Hi,
I've managed to build the docker and looking at it, it seems that it was built OK (folders and files in place).
opening the docker at /app and running 'ls' command, shows 4 files: train.py, infer.py, train.sh, infer.sh.
running 'bash train.sh' raises the error. running 'python train.py' runs the python correctly. adding 'echo $PWD' shows execution is in the correct path.
Running on windows. Any ideas on what am I doing wrong? Help is highly appreciated.
Thanks!
Created by Tomer Hermelin MLS Hi @so30 ,
It seems like a terminal issue, please see [this thread](https://superuser.com/questions/1172759/cygwin-error-failed-to-run-bin-bash-no-such-file-or-directory).
Best,
Yao
@yy6linda
Hi,
I tried the test docker image you suggested above, I still get the same error when trying to run "bash infer.sh":
': [Errno 2] No such file or directory
Are you positive it should work on windows system? Deleted message Today I tried again and did exactly as in the example:
```
User@DESKTOP-RT8ISJE MINGW64 /c/g/examples/covid19-question-1 (master)
$ docker build -t awesome-covid19-q1-model:v1 .
Sending build context to Docker daemon 19.46kB
Step 1/15 : FROM python:3.5
3.5: Pulling from library/python
d6ff36c9ec48: Already exists
c958d65b3090: Already exists
edaf0a6b092f: Already exists
80931cf68816: Already exists
bc1b8aca3825: Already exists
6bdbc0af74d9: Pulling fs layer
e6eb974ca946: Pulling fs layer
11740b0bcf22: Pulling fs layer
fc2b025653e5: Pulling fs layer
fc2b025653e5: Waiting
11740b0bcf22: Verifying Checksum
11740b0bcf22: Download complete
fc2b025653e5: Verifying Checksum
fc2b025653e5: Download complete
e6eb974ca946: Verifying Checksum
e6eb974ca946: Download complete
6bdbc0af74d9: Verifying Checksum
6bdbc0af74d9: Download complete
6bdbc0af74d9: Pull complete
e6eb974ca946: Pull complete
11740b0bcf22: Pull complete
fc2b025653e5: Pull complete
Digest: sha256:f451b0c1912e175444848cfe3242ac225975c1d0613c20a2339dfdde5700c0be
Status: Downloaded newer image for python:3.5
---> 342dab296f53
Step 2/15 : LABEL challenge="covid19"
---> Running in c4e6f4cbab3e
Removing intermediate container c4e6f4cbab3e
---> 00e247432ab3
Step 3/15 : LABEL enable_training=true
---> Running in b14739eccd24
Removing intermediate container b14739eccd24
---> 4fe1d622e2e6
Step 4/15 : LABEL description="COVID diagnosis baseline prediction"
---> Running in aa60c896b3d9
Removing intermediate container aa60c896b3d9
---> 1551005ec1d8
Step 5/15 : LABEL ranked_features="cough,body temperature,hematocrit,diastolic blood pressure,systolic blood pressure"
---> Running in 3a2c576dfb7a
Removing intermediate container 3a2c576dfb7a
---> 983acf671726
Step 6/15 : LABEL references="https://www.medrxiv.org/content/10.1101/2020.03.19.20039099v1"
---> Running in 4e2314133884
Removing intermediate container 4e2314133884
---> 205d0c27e063
Step 7/15 : RUN pip install pandas numpy sklearn datetime joblib
---> Running in fee90707a8c7
Collecting pandas
Downloading pandas-0.25.3-cp35-cp35m-manylinux1_x86_64.whl (10.3 MB)
Collecting numpy
Downloading numpy-1.18.5-cp35-cp35m-manylinux1_x86_64.whl (19.9 MB)
Collecting sklearn
Downloading sklearn-0.0.tar.gz (1.1 kB)
Collecting datetime
Downloading DateTime-4.3-py2.py3-none-any.whl (60 kB)
Collecting joblib
Downloading joblib-0.14.1-py2.py3-none-any.whl (294 kB)
Collecting pytz>=2017.2
Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB)
Collecting python-dateutil>=2.6.1
Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting scikit-learn
Downloading scikit_learn-0.22.2.post1-cp35-cp35m-manylinux1_x86_64.whl (7.0 MB)
Collecting zope.interface
Downloading zope.interface-5.1.0-cp35-cp35m-manylinux2010_x86_64.whl (234 kB)
Collecting six>=1.5
Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting scipy>=0.17.0
Downloading scipy-1.4.1-cp35-cp35m-manylinux1_x86_64.whl (26.0 MB)
Requirement already satisfied: setuptools in /usr/local/lib/python3.5/site-packages (from zope.interface->datetime) (49.2.1)
Building wheels for collected packages: sklearn
Building wheel for sklearn (setup.py): started
Building wheel for sklearn (setup.py): finished with status 'done'
Created wheel for sklearn: filename=sklearn-0.0-py2.py3-none-any.whl size=1315 sha256=f0446bf63a4ed88006d4b5774d1df44a621cd570bc73cd282d0d10ccdcc1de22
Stored in directory: /root/.cache/pip/wheels/9e/ec/a6/33cdb5605b0b150074213e154792654a1006e6e6807dc7ca6f
Successfully built sklearn
Installing collected packages: pytz, numpy, six, python-dateutil, pandas, scipy, joblib, scikit-learn, sklearn, zope.interface, datetime
Successfully installed datetime-4.3 joblib-0.14.1 numpy-1.18.5 pandas-0.25.3 python-dateutil-2.8.1 pytz-2020.1 scikit-learn-0.22.2.post1 scipy-1.4.1 six-1.15.0 sklearn-0.0 zope.interface-5.1.0
Removing intermediate container fee90707a8c7
---> f30091eb37f1
Step 8/15 : RUN mkdir /app
---> Running in a3ca59cd7e48
Removing intermediate container a3ca59cd7e48
---> 09c8f2f8be57
Step 9/15 : WORKDIR /app
---> Running in 72ff51525b4d
Removing intermediate container 72ff51525b4d
---> ba7e25778a0b
Step 10/15 : COPY src/train.py .
---> 1ecc09f832ed
Step 11/15 : COPY src/infer.py .
---> fddc253fbf2c
Step 12/15 : COPY train.sh .
---> 6db936c3c12d
Step 13/15 : COPY infer.sh .
---> df79f7cc25ac
Step 14/15 : RUN chmod +x train.sh
---> Running in 20b62711a125
Removing intermediate container 20b62711a125
---> 4cc7ef493b37
Step 15/15 : RUN chmod +x infer.sh
---> Running in 19f4b75a4e18
Removing intermediate container 19f4b75a4e18
---> 339242fce781
Successfully built 339242fce781
Successfully tagged awesome-covid19-q1-model:v1
SECURITY WARNING: You are building a Docker image from Windows against a non-Windows Docker host. All files and directories added to build context will have '-rwxr-xr-x' permissions. It is recommended to double check and reset permissions for sensitive files and directories.
```
```
User@DESKTOP-RT8ISJE MINGW64 /c/g/examples/covid19-question-1 (master)
$ docker run \
> -v $(pwd)/synthetic_data/training:/data:ro \
> -v $(pwd)/output:/output:rw \
> -v $(pwd)/scratch:/scratch:rw \
> -v $(pwd)/model:/model:rw \
> awesome-covid19-q1-model:v1 bash /app/train.sh
**bash: C:/Program Files/Git/app/train.sh: No such file or directory**
```
@yy6linda
Can you help me please?
I installed linux and ran
```
bash train.sh
```
and again got the same error
: [Errno 2] No such file or directory
When I try to run
```
bash train.sh
```
i got
```
Permission denied or No such file directory (This depend on kind of terminal)
```
And I try to run this without docker
Does anyone have solution?
Hello
I have the same problem
I use docker on windows with "Cygwin64 Terminal" because it support linux syntax
I locate files according to requires, after row
```
docker build -t awesome-covid19-q1-model:v1 .
```
I have warning
'SECURITY WARNING: You are building a Docker image from Windows against a non-Win
dows Docker host. All files and directories added to build context will have '-r
wxr-xr-x' permissions. It is recommended to double check and reset permissions f
or sensitive files and directories.'
I don't know how serious this is, but after
```
docker run \
-v $(pwd)/synthetic_data/training:/data:ro \
-v $(pwd)/output:/output:rw \
-v $(pwd)/scratch:/scratch:rw \
-v $(pwd)/model:/model:rw \
awesome-covid19-q1-model:v1 bash /app/train.sh
```
get '': [Errno 2] No such file or directory'
Is this related to Windows?
Thank you Hi,
Thanks for all the help!
The first thing I've tried was the example command:
```
docker run \
-v $(pwd)/synthetic_data/training:/data:ro \
-v $(pwd)/output:/output:rw \
-v $(pwd)/scratch:/scratch:rw \
-v $(pwd)/model:/model:rw \
awesome-covid19-q1-model:v1 bash /app/train.sh
```
before I tried to pin down where my problem is (invoking the train.py file, specifically from the bash command).
I've also tried to run without mounting the folders, but it didn't make a difference as the problem is starting the py file (I've also added a print in the first line of the py file and it didn't trigger).
I think I'll erase everything and try again from the beginning, maybe I've corrupted some strings somehow. I will update if that helped.
Thanks! I did the same thing as what you were trying and didn't see the same error as what you have seen, here I suggest you do this simple practice without loading the data to see if you still have the same issue.
```
docker build -t test .
docker run -it test /bin/bash
```
Then you should be able to see:
```
root@afc19a3049e9:/app# ls
infer.py infer.sh train.py train.sh
root@afc19a3049e9:/app# bash infer.sh
Load measurement.csv
Traceback (most recent call last):
File "/app/infer.py", line 9, in
```
The bash file is running.
Have you tried to download synthetic data and run these commands below:
```
docker run \
-v $(pwd)/synthetic_data/training:/data:ro \
-v $(pwd)/output:/output:rw \
-v $(pwd)/scratch:/scratch:rw \
-v $(pwd)/model:/model:rw \
awesome-covid19-q1-model:v1 bash /app/train.sh
```
```
docker run \
-v $(pwd)/synthetic_data/evaluation:/data:ro \
-v $(pwd)/output:/output:rw \
-v $(pwd)/scratch:/scratch:rw \
-v $(pwd)/model:/model:rw \
awesome-covid19-q1-model:v1 bash /app/infer.sh
```
Do they work?
Thanks!
This was trying to run the example model here: https://github.com/Sage-Bionetworks-Challenges/ehr-dream-challenges/tree/master/examples/covid19-question-1
Tried to run it step by step.
cmd prints:
Error:
```
root@a5df190a004b:/app# bash infer.sh
': [Errno 2] No such file or directory
```
Context:
```
C:\src\MastersCourses\Clinical\Challenge\ehr-dream-challenges\examples\covid19-question-1>docker build -t awesome-covid19-q1-model:v1 .
Sending build context to Docker daemon 6.697GB
Step 1/15 : FROM python:3.5
---> d002b97d4a21
Step 2/15 : LABEL challenge="covid19"
---> Using cache
---> fdf0c6aa68d0
Step 3/15 : LABEL enable_training=true
---> Using cache
---> 49c22d3e6f83
Step 4/15 : LABEL description="COVID diagnosis baseline prediction"
---> Using cache
---> ddd1a31cb1bb
Step 5/15 : LABEL ranked_features="cough,body temperature,hematocrit,diastolic blood pressure,systolic blood pressure"
---> Using cache
---> 42501c671e1e
Step 6/15 : LABEL references="https://www.medrxiv.org/content/10.1101/2020.03.19.20039099v1"
---> Using cache
---> aca876020f62
Step 7/15 : RUN pip install pandas numpy sklearn datetime joblib
---> Using cache
---> 298c346ef4cd
Step 8/15 : RUN mkdir /app
---> Using cache
---> 0e14d2ec94fe
Step 9/15 : WORKDIR /app
---> Using cache
---> 74289b1ba6a0
Step 10/15 : COPY src/train.py .
---> 0aa8f1b7f02e
Step 11/15 : COPY src/infer.py .
---> 1a5f4439c9bf
Step 12/15 : COPY train.sh .
---> 04e01e9a3135
Step 13/15 : COPY infer.sh .
---> ba0c4481a002
Step 14/15 : RUN chmod +x train.sh
---> Running in 59d28037ae2c
Removing intermediate container 59d28037ae2c
---> 63a1c9fa0deb
Step 15/15 : RUN chmod +x infer.sh
---> Running in ca3137054058
Removing intermediate container ca3137054058
---> 58ea6cdd9f2a
Successfully built 58ea6cdd9f2a
Successfully tagged awesome-covid19-q1-model:v1
SECURITY WARNING: You are building a Docker image from Windows against a non-Windows Docker host. All files and directories added to build context will have '-rwxr-xr-x' permissions. It is recommended to double check and reset permissions for sensitive files and directories.
C:\src\MastersCourses\Clinical\Challenge\ehr-dream-challenges\examples\covid19-question-1>docker run -v C:\src\MastersCourses\Clinical\Challenge\ehr-dream-challenges\examples\covid19-question-1\synthetic_data\training:/data:ro -v C:\src\MastersCourses\Clinical\Challenge\ehr-dream-challenges\examples\covid19-question-1\output:/output:rw -v C:\src\MastersCourses\Clinical\Challenge\ehr-dream-challenges\examples\covid19-question-1\scratch:/scratch:rw -v C:\src\MastersCourses\Clinical\Challenge\ehr-dream-challenges\examples\covid19-question-1\model:/model:rw -it --entrypoint "/bin/bash" awesome-covid19-q1-model:v1
root@a5df190a004b:/app# bash train.sh
': [Errno 2] No such file or directory
root@a5df190a004b:/app# bash inger.sh
bash: inger.sh: No such file or directory
root@a5df190a004b:/app# bash infer.sh
': [Errno 2] No such file or directory
root@a5df190a004b:/app# cat infer.sh
#!/usr/bin/env bash
python /app/infer.py
root@a5df190a004b:/app# python /app/infer.py
Load measurement.csv
Load condition.csv
Killed
root@a5df190a004b:/app# ls
infer.py infer.sh train.py train.sh
root@a5df190a004b:/app#
```
Hi @MLS ,
I'm happy to help. Can you send me the error message you got for running 'bash train.sh' ? Also I recommend you to take a look at this [example Docker model](https://github.com/Sage-Bionetworks-Challenges/ehr-dream-challenges/tree/master/examples/covid19-question-1). Try if you run into the same error when running the example model.
Best,
Yao
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