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docker build fails #44

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MNEUW opened this issue Dec 20, 2020 · 19 comments
Open

docker build fails #44

MNEUW opened this issue Dec 20, 2020 · 19 comments

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@MNEUW
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MNEUW commented Dec 20, 2020 •
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Dear ost-team,

I tried to pull the docker image. Anyway by using docker pull buddyvolly/opensartoolkit still an old ost-version is installed. now I fail building the new version using the image here in this repository. By using docker build I always get the following errer-log at step 8/14:
`docker build /home/ost/OpenSarToolkit_master_20201220/
Sending build context to Docker daemon 54.87MB
Step 1/14 : FROM ubuntu:18.04
---> 2c047404e52d
Step 2/14 : LABEL maintainer="Petr Sevcik, EOX"
---> Using cache
---> e76d4f005833
Step 3/14 : LABEL OpenSARToolkit='0.10.1'
---> Using cache
---> 3962f459ecd1
Step 4/14 : WORKDIR /home/ost
---> Using cache
---> 693506450e9e
Step 5/14 : COPY snap7.varfile $HOME
---> Using cache
---> a9f658bc3602
Step 6/14 : ENV OTB_VERSION="7.1.0" TBX_VERSION="7" TBX_SUBVERSION="0"
---> Using cache
---> 76a4ec29a32c
Step 7/14 : ENV TBX="esa-snap_sentinel_unix_${TBX_VERSION}_${TBX_SUBVERSION}.sh" SNAP_URL="http://step.esa.int/downloads/${TBX_VERSION}.${TBX_SUBVERSION}/installers" OTB=OTB-${OTB_VERSION}-Linux64.run HOME=/home/ost PATH=$PATH:/home/ost/programs/snap/bin:/home/ost/programs/OTB-${OTB_VERSION}-Linux64/bin
---> Using cache
---> c642dd2a2adc
Step 8/14 : RUN groupadd -r ost && useradd -r -g ost ost && apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -yq python3 python3-pip git libgdal-dev python3-gdal libspatialindex-dev libgfortran3 wget unzip imagemagick nodejs npm
---> Running in d4c18ae031c0
Get:1 http://archive.ubuntu.com/ubuntu bionic InRelease [242 kB]
Get:2 http://security.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB]
Get:3 http://archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB]
Get:4 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]
Get:5 http://archive.ubuntu.com/ubuntu bionic/main amd64 Packages [1344 kB]
Get:6 http://archive.ubuntu.com/ubuntu bionic/multiverse amd64 Packages [186 kB]
Get:7 http://archive.ubuntu.com/ubuntu bionic/universe amd64 Packages [11.3 MB]
Get:8 http://archive.ubuntu.com/ubuntu bionic/restricted amd64 Packages [13.5 kB]
Get:9 http://archive.ubuntu.com/ubuntu bionic-updates/multiverse amd64 Packages [53.8 kB]
Get:10 http://archive.ubuntu.com/ubuntu bionic-updates/restricted amd64 Packages [266 kB]
Get:11 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 Packages [2136 kB]
Get:12 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 Packages [2244 kB]
Get:13 http://archive.ubuntu.com/ubuntu bionic-backports/universe amd64 Packages [11.4 kB]
Get:14 http://archive.ubuntu.com/ubuntu bionic-backports/main amd64 Packages [11.3 kB]
Get:15 http://security.ubuntu.com/ubuntu bionic-security/restricted amd64 Packages [237 kB]
Get:16 http://security.ubuntu.com/ubuntu bionic-security/main amd64 Packages [1816 kB]
Get:17 http://security.ubuntu.com/ubuntu bionic-security/universe amd64 Packages [1372 kB]
Get:18 http://security.ubuntu.com/ubuntu bionic-security/multiverse amd64 Packages [15.3 kB]
Fetched 21.5 MB in 2s (9791 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
libgdal-dev : Depends: default-libmysqlclient-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
The command '/bin/sh -c groupadd -r ost && useradd -r -g ost ost && apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -yq python3 python3-pip git libgdal-dev python3-gdal libspatialindex-dev libgfortran3 wget unzip imagemagick nodejs npm' returned a non-zero code: 100
`

may you have a hint what I'm doing wrong.
best M
@BuddyVolly
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BuddyVolly commented Dec 21, 2020 •
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Hi Mneuw,

sorry for running into this. You are doing nothing wrong. Just usual clash of dependencies, especially when you are working with gdal...there are some dependency issues between gdal and nodejs/npm.
Unfortunately I am not having too much time to look into this right now.
Could you check if removing the gdal related stuff in the 8th RUN solves this?
i.e. delete those 2 entries: libgdal-dev python3-gdal

gdal should later then be automatically installed via pip (so no additional entry needed).

Please let me know how that goes. And I hope that solves it.
Cheers

@MNEUW
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MNEUW commented Dec 21, 2020 •
edited
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Finally got it to run:)

needed to modify the dockerfile quite a bit:

  1. updated to OTB Version 7.2.0 because wget couldn't find the old one? you think this could cause problems?
  2. removed libgdal-dev but needed python3-gdal
  3. added a RUN to add nodejs >= v.10 (was required for installation)
  4. added pip update > maybe this is already newest version and not necessary
  5. removed last line jupyter nbextension enable --py widgetsnbextension because of an error. are these extensions important?

FROM ubuntu:18.04

LABEL maintainer="Petr Sevcik, EOX"
LABEL OpenSARToolkit='0.10.1'

set work directory to home and download snap
WORKDIR /home/ost

copy the snap installation config file into the container
COPY snap7.varfile $HOME

update variables
ENV OTB_VERSION="7.2.0"
TBX_VERSION="7"
TBX_SUBVERSION="0"
ENV TBX="esa-snap_sentinel_unix_${TBX_VERSION}_${TBX_SUBVERSION}.sh"
SNAP_URL="http://step.esa.int/downloads/${TBX_VERSION}.${TBX_SUBVERSION}/installers"
OTB=OTB-${OTB_VERSION}-Linux64.run
HOME=/home/ost
PATH=$PATH:/home/ost/programs/snap/bin:/home/ost/programs/OTB-${OTB_VERSION}-Linux64/bin

install all dependencies
RUN groupadd -r ost &&
useradd -r -g ost ost &&
apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -yq
python3
python3-pip
git
python3-gdal
libspatialindex-dev
libgfortran3
wget
unzip
imagemagick
npm
curl

RUN apt-get update &&
curl -sL https://deb.nodesource.com/setup_10.x | bash - &&
apt-get -y install nodejs &&
ln -s /usr/bin/nodejs /usr/local/bin/node

RUN alias python=python3 &&
rm -rf /var/lib/apt/lists/* &&
python3 -m pip install -U pip &&
python3 -m pip install -U setuptools &&
python3 -m pip install jupyterlab &&
mkdir /home/ost/programs &&
wget $SNAP_URL/$TBX && \
chmod +x $TBX &&
./$TBX -q -varfile snap7.varfile &&
rm $TBX &&
rm snap7.varfile &&
cd /home/ost/programs &&
wget https://www.orfeo-toolbox.org/packages/${OTB} && \
chmod +x $OTB &&
./${OTB} &&
rm -f OTB-${OTB_VERSION}-Linux64.run

update snap to latest version
RUN /home/ost/programs/snap/bin/snap --nosplash --nogui --modules --update-all 2>&1 | while read -r line; do
echo "$line" &&
[ "$line" = "updates=0" ] && sleep 2 && pkill -TERM -f "snap/jre/bin/java";
done; exit 0

set usable memory to 12G
RUN echo "-Xmx36G" > /home/ost/programs/snap/bin/gpt.vmoptions

get OST and tutorials
RUN python3 -m pip install git+https://github.com/ESA-PhiLab/OpenSarToolkit.git &&
git clone https://github.com/ESA-PhiLab/OST_Notebooks &&
jupyter labextension install @jupyter-widgets/jupyterlab-manager

EXPOSE 8888
CMD jupyter lab --ip='0.0.0.0' --port=8888 --no-browser --allow-root

best
M

@BuddyVolly
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Hi,

responding to the numbers above:

  1. not at all. Orfeo is needed during mosaicking. So 7.2. is fine. it needs to ship with otbcli_Mosaic function (which it does)
    2.ok
  2. ok
  3. shouldn't do a harm
  4. ok, you might have visualization issues of the progress bar during download. but the download itself should still work

@MNEUW
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MNEUW commented Dec 22, 2020

Thanks a lot, all clear now for me!

@BuddyVolly
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great, let us know if there are further issues and have a great christmas time.

@MNEUW
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MNEUW commented Dec 23, 2020 •
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ok!! I just tried the S1GRD_Batch-processing and encountered that the grds_to_ards-module doesn't work for the RTC-Gamma0 product type. For some reason it produces only NA-layers. Contrary it runs perfectly for the GTC-Gamma product.
And I was wondering if and how it is possible to change to out_projection for the ard-products e.g. to WGS 1984 UTM Zone 33N?

Anyway it's a great toolkit! wish you a pleasent christmas 2020!!

Best Martin

@BuddyVolly
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hmm, in the docker file there is still the update of snap . uncomment following lines and build again. There are some issues with the latest version of snap that I still need to fix (when I have time)

RUN /home/ost/programs/snap/bin/snap --nosplash --nogui --modules --update-all 2>&1 | while read -r line; do
echo "$line" &&
[ "$line" = "updates=0" ] && sleep 2 && pkill -TERM -f "snap/jre/bin/java";
done; exit 0

@BuddyVolly
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BuddyVolly commented Dec 23, 2020 •
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then try to use this notebook as template:
https://github.com/ESA-PhiLab/OST_Notebooks/blob/master/4c%20-%20Sentinel-1%20GRD%20Batch%20-%20Timescan.ipynb

you need to change aoi, start,end and project_dir of course
for me this works.

Check out also the other notebooks. Should not take you more than a day to go through, and will hopefully help to get the concept. Most trickiest parts are the refine inventory and the ard parameters. the rest is just code execution

happy christmas to you, too!

@BuddyVolly
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and yes, you can set the out projection by using the EPSG code. so Lat/Lon is 4326, UTM 33N is 32633

e.g. s1.ard_parameters['single_ARD']['dem']['out_projection'] = '32633'

@MNEUW
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MNEUW commented Dec 26, 2020 •
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Now after getting back to SNAP version 7 I'm running into the following error while executing grds_to_ards in your above shared notebook:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-26-b95cd587dd24> in <module>
      3     timeseries=True,
      4     timescan=True,
----> 5     overwrite=False
      6 )

/usr/local/lib/python3.6/dist-packages/ost/Project.py in grds_to_ards(self, inventory_df, timeseries, timescan, mosaic, overwrite, max_workers, executor_type)
    848         # time-series part
    849         if timeseries or timescan:
--> 850             grd_batch.ards_to_timeseries(inventory_df, self.config_file)
    851 
    852         if timescan:

/usr/local/lib/python3.6/dist-packages/ost/s1/grd_batch.py in ards_to_timeseries(inventory_df, config_file)
    146 
    147     # create all extents
--> 148     _create_extents(inventory_df, config_file)
    149 
    150     # update extents in case of ls_mask

/usr/local/lib/python3.6/dist-packages/ost/s1/grd_batch.py in _create_extents(inventory_df, config_file)
    186             fargs=([str(config_file), ])
    187     ):
--> 188         track, list_of_scenes, extent = task.result()
    189         out_dict['track'].append(track)
    190         out_dict['list_of_scenes'].append(list_of_scenes)

/usr/local/lib/python3.6/dist-packages/godale/_concurrent.py in result(self)
    154         """Return func result or raise Exception."""
    155         if self._exception:
--> 156             raise self._exception
    157         else:
    158             return self._result

AttributeError: 'DataFrame' object has no attribute 'crs'

I changed the crs of the inventory_pandas_dataframe o the same as the output projection with no effect.First results (ard products in snap-format) appear in the processing directory but timeseries and timescan products fails.

may you have an idea where this could come from? steps before while querring the S1-datasets I already encounter some crs-warnings:
` INFO (10:00:32): Created project directory at /home/ost/shared
INFO (10:00:32): Downloaded data will be stored in: /home/ost/shared/download.
INFO (10:00:32): Inventory files will be stored in: /home/ost/shared/inventory.
INFO (10:00:32): Processed data will be stored in: /home/ost/shared/processing.
INFO (10:00:32): Using /home/ost/shared/temp as directory for temporary files.

/usr/local/lib/python3.6/dist-packages/pyproj/crs/crs.py:53: FutureWarning: '+init=:' syntax is deprecated. ':' is the preferred initialization method. When making the change, be mindful of axis order changes: https://pyproj4.github.io/pyproj/stable/gotchas.html#axis-order-changes-in-proj-6
return _prepare_from_string(" ".join(pjargs))
/usr/local/lib/python3.6/dist-packages/pyproj/crs/crs.py:294: FutureWarning: '+init=:' syntax is deprecated. ':' is the preferred initialization method. When making the change, be mindful of axis order changes: https://pyproj4.github.io/pyproj/stable/gotchas.html#axis-order-changes-in-proj-6
projstring = _prepare_from_string(" ".join((projstring, projkwargs)))
/usr/local/lib/python3.6/dist-packages/geopandas/geodataframe.py:422: RuntimeWarning: Sequential read of iterator was interrupted. Resetting iterator. This can negatively impact the performance.
for feature in features_lst:

If you do not have a Copernicus Scihub user account go to: https://scihub.copernicus.eu and register

Your Copernicus Scihub Username: madduen
Your Copernicus Scihub Password: ·········

/usr/local/lib/python3.6/dist-packages/pyproj/crs/crs.py:53: FutureWarning: '+init=:' syntax is deprecated. ':' is the preferred initialization method. When making the change, be mindful of axis order changes: https://pyproj4.github.io/pyproj/stable/gotchas.html#axis-order-changes-in-proj-6
return _prepare_from_string(" ".join(pjargs))

INFO (10:00:42): Writing inventory data to geopackage file: /home/ost/shared/inventory/full.inventory.gpkg
INFO (10:00:42): Coverage analysis for ASCENDING tracks in VV VH polarisation.
INFO (10:00:42): 5 frames for ASCENDING tracks in VV VH polarisation.
INFO (10:00:42): 5 frames remain after double entry removal
INFO (10:00:42): Excluding track 146
INFO (10:00:42): 2 frames remain after non-AOI overlap
INFO (10:00:42): All remaining tracks fully overlap the AOI. Not removing anything.
INFO (10:00:42): 2 frames remain after removal of non-full AOI crossing

/usr/local/lib/python3.6/dist-packages/pyproj/crs/crs.py:53: FutureWarning: '+init=:' syntax is deprecated. ':' is the preferred initialization method. When making the change, be mindful of axis order changes: https://pyproj4.github.io/pyproj/stable/gotchas.html#axis-order-changes-in-proj-6
return _prepare_from_string(" ".join(pjargs))
/usr/local/lib/python3.6/dist-packages/ost/s1/refine_inventory.py:71: UserWarning: CRS mismatch between the CRS of left geometries and the CRS of right geometries.
Use to_crs() to reproject one of the input geometries to match the CRS of the other.

Left CRS: EPSG:4326
Right CRS: +init=epsg:4326 +no_defs +type=crs

inventory_df, aoi_gdf, how='left', op='intersects'

INFO (10:00:43): Found 2 full coverage mosaics.
INFO (10:00:43): Coverage analysis for DESCENDING tracks in VV VH polarisation.
INFO (10:00:43): 6 frames for DESCENDING tracks in VV VH polarisation.
INFO (10:00:43): 6 frames remain after double entry removal
INFO (10:00:43): Excluding track 124
INFO (10:00:43): Excluding track 22
INFO (10:00:43): 3 frames remain after non-AOI overlap
INFO (10:00:43): All remaining tracks fully overlap the AOI. Not removing anything.
INFO (10:00:43): 3 frames remain after removal of non-full AOI crossing

/usr/local/lib/python3.6/dist-packages/ost/s1/refine_inventory.py:71: UserWarning: CRS mismatch between the CRS of left geometries and the CRS of right geometries.
Use to_crs() to reproject one of the input geometries to match the CRS of the other.

Left CRS: EPSG:4326
Right CRS: +init=epsg:4326 +no_defs +type=crs

inventory_df, aoi_gdf, how='left', op='intersects'

INFO (10:00:43): Found 3 full coverage mosaics.`

@BuddyVolly
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Hi,

it is a problem that we do not fix the version of certain python packages. There have been huge changes to the pyproj lib. Almost all of the geolibs in python use this for projection related stuff, and the syntax changed. You could downgrade to Proj 4 somehow. But it will take me some time to fix all this, as at the moment I do not really have time for it.

Best,
Andreas

@MNEUW
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MNEUW commented Jan 29, 2021

ok thanks for your answer! just let me know when there is an update. meanwhile I'll try on my own start.
Best, M

@MNEUW
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MNEUW commented Feb 1, 2021 •
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Hm, all steps are working now except the creation of the image bounds for the time-series processing. So I think we do not need huge changes. What does this actually? align the scences to same extent? and which script/function is responsible for the job?may you have another hint where I can start digging. sorry for interrupting.

Best,
Martin

@BuddyVolly
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Hi, this step is needed to calculate the common minimum bound of all images in the time-series, as their extent may vary (slightly).
I think it uses geopandas for that, which is based on pyproj, which again had those huge changes. So I assume something related to this. Here you can find an example of this problem (as many have this) https://gis.stackexchange.com/questions/348997/constant-future-warnings-with-new-pyproj

@MNEUW
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MNEUW commented Jun 16, 2021 via email

@BuddyVolly
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Yes, the apihub URL changed https://scihub.copernicus.eu/news/News00868
I still did not have the time do update the toolkit. I am working on a release with the new SNAP 8 and will include this.

@MNEUW
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MNEUW commented Jun 17, 2021 via email

@BuddyVolly
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Hi Martin,
so there is a solution I think without having to change the code.
You can set the base url in the search function of your class instance.
Let's say you initialized your Sentinel1Batch to s1 then:
s1.search(base_url='https://scihub.copernicus.eu/dhus/')

However, setting the base_url for DOWNLOAD from scihub is NOT possible. But you can use ASF for download, if you haven't done so yet. You can download 10 files concurrently and it keeps all of the archive, as opposed to scihub where you only have the last year as it is a rolling archive. It is much faster.

Hope that helps,
Andreas

@MNEUW
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MNEUW commented Jun 21, 2021 via email

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