Singularity container fails

[richelbilderbeek]

Copied from this error log:

********************************
Run 'ormr::ormr_report'
********************************
Create the environment, will check if it already exists

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1080, in __call__
        return func(*args, **kwargs)
      File "/miniconda/lib/python3.9/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/miniconda/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
        return getattr(module, func_name)(args, parser)
      File "/miniconda/lib/python3.9/site-packages/conda/cli/main_run.py", line 25, in execute
        script_caller, command_args = wrap_subprocess_call(on_win, context.root_prefix, prefix,
      File "/miniconda/lib/python3.9/site-packages/conda/utils.py", line 403, in wrap_subprocess_call
        with Utf8NamedTemporaryFile(mode='w', prefix=tmp_prefix, delete=False) as fh:
      File "/miniconda/lib/python3.9/site-packages/conda/auxlib/compat.py", line 88, in Utf8NamedTemporaryFile
        return NamedTemporaryFile(
      File "/miniconda/lib/python3.9/tempfile.py", line 541, in NamedTemporaryFile
        (fd, name) = _mkstemp_inner(dir, prefix, suffix, flags, output_type)
      File "/miniconda/lib/python3.9/tempfile.py", line 251, in _mkstemp_inner
        fd = _os.open(file, flags, 0o600)
    OSError: [Errno 30] Read-only file system: '/opt/ormr/.tmp76bmdb24'

`$ /miniconda/bin/conda run --prefix /opt/ormr --no-capture-output python -c import os; print(os.environ['PATH'])`

The error occurs in the test section of the Singularity script, when running ormr::ormr_report(ormr_folder_name = "/opt/ormr", verbose = TRUE). What happens is that ormr_report tries to install conda again, instead of detecting it.

[richelbilderbeek]

Error originates in create_conda_env, as the next message is never shown:

[richelbilderbeek]

From here:

#!/bin/bash

# See also https://www.rocker-project.org/use/singularity/

# Main parameters for the script with default values
PORT=${PORT:-8787}
USER=$(whoami)
PASSWORD=${PASSWORD:-notsafe}
TMPDIR=${TMPDIR:-tmp}
CONTAINER="rstudio_latest.sif"  # path to singularity container (will be automatically downloaded)

# Set-up temporary paths
RSTUDIO_TMP="${TMPDIR}/$(echo -n $CONDA_PREFIX | md5sum | awk '{print $1}')"
mkdir -p $RSTUDIO_TMP/{run,var-lib-rstudio-server,local-share-rstudio}

R_BIN=$CONDA_PREFIX/bin/R
PY_BIN=$CONDA_PREFIX/bin/python

if [ ! -f $CONTAINER ]; then
	singularity build --fakeroot $CONTAINER Singularity
fi

if [ -z "$CONDA_PREFIX" ]; then
  echo "Activate a conda env or specify \$CONDA_PREFIX"
  exit 1
fi

echo "Starting rstudio service on port $PORT ..."
singularity exec \
	--bind $RSTUDIO_TMP/run:/run \
	--bind $RSTUDIO_TMP/var-lib-rstudio-server:/var/lib/rstudio-server \
	--bind /sys/fs/cgroup/:/sys/fs/cgroup/:ro \
	--bind database.conf:/etc/rstudio/database.conf \
	--bind rsession.conf:/etc/rstudio/rsession.conf \
	--bind $RSTUDIO_TMP/local-share-rstudio:/home/rstudio/.local/share/rstudio \
	--bind ${CONDA_PREFIX}:${CONDA_PREFIX} \
	--bind $HOME/.config/rstudio:/home/rstudio/.config/rstudio \
        `# add additional bind mount required for your use-case` \
	--bind /data:/data \
	--env CONDA_PREFIX=$CONDA_PREFIX \
	--env RSTUDIO_WHICH_R=$R_BIN \
	--env RETICULATE_PYTHON=$PY_BIN \
	--env PASSWORD=$PASSWORD \
	--env PORT=$PORT \
	--env USER=$USER \
	rstudio_latest.sif \
	/init.sh

[richelbilderbeek]

So it is reticulate::use_condaenv that causes the crash:

[richelbilderbeek]

Already at https://github.com/richelbilderbeek/reticulate_on_singularity this has been failing.

Here is the most relevant part of the Singularity script:

    # Install reticulate
    Rscript -e 'install.packages("reticulate")'

    # Create the Conda environment at a system folder
    Rscript -e 'reticulate::conda_create(envname = "/opt/ormr")'
    Rscript -e 'reticulate::use_condaenv(condaenv = "/opt/ormr")'

Error from here:

****************************
Run 'reticulate::use_condaenv'
****************************

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1080, in __call__
        return func(*args, **kwargs)
      File "/miniconda/lib/python3.9/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/miniconda/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
        return getattr(module, func_name)(args, parser)
      File "/miniconda/lib/python3.9/site-packages/conda/cli/main_run.py", line 25, in execute
        script_caller, command_args = wrap_subprocess_call(on_win, context.root_prefix, prefix,
      File "/miniconda/lib/python3.9/site-packages/conda/utils.py", line 403, in wrap_subprocess_call
        with Utf8NamedTemporaryFile(mode='w', prefix=tmp_prefix, delete=False) as fh:
      File "/miniconda/lib/python3.9/site-packages/conda/auxlib/compat.py", line 88, in Utf8NamedTemporaryFile
        return NamedTemporaryFile(
      File "/miniconda/lib/python3.9/tempfile.py", line 541, in NamedTemporaryFile
        (fd, name) = _mkstemp_inner(dir, prefix, suffix, flags, output_type)
      File "/miniconda/lib/python3.9/tempfile.py", line 251, in _mkstemp_inner
        fd = _os.open(file, flags, 0o600)
    OSError: [Errno 30] Read-only file system: '/opt/ormr/.tmppbootsp1'

`$ /miniconda/bin/conda run --prefix /opt/ormr --no-capture-output python -c import os; print(os.environ['PATH'])`

  environment variables:
                 CIO_TEST=<not set>
               CONDA_ROOT=/miniconda
           CURL_CA_BUNDLE=<not set>
        GITHUB_EVENT_PATH=/github/workflow/event.json
              GITHUB_PATH=/__w/_temp/_runner_file_commands/add_path_df883f6b-edaa-4c5d-980d-a08c
                          62a26ace
                   GOPATH=/go
          LD_LIBRARY_PATH=/usr/lib/R/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-
                          java/lib/server:/.singularity.d/libs
                     PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>
             SUDO_COMMAND=/usr/local/bin/singularity --quiet build ormr.sif Singularity
                 SUDO_GID=0
                 SUDO_UID=0
                SUDO_USER=root
                USER_PATH=/go/bin:/usr/local/go/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/us
                          r/bin:/sbin:/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/loc
                          al/sbin

     active environment : None
       user config file : /root/.condarc
 populated config files : 
          conda version : 4.11.0
    conda-build version : not installed
         python version : 3.9.5.final.0
       virtual packages : __linux=5.11.0=0
                          __glibc=2.33=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /miniconda  (read only)
      conda av data dir : /miniconda/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /miniconda/pkgs
                          /root/.conda/pkgs
       envs directories : /root/.conda/envs
                          /miniconda/envs
               platform : linux-64
             user-agent : conda/4.11.0 requests/2.27.1 CPython/3.9.5 Linux/5.11.0-1027-azure debian/ glibc/2.33
                UID:GID : 0:0
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

Error in Sys.setenv(PATH = new_path) : wrong length for argument
Calls: <Anonymous> ... use_python -> python_config -> python_munge_path -> Sys.setenv
In addition: Warning message:
In system2(conda, c("run", in_env, run_args, shQuote(cmd), args),  :
  running command ''/miniconda/bin/conda' run --prefix '/opt/ormr' --no-capture-output 'python' -c "import os; print(os.environ['PATH'])"' had status 1
Execution halted

[richelbilderbeek]

This Issue depends on richelbilderbeek/reticulate_on_singularity#1

[richelbilderbeek]

List of places where similar problems are posted:

• GenoCAE, Docker
• GenoCAE, regular build
• ormr
• reticulate_on_singularity
• Stack Overflow