I tried to submit my image again this time I got an e-mail message with error message. I am happy because at least I made a progress compared to having nothing:) Here is the message I received:
{"message":"oci runtime error: exec: "/train.sh": stat /train.sh: no such file or directory"}
Now in my Docker file I have the following lines at the bottom (just adapted from the Tensorflow example in the Challenge Docker):
COPY preprocess.sh .
COPY extract_resize_nolabels.py .
COPY DREAM_DM_starter_tf.py .
COPY train.sh .
COPY test.sh .
COPY score_sc1.sh .
This builds successfully when I use the following command
nvidia-docker build -t docker.synapse.org/syn7286737/dm_docker .
But the following does not build successfully:
COPY preprocess.sh /preprocess.sh
COPY extract_resize_no_labels.py /extract_resize_no_labels.py
COPY DREAM_DM_starter_tf.py /DREAM_DM_starter_tf.py
COPY train.sh /train.sh
COPY test.sh /test.sh
COPY score_sc1.sh /score_sc1.sh
Giving me this error:
Step 21 : COPY preprocess.sh /preprocess.sh
stat /var/lib/docker/aufs/mnt/24f7c58141a6c7790e4311ddc341121396e7cbadafb558a0bab3be963366086a/preprocess.sh: no such file or directory
Although these files are indeed inside my docker folder (the folder I am using to perform the build)
Including
WORKDIR /
before these COPY commands (as shown in the example Docker container) did not build either. I will appreciate if you can help me to resolve this. I can share the full Dockerfile if that would be useful. BTW, I push using the following commands:
nvidia-docker login docker.synapse.org
nvidia-docker push docker.synapse.org/syn7286737/dm_docker
Thanks.
Created by Zafer Aydin zaferaydin Hi Xiaoming,
Yes I solved the problem. You can read my previous response above. You have a slightly different version though: a runtime error. I also don't know how you copy your train.sh file. I used
WORKDIR /
COPY train.sh .
instead of
COPY train.sh /train.sh
I think I also got a similar problem with the second one but the first one worked for me. Hi Zafer Aydin,
I have met the same problem as yours:
**{"message":"oci runtime error: exec: "/train.sh": stat /train.sh: no such file or directory"}**
I am wondering whether you have solved it or not?
Best,
Xiaoming Dear Zafer,
Great! Thanks for letting us know!
Best,
Thomas I solved this problem. It is related to the nvidia-docker version. The problem goes away when I restart the docker by
sudo service docker restart
There is a thread about this error here:
https://github.com/docker/docker/issues/25925
Yes that's the command I am using. Today I tried to install nvidia-docker from the source but received the same problem. Here is the ls result from the same directory:
total 5790
drwxr-xr-x 2 zafer zafer 19 Kas 1 17:31 .
drwxrwxr-x 7 zafer zafer 8 Eki 27 06:51 ..
-rwxr-xr-x 1 zafer zafer 17042396 Eyl 29 19:33 111363.dcm
-rwxr-xr-x 1 zafer zafer 118 Eyl 30 09:11 bashrc
-rwxr-xr-x 1 zafer zafer 1146 Eyl 30 09:15 dicom_to_jpeg.py
-rwxr-xr-x 1 zafer zafer 1786 Kas 1 16:43 Dockerfile
-rwxr-xr-x 1 zafer zafer 31383 Eki 1 09:39 DREAM_DM_starter_tf.py
-rwxr-xr-x 1 zafer zafer 1406 Eyl 29 15:33 extract_resize_nolabels.py
-rwxr-xr-x 1 zafer zafer 1536 Eyl 30 09:17 generate_label_files.py
-rwxr-xr-x 1 zafer zafer 1736 Eyl 30 09:17 generate_labels.py
-rwxr-xr-x 1 zafer zafer 498 Eki 1 09:35 preprocess.sh
-rwxr-xr-x 1 zafer zafer 65 Eyl 30 19:33 run_build
-rw-rw-r-- 1 zafer zafer 3633 Kas 1 16:45 run_build2.log
-rwxr-xr-x 1 zafer zafer 12759 Eyl 30 21:55 run_build.log
-rwxr-xr-x 1 zafer zafer 111 Eki 1 09:45 run_push
-rwxr-xr-x 1 zafer zafer 307 Eyl 29 15:17 saved
-rwxr-xr-x 1 zafer zafer 219 Eki 1 09:40 score_sc1.sh
-rwxr-xr-x 1 zafer zafer 230 Eki 1 09:44 test.sh
-rwxr-xr-x 1 zafer zafer 281 Eki 1 09:43 train.sh
and here is the output from nvidia-docker volume ls
DRIVER VOLUME NAME
Can it be because there are no recognized drives? Dear Zafer,
Please kindly also provide me with the command you used to build the docker. Was it:
`nvidia-docker build -t docker.synapse.org/syn7286737/dm_docker .`
Could you also do an `ls` in the current directory. I'm not entirely sure what is happening
Best,
Thomas I uploaded it to my project folder. Its ID is syn7487728. Many thanks. Dear Zafer,
This is my session:
```
$ ls
111363.dcm dicom_to_jpeg.py preprocess.sh saved
DREAM_DM_starter_tf.py extract_resize_nolabels.py run_build score_sc1.sh
Dockerfile generate_label_files.py run_build.log test.sh
bashrc generate_labels.py run_push train.sh
$ docker build -t docker.synapse.org/syn12345/dm_docker .
Sending build context to Docker daemon 17.11 MB
Step 1 : FROM tleyden5iwx/ubuntu-cuda
---> 0027e029bd6c
Step 2 : RUN apt-get update && apt-get install -y bc cmake curl gcc-4.6 g++-4.6 gcc-4.6-multilib g++-4.6-multilib gfortran git libprotobuf-dev libleveldb-dev libsnappy-dev libopencv-dev libboost-all-dev libhdf5-serial-dev liblmdb-dev libjpeg62 libfreeimage-dev libatlas-base-dev pkgconf protobuf-compiler python-dev python-pip unzip wget
---> Using cache
---> 9904f08d88a7
Step 3 : RUN echo "/usr/lib/x86_64-linux-gnu" > /etc/ld.so.conf.d/cuda.conf && ldconfig
---> Using cache
---> 1c1a6280185f
Step 4 : RUN echo "nameserver 208.67.222.222" >/etc/resolv.conf
---> Using cache
---> d99ef34738df
Step 5 : RUN apt-get install automake 1.14 -y
---> Using cache
---> 60f7b33e88cc
Step 6 : RUN pip install pydicom
---> Using cache
---> 47642dcfeef1
Step 7 : RUN apt-get build-dep -y python-matplotlib
---> Using cache
---> 3cd071394352
Step 8 : RUN pip install synapseclient
---> Using cache
---> 74f9a3e6faec
Step 9 : RUN pip install lmdb
---> Using cache
---> cec0e6a10095
Step 10 : RUN apt-get install python-opencv
---> Using cache
---> f5e5ada6e402
Step 11 : RUN ln /dev/null /dev/raw1394
---> Using cache
---> 310de64cb2d0
Step 12 : RUN pip install scipy
---> Using cache
---> 3faf61339c3c
Step 13 : RUN pip install sklearn
---> Using cache
---> a77968718d3e
Step 14 : RUN pip install openpyxl
---> Using cache
---> 35a24ca96da3
Step 15 : FROM tensorflow/tensorflow:0.9.0-gpu
---> 4a52aeda07e6
Step 16 : MAINTAINER Darvin Yi
---> Using cache
---> 56d7789bcd99
Step 17 : RUN pip install --upgrade pip
---> Using cache
---> 933858beacd2
Step 18 : RUN pip install pydicom
---> Using cache
---> 0ff0461baefa
Step 19 : RUN pip install -U scikit-learn
---> Using cache
---> b2f9c702d212
Step 20 : RUN pip install tflearn #git+https://github.com/tflearn/tflearn.git
---> Using cache
---> a14500a3bc36
Step 21 : COPY preprocess.sh /preprocess.sh
---> Using cache
---> 40b2b649ec4a
Step 22 : COPY extract_resize_nolabels.py .
---> Using cache
---> 9b5aed5735f9
Step 23 : COPY DREAM_DM_starter_tf.py .
---> Using cache
---> e42e47da829f
Step 24 : COPY train.sh .
---> Using cache
---> 1f47673afffb
Step 25 : COPY test.sh .
---> Using cache
---> 7ac602947523
Step 26 : COPY score_sc1.sh .
---> Using cache
---> 9b2c4341a46b
Successfully built 9b2c4341a46b
```
Could you print out your entire docker build log?
Best,
Thomas Dear Zafer,
Apologies for the delay. I was unable to reproduce your error. I ran docker build on the folder you gave and it successfully built all the way through.
Best,
Thomas Here it is syn7446136. I am using Ubuntu 16.04.1 LTS xenial. Thanks. Dear Zafer,
Please put the contents of your docker folder in a zipped file, put it onto synapse and share it with me so that I can try to debug your docker file, or put it on github where I can clone your repo. At first glance, I am unsure of what is going on, the only thing I can think of is if `preprocess.sh` isn't actually in your docker folder, but you said that it is.
Best,
Thomas