[WISE Bug]: on base ubuntu:20.04 Docker Image (not in github) install missing libgomp.so.1 #171
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this seems to be a common issue when: |
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workaround to get container working: |
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this is proven fixed. This container is vanilla Ubuntu 20.04 with no libgomp installed. |
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@RobBryce sadly this is still not working right. I thought you solved it, BUT it was me installing build essentials that satisfied the missing libgomp dependancy, so this is still broken as of v1.0.6-beta.1 |
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Not enough information is provided to act on this issue. Since you are currently the only one experiencing this issue please describe the system and the issue you are seeing. What is the OS version/build date? Are there any errors/warnings during the install process? Is any version of libgomp1 available after the install? Are you installing anything else when testing or is this just the 1.0.6-beta.1 version of WISE on an unmodified Ubuntu 20.04 container? Does installing libgomp1 manually still resolve the issue? What version of libgomp1 is installed when installing manually? |
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@tredpath Both Alex and myself have found this. Alex today on latest:
Me:
Alex:
Then I made a new test for this issue without the installation of build essentals on latest > base_typescript@1.0.0 test-wise
> node dist/test.wise.js
Clearing old results
Running the job
error: Command failed: /usr/bin/wise ~/app_data/testjob/job.fgmj
{"message":"Command failed: /usr/bin/wise ~/app_data/testjob/job.fgmj\n","name":"Error"}
error: Command failed: /usr/bin/wise ~/app_data/testjob/job.fgmj --validate
stderr:
{"message":"Command failed: /usr/bin/wise ~/app_data/testjob/job.fgmj --validate\n","name":"Error"}@tredpath You are also free to grab the wise_demo and run it yourself.
2004 works because it has build essentials Step 18/33 : RUN apt install -y /tmp/WISE/wise-ubuntu2004.deb
---> Running in 3e56d257986d
WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
gdal-data libaec0 libarmadillo9 libarpack2 libblas3 libcfitsio8 libcharls2
libcurl3-gnutls libdap25 libdapclient6v5 libepsilon1 libfreexl1 libfyba0
libgdal26 libgeos-3.8.0 libgeos-c1v5 libgeotiff5 libgfortran5 libgomp1
libhdf4-0-alt libhdf5-103 libkmlbase1 libkmldom1 libkmlengine1 liblapack3
libltdl7 libminizip1 libmysqlclient21 libnetcdf15 libnuma1 libodbc1
libogdi4.1 libopenjp2-7 libpoppler97 libpq5 libproj15 libqhull7 libquadmath0
libspatialite7 libsuperlu5 libsz2 liburiparser1 libxerces-c3.2 mysql-common
odbcinst odbcinst1debian2 poppler-data proj-bin proj-data
Suggested packages:
geotiff-bin gdal-bin libgeotiff-epsg libhdf4-doc libhdf4-alt-dev hdf4-tools
libmyodbc odbc-postgresql tdsodbc unixodbc-bin ogdi-bin poppler-utils
ghostscript fonts-japanese-mincho | fonts-ipafont-mincho
fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai
fonts-arphic-uming fonts-nanum
The following NEW packages will be installed:
gdal-data libaec0 libarmadillo9 libarpack2 libblas3 libcfitsio8 libcharls2
libcurl3-gnutls libdap25 libdapclient6v5 libepsilon1 libfreexl1 libfyba0
libgdal26 libgeos-3.8.0 libgeos-c1v5 libgeotiff5 libgfortran5 libgomp1
libhdf4-0-alt libhdf5-103 libkmlbase1 libkmldom1 libkmlengine1 liblapack3
libltdl7 libminizip1 libmysqlclient21 libnetcdf15 libnuma1 libodbc1
libogdi4.1 libopenjp2-7 libpoppler97 libpq5 libproj15 libqhull7 libquadmath0
libspatialite7 libsuperlu5 libsz2 liburiparser1 libxerces-c3.2 mysql-common
odbcinst odbcinst1debian2 poppler-data proj-bin proj-data wise
0 upgraded, 50 newly installed, 0 to remove and 4 not upgraded.
...
Get:49 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libgomp1 amd64 10.3.0-1ubuntu1~20.04 [102 kB]
...
Selecting previously unselected package libgomp1:amd64.
Preparing to unpack .../47-libgomp1_10.3.0-1ubuntu1~20.04_amd64.deb ...
Unpacking libgomp1:amd64 (10.3.0-1ubuntu1~20.04) ... |
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The libgomp1 issue was resolved in WISE-Developers/WISE_Application#34 but other issues came up with read/write driver lists. With the 1.0.6-beta.2 installer on the ubuntu:20.04 docker container with just Java and W.I.S.E. installed it will validate and run the FGM here. I didn't use your Dockerfile I ran the install and execution commands manually after Running it generated the following files: |
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I made some tweaks to the JS API mostly to make it easier to start example_job.js in a test environment. My minimal docker container to create and run an FGM is: FROM ubuntu:20.04
SHELL ["/bin/bash", "-c"]
# Set the timezone
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
# Install dependencies, most importantly for WISE is Java (I use 11 but any should work)
RUN apt update && apt install -y --no-install-recommends \
openjdk-11-jre \
wget \
zip \
unzip \
apt-transport-https \
ca-certificates \
git \
jq
# Install NodeJS
RUN wget https://deb.nodesource.com/setup_16.x && bash setup_16.x && apt install -y nodejs
# Create some directories that will be needed later
RUN mkdir -p /opt/wise && mkdir -p /opt/builder && mkdir -p /opt/jobs && mkdir -p /opt/jobs/examples/test
# Download the WISE JS API and unzip the example job data
RUN git clone https://github.com/WISE-Developers/WISE_JS_API.git /opt/api && unzip /opt/api/files/dogrib.zip -d /opt/jobs/examples/test
# Install the dependencies for the WISE JS API
RUN npm --prefix /opt/api i && npm config set WISE_JS_API:job_directory /opt/jobs
# Download the most recent WISE Builder archive
RUN wget -nv $(wget -nv -O - https://api.github.com/repos/WISE-Developers/WISE_Builder_Component/releases/latest | jq -r '.assets[] | select(.name | contains("WISE_Builder-")) | .browser_download_url') -O /opt/builder/builder.zip
# Unzip the WISE Builder archive
RUN unzip /opt/builder/builder.zip -d /opt/builder && rm /opt/builder/builder.zip
# Download the most recent WISE Application installer
RUN wget -nv $(wget -nv -O - https://api.github.com/repos/WISE-Developers/WISE_Application/releases/latest | jq -r '.assets[] | select(.name | contains("wise-ubuntu2004-")) | .browser_download_url') -O /opt/wise/wise.deb
# Install WISE
RUN apt install -y /opt/wise/wise.deb
# Create a config file that will be used by the JS API and WISE Builder. I haven't configured the MQTT options which will cause some warnings in the build process later but the test will still work.
# To add MQTT options, add the following to the config.json file just before "signals": "mqtt": {"hostname": "example.ca","port": 1883,"topic": "wise","verbosity": "INFO","qos": 1,"username": "username","password": "password"},
RUN echo '{"log": {"filename": "logfile.log","verbosity": "WARN"},"signals": {"start": "start.txt","complete": "complete.txt"},"hardware": {"processes": 1,"cores": 2},"builder": {"hostname": "127.0.0.1","port": 32479},"exampleDirectory": "/opt/jobs/examples","alreadyV2": true}' > /opt/jobs/config.json
# Copy the default.json file from the WISE JS API to the jobs directory
RUN cp /opt/api/files/defaults.json /opt/jobs/defaults.json
# Run in the API directory
WORKDIR /opt/api
# Start WISE Builder in the background, execute the example job, and then kill WISE Builder. This is where some warnings will be generated about not being able to connect to MQTT but they can be ignored as the job is successfully created
RUN nohup java -jar /opt/builder/WISE_Builder.jar -o json_v2 -j /opt/jobs -l 32479 2>&1 >/dev/null & echo $! > builder_pid.txt && sleep 5 && node /opt/api/dist/example_job.js && kill $(cat builder_pid.txt) && rm builder_pid.txt
# Run WISE on the most recent job in the jobs directory
RUN wise -r 4 -f 0 -t $(find /opt/jobs/ -maxdepth 1 -type d -name 'job_*' -print -quit)/job.fgmjI built this with the following docker compose file version: '3.1'
services:
test:
build:
context: .
dockerfile: wise.Dockerfile
volumes:
- job_data:/opt/jobs
volumes:
job_data:I ran it with |
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now I need to add the docker stuff to the wise demo! |
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What happened?
created a fresh docker container on image ubuntu:20.04 from dockerhub.
updated apt
installed wget
pulled wise-ubuntu2004-1.0.0-beta.deb
installed it
ran wise --version and got:
/usr/lib/wise/wise: error while loading shared libraries: libgomp.so.1: cannot open shareThis does not happen in ubuntu 20.04 on github:
Version
(Ubuntu 2020) v1.0.0-beta
What component are you seeing the problem on?
No response
Relevant log output
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