479, in forward
mask0 = singa.LTFloat(x, self.min)
TypeError: in method 'LTFloat', argument 2 of type 'float'
======================================================================
ERROR: test_clip_default (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1946, in test_clip_default
name='test_clip_default_min')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 55, in expect
outputs_dict = sonnx.run_node(onnx_node, input_tensors, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1300, in run_node
return cls._run_node(onnx_node, inputs, handle, forward, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1324, in _run_node
outputs = forward(*inputs) if handle is None else forward(
TypeError: clip() missing 1 required positional argument: 'max'
======================================================================
FAIL: test_pow (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1851, in test_pow
expect(node, inputs=[x, y], outputs=[z], name='test_pow_example')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 59, in expect
decimal=5)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/numpy/testing/utils.py", line 918, in assert_array_almost_equal
precision=decimal)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/numpy/testing/utils.py", line 739, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 5 decimals
(mismatch 33.33333333333333%)
x: array([ 1., 32., 729.], dtype=float32)
y: array([ 1. , 32. , 729.00006], dtype=float32)
----------------------------------------------------------------------
Ran 400 tests in 1.563s
```
P.S. The above remaining two test case error occurs also in docker container enivornment without conda, so needed to be fixed.
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[GitHub] [singa] chrishkchris edited a comment on issue #631: Is there any
runtime problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris edited a comment on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601537054
In conclusion, I have posted an conda package versions' combinations that works for SINGA and onnx in conda environment, so I close this issue. The change of conda package version is addressed in #624
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[GitHub] [singa] joddiy commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
joddiy commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601078305
Hi, all, please use onnx==1.5.0, we now support op set of version 10 for onnx 1.5.0.
https://github.com/onnx/onnx/blob/master/docs/Versioning.md#released-versions
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[GitHub] [singa] nudles edited a comment on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
nudles edited a comment on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601028209
which version of onnx are you using?
you may need to use the onnx that is compatible with SINGA.
Protobuf has many versions. It is a bit difficult to make other dependencies compatible with some protobuf versions.
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[GitHub] [singa] nudles commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
nudles commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601028209
which version of onnx are you using?
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[GitHub] [singa] chrishkchris commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601091210
so in the dockerfile (everyone is using for development) we may need to set to onnx==1.5.0
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[GitHub] [singa] chrishkchris commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601029801
https://github.com/apache/singa/blob/dev/tool/conda/singa/meta.yaml
currently our conda metal.yaml is using
- libprotobuf 3.6.1
- onnx >=1.3.0
maybe the two are not compatible
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[GitHub] [singa] chrishkchris commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601088702
> Hi, all, please use onnx==1.5.0, we now support op set of version 10 for onnx 1.5.0.
> https://github.com/onnx/onnx/blob/master/docs/Versioning.md#released-versions
got it, I will fix the conda version of onnx to 1.5.0. Thanks a lot
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[GitHub] [singa] chrishkchris commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601040486
OK, from the Travis CI build log the onnx version was onnx-1.6.0-py36he1b5a44_0
seems that protobuf is not specified (then should be the most latest version), so I may try to use later version.
```
dcsysh@panda8:~$ conda search onnx=1.6.0=py36he1b5a44_0 --info
Loading channels: done
onnx 1.6.0 py36he1b5a44_0
-------------------------
file name : onnx-1.6.0-py36he1b5a44_0.tar.bz2
name : onnx
version : 1.6.0
build : py36he1b5a44_0
build number: 0
size : 2.9 MB
license : MIT
subdir : linux-64
url : https://conda.anaconda.org/conda-forge/linux-64/onnx-1.6.0-py36he1b5a44_0.tar.bz2
md5 : 26073522c9dcaa50a8894c762668d7da
timestamp : 2019-09-28 06:49:12 UTC
constraints :
- python_abi * *_cp36m
dependencies:
- libgcc-ng >=7.3.0
- libstdcxx-ng >=7.3.0
- numpy
- protobuf
- python >=3.6,<3.7.0a0
- six
```
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[GitHub] [singa] chrishkchris edited a comment on issue #631: Is there any
runtime problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris edited a comment on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601023271
https://blog.csdn.net/kailvechao1536/article/details/103538689 this blog says that changes to protobuf 3.9 can solve problem for onnx
or this onnx issue
https://github.com/onnx/onnx/issues/2434
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[GitHub] [singa] chrishkchris commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601023271
https://blog.csdn.net/kailvechao1536/article/details/103538689 this blog says that changes to protobuf 3.9 can solve problem for onnx
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[GitHub] [singa] chrishkchris edited a comment on issue #631: Is there any
runtime problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris edited a comment on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601523589
After quite a exhaustive search of conda package versions' combinations, I found that this seems to be working for both onnx and singa:
```
host:
- swig 3.0.12
- openblas 0.3.9
- protobuf 3.9.2
- glog 0.3.5
- numpy 1.11.3
- cudnn {{ cudnn }} # ['cudnn' in str(build_str)]
- dnnl {{ dnnl }}
- python {{ python }}
run:
- {{ pin_compatible('glog', max_pin='x.x') }}
- {{ pin_compatible('numpy', max_pin='x.x') }}
- {{ pin_compatible('dnnl', max_pin='x.x') }}
- cudnn {{ cudnn }} # ['cudnn' in str(build_str)]
- python {{ python }}
- libprotobuf 3.9.2
- libopenblas 0.3.9
- pillow
- future
- tqdm
- onnx 1.6.0
- deprecated 1.2.7
```
onnx 1.5 fails one more test case due to numerical error, so I choose onnx 1.6
However, now there are still two errors in the test case I am investigating why:
```
+ python run.py
..............................................................................................................................EE...................................................F............................................................................................................................................................................................................................
======================================================================
ERROR: test_clip (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1896, in test_clip
name='test_clip_example')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 55, in expect
outputs_dict = sonnx.run_node(onnx_node, input_tensors, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1300, in run_node
return cls._run_node(onnx_node, inputs, handle, forward, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1324, in _run_node
outputs = forward(*inputs) if handle is None else forward(
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 499, in clip
return Clip(min, max)(x)[0]
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 245, in __call__
return self._do_forward(*xs)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 295, in _do_forward
ys = self.forward(*xs)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 479, in forward
mask0 = singa.LTFloat(x, self.min)
TypeError: in method 'LTFloat', argument 2 of type 'float'
======================================================================
ERROR: test_clip_default (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1946, in test_clip_default
name='test_clip_default_min')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 55, in expect
outputs_dict = sonnx.run_node(onnx_node, input_tensors, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1300, in run_node
return cls._run_node(onnx_node, inputs, handle, forward, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1324, in _run_node
outputs = forward(*inputs) if handle is None else forward(
TypeError: clip() missing 1 required positional argument: 'max'
======================================================================
FAIL: test_pow (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1851, in test_pow
expect(node, inputs=[x, y], outputs=[z], name='test_pow_example')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 59, in expect
decimal=5)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/numpy/testing/utils.py", line 918, in assert_array_almost_equal
precision=decimal)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/numpy/testing/utils.py", line 739, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 5 decimals
(mismatch 33.33333333333333%)
x: array([ 1., 32., 729.], dtype=float32)
y: array([ 1. , 32. , 729.00006], dtype=float32)
----------------------------------------------------------------------
Ran 400 tests in 1.563s
```
P.S. The above remaining two test case error on test_clip (onnx backend @joddiy) occurs also in docker container enivornment without conda, so needed to be fixed.
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[GitHub] [singa] chrishkchris edited a comment on issue #631: Is there any
runtime problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris edited a comment on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601523589
After quite a exhaustive search of conda package versions' combinations, I found that this seems to be working for both onnx and singa:
```
host:
- swig 3.0.12
- openblas 0.3.9
- protobuf 3.9.2
- glog 0.3.5
- numpy 1.11.3
- cudnn {{ cudnn }} # ['cudnn' in str(build_str)]
- dnnl {{ dnnl }}
- python {{ python }}
run:
- {{ pin_compatible('glog', max_pin='x.x') }}
- {{ pin_compatible('numpy', max_pin='x.x') }}
- {{ pin_compatible('dnnl', max_pin='x.x') }}
- cudnn {{ cudnn }} # ['cudnn' in str(build_str)]
- python {{ python }}
- libprotobuf 3.9.2
- libopenblas 0.3.9
- pillow
- future
- tqdm
- onnx 1.6.0
- deprecated 1.2.7
```
onnx 1.5 fails one more test case due to numerical error, so I choose onnx 1.6
However, now there are still two errors in the test case I am investigating why:
```
+ python run.py
..............................................................................................................................EE...................................................F............................................................................................................................................................................................................................
======================================================================
ERROR: test_clip (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1896, in test_clip
name='test_clip_example')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 55, in expect
outputs_dict = sonnx.run_node(onnx_node, input_tensors, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1300, in run_node
return cls._run_node(onnx_node, inputs, handle, forward, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1324, in _run_node
outputs = forward(*inputs) if handle is None else forward(
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 499, in clip
return Clip(min, max)(x)[0]
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 245, in __call__
return self._do_forward(*xs)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 295, in _do_forward
ys = self.forward(*xs)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 479, in forward
mask0 = singa.LTFloat(x, self.min)
TypeError: in method 'LTFloat', argument 2 of type 'float'
======================================================================
ERROR: test_clip_default (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1946, in test_clip_default
name='test_clip_default_min')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 55, in expect
outputs_dict = sonnx.run_node(onnx_node, input_tensors, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1300, in run_node
return cls._run_node(onnx_node, inputs, handle, forward, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1324, in _run_node
outputs = forward(*inputs) if handle is None else forward(
TypeError: clip() missing 1 required positional argument: 'max'
======================================================================
FAIL: test_pow (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1851, in test_pow
expect(node, inputs=[x, y], outputs=[z], name='test_pow_example')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 59, in expect
decimal=5)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/numpy/testing/utils.py", line 918, in assert_array_almost_equal
precision=decimal)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/numpy/testing/utils.py", line 739, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 5 decimals
(mismatch 33.33333333333333%)
x: array([ 1., 32., 729.], dtype=float32)
y: array([ 1. , 32. , 729.00006], dtype=float32)
----------------------------------------------------------------------
Ran 400 tests in 1.563s
```
P.S. The above remaining two test case error on test_clip occurs also in docker container enivornment without conda, so needed to be fixed.
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[GitHub] [singa] nudles commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
nudles commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601030792
you can compare the libprotobuf of SINGA and onnx via methods here https://github.com/conda/conda/issues/2361
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[GitHub] [singa] chrishkchris commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601048021
So I will try the conda build singa onnx test case with protobuf 3.11.3 first
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[GitHub] [singa] chrishkchris edited a comment on issue #631: Is there any
runtime problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris edited a comment on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601043209
Also, our singa dockerfile is using `pip3 install protobuf`, so I may get the same version to conda
Currently, the pip install protobuf version is 3.11.3, but our conda package uses 3.6.1, so it may be better to upgrade
```
(builder) dcsysh@panda8:~$ pip install protobuf
Collecting protobuf
Downloading protobuf-3.11.3-cp36-cp36m-manylinux1_x86_64.whl (1.3 MB)
|████████████████████████████████| 1.3 MB 4.0 MB/s
Requirement already satisfied: six>=1.9 in ./anaconda3/envs/builder/lib/python3.6/site-packages (from protobuf) (1.14.0)
Requirement already satisfied: setuptools in ./anaconda3/envs/builder/lib/python3.6/site-packages (from protobuf) (45.2.0.post20200210)
Installing collected packages: protobuf
Successfully installed protobuf-3.11.3
```
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[GitHub] [singa] chrishkchris commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601043209
Also, our singa dockerfile is using `pip3 install protobuf`, so I may get the same version to conda
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[GitHub] [singa] chrishkchris closed issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris closed issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631
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[GitHub] [singa] chrishkchris commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601006300
maybe the version of protobuf does not match, but I am not sure
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[GitHub] [singa] chrishkchris edited a comment on issue #631: Is there any
runtime problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris edited a comment on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601006300
maybe the version of protobuf used in conda package does not match, but I am not sure
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[GitHub] [singa] chrishkchris commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601523589
After quite a exhaustive search of conda package versions' combinations, I found that this seems to be working for both onnx and singa:
```
host:
- swig 3.0.12
- openblas 0.3.9
- protobuf 3.9.2
- glog 0.3.5
- numpy 1.11.3
- cudnn {{ cudnn }} # ['cudnn' in str(build_str)]
- dnnl {{ dnnl }}
- python {{ python }}
run:
- {{ pin_compatible('glog', max_pin='x.x') }}
- {{ pin_compatible('numpy', max_pin='x.x') }}
- {{ pin_compatible('dnnl', max_pin='x.x') }}
- cudnn {{ cudnn }} # ['cudnn' in str(build_str)]
- python {{ python }}
- libprotobuf 3.9.2
- libopenblas 0.3.9
- pillow
- future
- tqdm
- onnx 1.6.0
- deprecated 1.2.7
```
onnx 1.5 fails one more test case due to numerical error, so I choose onnx 1.6
However, now there are still two errors in the test case I am investigating why:
```
+ python run.py
..............................................................................................................................EE...................................................F............................................................................................................................................................................................................................
======================================================================
ERROR: test_clip (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1896, in test_clip
name='test_clip_example')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 55, in expect
outputs_dict = sonnx.run_node(onnx_node, input_tensors, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1300, in run_node
return cls._run_node(onnx_node, inputs, handle, forward, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1324, in _run_node
outputs = forward(*inputs) if handle is None else forward(
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 499, in clip
return Clip(min, max)(x)[0]
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 245, in __call__
return self._do_forward(*xs)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 295, in _do_forward
ys = self.forward(*xs)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/autograd.py", line 479, in forward
mask0 = singa.LTFloat(x, self.min)
TypeError: in method 'LTFloat', argument 2 of type 'float'
======================================================================
ERROR: test_clip_default (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1946, in test_clip_default
name='test_clip_default_min')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 55, in expect
outputs_dict = sonnx.run_node(onnx_node, input_tensors, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1300, in run_node
return cls._run_node(onnx_node, inputs, handle, forward, opset_version)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/singa/sonnx.py", line 1324, in _run_node
outputs = forward(*inputs) if handle is None else forward(
TypeError: clip() missing 1 required positional argument: 'max'
======================================================================
FAIL: test_pow (test_onnx_backend.TestPythonOnnxBackend)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 1851, in test_pow
expect(node, inputs=[x, y], outputs=[z], name='test_pow_example')
File "/root/miniconda/conda-bld/singa_1584677090067/test_tmp/test/python/test_onnx_backend.py", line 59, in expect
decimal=5)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/numpy/testing/utils.py", line 918, in assert_array_almost_equal
precision=decimal)
File "/root/miniconda/conda-bld/singa_1584677090067/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/python3.6/site-packages/numpy/testing/utils.py", line 739, in assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not almost equal to 5 decimals
(mismatch 33.33333333333333%)
x: array([ 1., 32., 729.], dtype=float32)
y: array([ 1. , 32. , 729.00006], dtype=float32)
----------------------------------------------------------------------
Ran 400 tests in 1.563s
```
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[GitHub] [singa] chrishkchris commented on issue #631: Is there any runtime
problem of onnx in Travis CI built SINGA CPU version related to
libprotobuf.so.20?
Posted by GitBox <gi...@apache.org>.
chrishkchris commented on issue #631: Is there any runtime problem of onnx in Travis CI built SINGA CPU version related to libprotobuf.so.20?
URL: https://github.com/apache/singa/issues/631#issuecomment-601537054
In conclusion, I have posted an conda package versions' combinations that works for SINGA and onnx in conda environment, so I close this issue.
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