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Joonasko / WISE

DestinE WISE development
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Add packaging to WISE #1

Open jaantollander opened 1 week ago

jaantollander commented 1 week ago

The develop branch contains changes required for packaging WISE. We should test the package before merging the changes to main branch.

You can try installing the package using: 

pip3 install git+https://github.com/Joonasko/WISE.git@develop

Or clone the develop branch and install to the editable mode:

pip3 install --editable .

Installing wise will now install run_wise command to the shell.

run_wise --help

Ping: @Joonasko @spolade

Joonasko commented 6 days ago

Do you mean testing this on my own pc or LUMI (or the virtual machine?)

When I ran it on my own pc, the installation seems to have been successful:

:~$ run_wise --help usage: run_wise [-h] -year_start YEAR_START -month_start MONTH_START -day_start DAY_START -year_end YEAR_END -month_end MONTH_END -day_end DAY_END

Runscript for data notifier job.

options: -h, --help show this help message and exit -year_start YEAR_START Input year start -month_start MONTH_START Input month start -day_start DAY_START Input day start -year_end YEAR_END Input year end -month_end MONTH_END Input month end -day_end DAY_END Input day end

Should I try it also on LUMI, and how should I proceed from here? There should be a working version of the application by the end of this week (29.11.), so should I use the older version, or could we setup this one before that?

@jaantollander

jaantollander commented 4 days ago

Try this container image for testing the develop version on LUMI: /projappl/project_465000454/containers_dev/wildfires_wise/develop_python-3.11_ubuntu-22.04_358aea939ba8.sif

Joonasko commented 4 days ago

I tried running a small test using that container, but it fails due to a segmentation fault:

kolstela@uan03:/projappl/project_465000454/containers_dev/wildfires_wise> singularity shell --bind '/projappl/project_465000454/kolstela/wise_lumi_container/wise_lumi_files:/testjobs' --bind '/scratch/project_465000454/kolstela/wise_outputs:/testjobs/testjobs/area1/Outputs' --bind '/scratch/project_465000454/kolstela/wise_outputs:/testjobs/testjobs/area2/Outputs' --bind '/scratch/project_465000454/kolstela/wise_outputs:/testjobs/testjobs/area3/Outputs' --bind '/scratch/project_465000454/tmp/a1vz:/input_data' develop_python-3.11_ubuntu-22.04_358aea939ba8.sif
Apptainer> run_wise -year_start 1990 -year_end 1990 -month_start 06 -month_end 06 -day_start 06 -day_end 06
running run_wise.py
running ncdf_edits_multiarea.py
ncdf_edits_multiarea.py done, starting modify_fgmj.py
running .fgmj modifier
fgmj file modified
fgmj file modified
fgmj file modified
modify_fgmj.py done
launching WISE runs
/usr/bin/wise: line 2: 186817 Segmentation fault      LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/wise /usr/lib/wise/wise "$@"
/usr/bin/wise: line 2: 191468 Segmentation fault      LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/wise /usr/lib/wise/wise "$@"
/usr/bin/wise: line 2: 191688 Segmentation fault      LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/wise /usr/lib/wise/wise "$@"

I ran ldd for the wise installation in the container, it seems to be missing some dependencies (libfuel, libfwi etc)? I got the following:

Apptainer> ldd /usr/lib/wise/wise
        linux-vdso.so.1 (0x00007ffc3f319000)
        libfwi.so.1 => not found
        libfuel.so.1 => not found
        libgrid.so.1 => not found
        libproject.so.1 => not found
        libkmllib.so.1 => not found
        libREDappWrapper.so.1 => not found
        libWTime.so.2 => not found
        libMultithread.so.1 => not found
        libhssmath.so.4 => not found
        libhssgeography.so.2 => not found
        libpaho-mqtt3a.so.1 => not found
        libpaho-mqttpp3.so.1 => not found
        libgdal.so.30 => /lib/libgdal.so.30 (0x00007f40d6888000)
        libboost_program_options.so.1.81.0 => not found
        libquadmath.so.0 => /lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f40d683e000)
        libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f40d6612000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f40d652b000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f40d650b000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f40d62e2000)
        libheif.so.1 => /lib/x86_64-linux-gnu/libheif.so.1 (0x00007f40d625f000)
        libarmadillo.so.10 => /lib/libarmadillo.so.10 (0x00007f40d624b000)
        libpoppler.so.118 => /lib/x86_64-linux-gnu/libpoppler.so.118 (0x00007f40d5eef000)
        libjson-c.so.5 => /lib/x86_64-linux-gnu/libjson-c.so.5 (0x00007f40d5edc000)
        libfreexl.so.1 => /lib/x86_64-linux-gnu/libfreexl.so.1 (0x00007f40d5ed0000)
        libqhull_r.so.8.0 => /lib/x86_64-linux-gnu/libqhull_r.so.8.0 (0x00007f40d5e5d000)
        libgeos_c.so.1 => /lib/x86_64-linux-gnu/libgeos_c.so.1 (0x00007f40d5e1e000)
        libwebp.so.7 => /lib/x86_64-linux-gnu/libwebp.so.7 (0x00007f40d5db1000)
        libodbc.so.2 => /lib/x86_64-linux-gnu/libodbc.so.2 (0x00007f40d5d40000)
        libodbcinst.so.2 => /lib/x86_64-linux-gnu/libodbcinst.so.2 (0x00007f40d5d2b000)
        libkmlbase.so.1 => /lib/x86_64-linux-gnu/libkmlbase.so.1 (0x00007f40d5d0e000)
        libkmldom.so.1 => /lib/x86_64-linux-gnu/libkmldom.so.1 (0x00007f40d5c6e000)
        libkmlengine.so.1 => /lib/x86_64-linux-gnu/libkmlengine.so.1 (0x00007f40d5c35000)
        libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f40d5c04000)
        libxerces-c-3.2.so => /lib/x86_64-linux-gnu/libxerces-c-3.2.so (0x00007f40d58ae000)
        libopenjp2.so.7 => /lib/x86_64-linux-gnu/libopenjp2.so.7 (0x00007f40d5856000)
        libnetcdf.so.19 => /usr/local/lib/libnetcdf.so.19 (0x00007f40d5680000)
        libhdf5_serial.so.103 => /lib/x86_64-linux-gnu/libhdf5_serial.so.103 (0x00007f40d52ec000)
        libmfhdfalt.so.0 => /lib/libmfhdfalt.so.0 (0x00007f40d52c2000)
        libdfalt.so.0 => /lib/libdfalt.so.0 (0x00007f40d521d000)
        libogdi.so.4.1 => /lib/libogdi.so.4.1 (0x00007f40d51ff000)
        libgif.so.7 => /lib/x86_64-linux-gnu/libgif.so.7 (0x00007f40d51f4000)
        libcharls.so.2 => /lib/x86_64-linux-gnu/libcharls.so.2 (0x00007f40d51a3000)
        libgeotiff.so.5 => /lib/x86_64-linux-gnu/libgeotiff.so.5 (0x00007f40d516e000)
        libpng16.so.16 => /lib/x86_64-linux-gnu/libpng16.so.16 (0x00007f40d5133000)
        libcfitsio.so.9 => /lib/x86_64-linux-gnu/libcfitsio.so.9 (0x00007f40d4e2c000)
        libpq.so.5 => /lib/x86_64-linux-gnu/libpq.so.5 (0x00007f40d4dd5000)
        liblz4.so.1 => /lib/x86_64-linux-gnu/liblz4.so.1 (0x00007f40d4db5000)
        libblosc.so.1 => /lib/x86_64-linux-gnu/libblosc.so.1 (0x00007f40d4da4000)
        liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00007f40d4d79000)
        libproj.so.22 => /lib/x86_64-linux-gnu/libproj.so.22 (0x00007f40d4a10000)
        libsqlite3.so.0 => /lib/x86_64-linux-gnu/libsqlite3.so.0 (0x00007f40d48c3000)
        libtiff.so.5 => /lib/x86_64-linux-gnu/libtiff.so.5 (0x00007f40d4839000)
        libjpeg.so.8 => /lib/x86_64-linux-gnu/libjpeg.so.8 (0x00007f40d47b8000)
        libdeflate.so.0 => /lib/x86_64-linux-gnu/libdeflate.so.0 (0x00007f40d4794000)
        libspatialite.so.7 => /lib/x86_64-linux-gnu/libspatialite.so.7 (0x00007f40d3fb2000)
        libpcre2-8.so.0 => /lib/x86_64-linux-gnu/libpcre2-8.so.0 (0x00007f40d3f1b000)
        libcurl.so.4 => /lib/x86_64-linux-gnu/libcurl.so.4 (0x00007f40d3e74000)
        libfyba.so.0 => /lib/x86_64-linux-gnu/libfyba.so.0 (0x00007f40d3e1a000)
        libxml2.so.2 => /lib/x86_64-linux-gnu/libxml2.so.2 (0x00007f40d3c38000)
        libmysqlclient.so.21 => /lib/x86_64-linux-gnu/libmysqlclient.so.21 (0x00007f40d35ab000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f40d358f000)
        libzstd.so.1 => /lib/x86_64-linux-gnu/libzstd.so.1 (0x00007f40d34c0000)
        libcrypto.so.3 => /lib/x86_64-linux-gnu/libcrypto.so.3 (0x00007f40d307c000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f40d8135000)
        libaom.so.3 => /lib/x86_64-linux-gnu/libaom.so.3 (0x00007f40d2b0a000)
        libde265.so.0 => /lib/x86_64-linux-gnu/libde265.so.0 (0x00007f40d2a56000)
        libx265.so.199 => /lib/x86_64-linux-gnu/libx265.so.199 (0x00007f40d1af1000)
        libdav1d.so.5 => /lib/x86_64-linux-gnu/libdav1d.so.5 (0x00007f40d196b000)
        libblas.so.3 => /lib/x86_64-linux-gnu/libblas.so.3 (0x00007f40d18c5000)
        liblapack.so.3 => /lib/x86_64-linux-gnu/liblapack.so.3 (0x00007f40d118a000)
        libarpack.so.2 => /lib/x86_64-linux-gnu/libarpack.so.2 (0x00007f40d1142000)
        libsuperlu.so.5 => /lib/x86_64-linux-gnu/libsuperlu.so.5 (0x00007f40d10d0000)
        libfreetype.so.6 => /lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007f40d1008000)
        libfontconfig.so.1 => /lib/x86_64-linux-gnu/libfontconfig.so.1 (0x00007f40d0fbe000)
        liblcms2.so.2 => /lib/x86_64-linux-gnu/liblcms2.so.2 (0x00007f40d0f5c000)
        libnss3.so => /lib/x86_64-linux-gnu/libnss3.so (0x00007f40d0e29000)
        libsmime3.so => /lib/x86_64-linux-gnu/libsmime3.so (0x00007f40d0dff000)
        libplc4.so => /lib/x86_64-linux-gnu/libplc4.so (0x00007f40d0df8000)
        libnspr4.so => /lib/x86_64-linux-gnu/libnspr4.so (0x00007f40d0db8000)
        libgeos.so.3.10.2 => /lib/x86_64-linux-gnu/libgeos.so.3.10.2 (0x00007f40d0bad000)
        libltdl.so.7 => /lib/x86_64-linux-gnu/libltdl.so.7 (0x00007f40d0ba0000)
        libminizip.so.1 => /lib/x86_64-linux-gnu/libminizip.so.1 (0x00007f40d0800000)
        liburiparser.so.1 => /lib/x86_64-linux-gnu/liburiparser.so.1 (0x00007f40d0b89000)
        libcurl-gnutls.so.4 => /lib/x86_64-linux-gnu/libcurl-gnutls.so.4 (0x00007f40d0ae7000)
        libicuuc.so.70 => /lib/x86_64-linux-gnu/libicuuc.so.70 (0x00007f40d0605000)
        libhdf5_hl.so.310 => /usr/local/lib/libhdf5_hl.so.310 (0x00007f40d0ac0000)
        libhdf5.so.310 => /usr/local/lib/libhdf5.so.310 (0x00007f40d01ab000)
        libsz.so.2 => /lib/x86_64-linux-gnu/libsz.so.2 (0x00007f40d0abb000)
        libtirpc.so.3 => /lib/x86_64-linux-gnu/libtirpc.so.3 (0x00007f40d0a8d000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f40d0a88000)
        libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00007f40d0a73000)
        libssl.so.3 => /lib/x86_64-linux-gnu/libssl.so.3 (0x00007f40d0107000)
        libgssapi_krb5.so.2 => /lib/x86_64-linux-gnu/libgssapi_krb5.so.2 (0x00007f40d0a1f000)
        libldap-2.5.so.0 => /lib/x86_64-linux-gnu/libldap-2.5.so.0 (0x00007f40d00a8000)
        libsnappy.so.1 => /lib/x86_64-linux-gnu/libsnappy.so.1 (0x00007f40d0a15000)
        libjbig.so.0 => /lib/x86_64-linux-gnu/libjbig.so.0 (0x00007f40d0097000)
        librttopo.so.1 => /lib/x86_64-linux-gnu/librttopo.so.1 (0x00007f40d0024000)
        libnghttp2.so.14 => /lib/x86_64-linux-gnu/libnghttp2.so.14 (0x00007f40cfffa000)
        libidn2.so.0 => /lib/x86_64-linux-gnu/libidn2.so.0 (0x00007f40cffd9000)
        librtmp.so.1 => /lib/x86_64-linux-gnu/librtmp.so.1 (0x00007f40cffba000)
        libssh.so.4 => /lib/x86_64-linux-gnu/libssh.so.4 (0x00007f40cff4d000)
        libpsl.so.5 => /lib/x86_64-linux-gnu/libpsl.so.5 (0x00007f40cff39000)
        liblber-2.5.so.0 => /lib/x86_64-linux-gnu/liblber-2.5.so.0 (0x00007f40cff28000)
        libbrotlidec.so.1 => /lib/x86_64-linux-gnu/libbrotlidec.so.1 (0x00007f40cff1a000)
        libfyut.so.0 => /lib/x86_64-linux-gnu/libfyut.so.0 (0x00007f40cff0f000)
        libfygm.so.0 => /lib/x86_64-linux-gnu/libfygm.so.0 (0x00007f40cff06000)
        libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007f40cfef2000)
        libnuma.so.1 => /lib/x86_64-linux-gnu/libnuma.so.1 (0x00007f40cfee5000)
        libgfortran.so.5 => /lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007f40cfc0a000)
        libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00007f40cfc01000)
        libnssutil3.so => /lib/x86_64-linux-gnu/libnssutil3.so (0x00007f40cfbce000)
        libplds4.so => /lib/x86_64-linux-gnu/libplds4.so (0x00007f40cfbc9000)
        libnettle.so.8 => /lib/x86_64-linux-gnu/libnettle.so.8 (0x00007f40cfb83000)
        libgnutls.so.30 => /lib/x86_64-linux-gnu/libgnutls.so.30 (0x00007f40cf998000)
        libicudata.so.70 => /lib/x86_64-linux-gnu/libicudata.so.70 (0x00007f40cdd7a000)
        libaec.so.0 => /lib/x86_64-linux-gnu/libaec.so.0 (0x00007f40cdd71000)
        libkrb5.so.3 => /lib/x86_64-linux-gnu/libkrb5.so.3 (0x00007f40cdca6000)
        libk5crypto.so.3 => /lib/x86_64-linux-gnu/libk5crypto.so.3 (0x00007f40cdc77000)
        libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2 (0x00007f40cdc71000)
        libkrb5support.so.0 => /lib/x86_64-linux-gnu/libkrb5support.so.0 (0x00007f40cdc63000)
        libsasl2.so.2 => /lib/x86_64-linux-gnu/libsasl2.so.2 (0x00007f40cdc48000)
        libunistring.so.2 => /lib/x86_64-linux-gnu/libunistring.so.2 (0x00007f40cda9c000)
        libhogweed.so.6 => /lib/x86_64-linux-gnu/libhogweed.so.6 (0x00007f40cda54000)
        libgmp.so.10 => /lib/x86_64-linux-gnu/libgmp.so.10 (0x00007f40cd9d2000)
        libbrotlicommon.so.1 => /lib/x86_64-linux-gnu/libbrotlicommon.so.1 (0x00007f40cd9af000)
        libp11-kit.so.0 => /lib/x86_64-linux-gnu/libp11-kit.so.0 (0x00007f40cd874000)
        libtasn1.so.6 => /lib/x86_64-linux-gnu/libtasn1.so.6 (0x00007f40cd85a000)
        libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1 (0x00007f40cd853000)
        libffi.so.8 => /lib/x86_64-linux-gnu/libffi.so.8 (0x00007f40cd846000)

I do not know if this is actually the fault of the missing dependencies (I also tried running this locally in case I could not get memory from LUMI), but still ended up in the same error and it dumped the core. I do not know if this is of any help, but here is my def file for creating a container with a working version of WISE:

BootStrap: library
From: ubuntu:22.04

%runscript
  wise -r 4 -f 0 -t /testjobs/area1/job.fgmj

%post

  mkdir -p /opt/jobs/examples
  mkdir -p /wise_deb
  mkdir -p /testjobs
  apt-get update && apt-get install -y libgdal30
  apt-get install wget
  apt-get install unzip
  apt-get -y install nodejs
  apt-get -y install default-jre
  apt-get -y install npm
  apt-get install -y python3
  apt-get -y install vim
  apt-get -y install python3-pip
  pip3 install netCDF4
  pip3 install xarray
  pip3 install argparse
  pip3 install numpy
  pip3 install pandas
  pip3 install datetime
  pip3 install fiona pyogrio
  pip3 install rasterio
  pip3 install pytest    

  wget -c https://github.com/WISE-Developers/WISE_Application/releases/download/1.0.6-beta.5/wise-ubuntu2204-1.0.6-beta.5.deb -O wise_deb/wise_ubuntu2204.deb

  apt-get install -y /wise_deb/wise_ubuntu2204.deb

  apt-get install -y build-essential git
  git clone https://github.com/WISE-Developers/WISE_Application.git wise_git_test

  #npm audit fix --force

  mkdir -p /opt/wise && mkdir -p /opt/builder %% mkdir -p /opt/jobs && mkdir -p /opt/jobs/examples/test

  wget -c https://raw.githubusercontent.com/WISE-Developers/wise_demo/main/demo_data/test_helpers/sample_config.json -O /opt/jobs/config.json

  wget -c https://github.com/WISE-Developers/WISE_Builder_Component/releases/download/1.0.6-beta.5/WISE_Builder-1.0.6-beta.5.zip -o WISE_Builder-1.0.6-beta.5.zip

  unzip WISE_Builder*.zip -d /opt/builder && rm WISE_Builder*.zip

  git clone https://github.com/WISE-Developers/WISE_JS_API.git /opt/api && unzip /opt/api/files/dogrib.zip -d /opt/jobs/examples/test

  cp /opt/api/files/defaults.json /opt/jobs/defaults.json

  npm --prefix /opt/api i && npm config set WISE_JS_API:job_directory /opt/jobs

  chmod 777 /opt/builder/WISE_Builder.jar
  chmod -R 777 /opt/builder/WISE_Builder_lib/

  java -jar /opt/builder/WISE_Builder.jar --version

 # cd /opt/api;
 # 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;

%files
#testjobs testjobs 
%environment

@jaantollander

Joonasko commented 4 days ago

Actually I checked a working container installation of WISE and it is missing the same dependencies so that is not the issue. Here is the output from running the container you provided (I ran on my own pc):


joonasko@kostelj22k:/mnt/d/wise_development/wise_container$ singularity shell --bind wise_lumi_files:/testjobs --bind wise_outputs:/testjobs/testjobs/area1/Outputs --bind wise_outputs:/testjobs/testjobs/area2/Outputs --bind wise_outputs:/testjobs/testjobs/area3/Outputs --bind a1vz_nc_files:/input_data wise_jaan.sif
Apptainer> ls
a1vz_nc_files  wise_jaan.sif  wise_lumi_files  wise_outputs
Apptainer> run_wise
ruusage: run_wise [-h] -year_start YEAR_START -month_start MONTH_START -day_start DAY_START -year_end YEAR_END -month_end MONTH_END -day_end DAY_END
run_wise: error: the following arguments are required: -year_start, -month_start, -day_start, -year_end, -month_end, -day_end
Apptainer> run_wise -year_start 1990 -year_end 1990 -month_start 06 -month_end 06 -day_start 06 -day_end 06
running run_wise.py
running ncdf_edits_multiarea.py
ncdf_edits_multiarea.py done, starting modify_fgmj.py
running .fgmj modifier
fgmj file modified
fgmj file modified
fgmj file modified
modify_fgmj.py done
launching WISE runs
/usr/bin/wise: line 2:   981 Segmentation fault      (core dumped) LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/wise /usr/lib/wise/wise "$@"
/usr/bin/wise: line 2:  1014 Segmentation fault      (core dumped) LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/wise /usr/lib/wise/wise "$@"
/usr/bin/wise: line 2:  1041 Segmentation fault      (core dumped) LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/wise /usr/lib/wise/wise "$@"
jaantollander commented 4 days ago

Thanks for testing. We need to investigate this further.

jaantollander commented 3 days ago

Wise dependencies are not the issue. The /usr/bin/wise executable is a Bash script that runs as follows:

#!/bin/bash
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/wise /usr/lib/wise/wise "$@"
Joonasko commented 3 days ago

I tested the input data using my own container, and then again with the one you provided. I used both with singularity shell, binded the same input and output directories and ran the same testcase (area1) with the same data. The "Warning 1: Self-intersection..." means that the model is correctly calculating the fire spread, but in the second test it again gives the "Segmentation fault (core dumped) error:

joonasko@kostelj22k:/mnt/d/wise_development/wise_container$ singularity shell --bind wise_lumi_files:/testjobs --bind wise_outputs:/testjobs/testjobs/area1/Outputs --bind wise_outputs:/testjobs/testjobs/area2/Outputs --bind wise_outputs:/testjobs/testjobs/area3/Outputs --bind a1vz_nc_files:/input_data ../wise_local.sif
Singularity> ls
a1vz_nc_files  wise_jaan.sif  wise_lumi_files  wise_outputs
Singularity> wise /testjobs/test
test.txt  testjobs/
Singularity> wise /testjobs/testjobs/area1/job.fgmj

Warning 1: Self-intersection at or near point 24.153023160103128 64.00681670767473
Warning 1: Self-intersection at or near point 24.153023160103128 64.00681670767473
Warning 1: Self-intersection at or near point 24.148732825123346 64.005241633507239
Warning 1: Self-intersection at or near point 24.156380229055046 64.005979798088092
Warning 1: Ring Self-intersection at or near point 24.158934098172498 64.003244716210048
Warning 1: Self-intersection at or near point 24.153023160103128 64.00681670767473
^Z
[1]+  Stopped                 wise /testjobs/testjobs/area1/job.fgmj
Singularity> exit
exit
There are stopped jobs.
Singularity> exit
exit
joonasko@kostelj22k:/mnt/d/wise_development/wise_container$ singularity shell --bind wise_lumi_files:/testjobs --bind wise_outputs:/testjobs/testjobs/area1/Outputs --bind wise_outputs:/testjobs/testjobs/area2/Outputs --bind wise_outputs:/testjobs/testjobs/area3/Outputs --bind a1vz_nc_files:/input_data wise_jaan.sif
Apptainer> wise /testjobs/testjobs/area1/job.fgmj

/usr/bin/wise: line 2:   339 Segmentation fault      (core dumped) LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/wise /usr/lib/wise/wise "$@"

Is there anything I can do to help testing this?

jaantollander commented 3 days ago

I'll downgrade the WISE_Application version to 1.0.6-beta.5. My container is using 1.0.6-beta.6, maybe that is causing the issue.

jaantollander commented 3 days ago

I deployed new container /projappl/project_465000454/containers_dev/wildfires_wise/develop_python-3.11_ubuntu-22.04_117e590badbc.sif with version 1.0.6-beta.5. Try it to see if it no longer segfaults, otherwise we need to dig deeper.

Joonasko commented 3 days ago

Thanks Jaan, I tested the new container but it still ends up in the same error:

joonasko@kostelj22k:/mnt/d/wise_development/wise_container$ singularity shell --bind wise_lumi_files:/testjobs --bind wise_outputs:/testjobs/testjobs/area1/Outputs --bind wise_outputs:/testjobs/testjobs/area2/Outputs --bind wise_outputs:/testjobs/testjobs/area3/Outputs --bind a1vz_nc_files:/input_data wise_jaan_beta_5.sif
Apptainer> wise /testjobs/testjobs/area1/job.fgmj
/usr/bin/wise: line 2:  3707 Segmentation fault      (core dumped) LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/wise /usr/lib/wise/wise "$@"

I checked and this is the same WISE version I have been working with.

I am doing these tests on my own pc, not LUMI. But that should not be an issue with the containers? Can I produce some error / log messages for you somehow to give more information?