run_multi_step_test for make_fragments failed while running 1.submit.py...Aborting!
Running 1.submit.py...
Command line: cd /home/benchmark/working_dir && unset __PYVENV_LAUNCHER__ && . /home/benchmark/prefix/nobu-5/linux/python_virtual_environments/python-3.8/f7290385dceb30c19a02dbf8bd4617f9/bin/activate && python 1.submit.py
Loaded variables from 0.compile.output.json: dict_keys(['build_command_line', 'output', 'res'])
FRAG DB PREFIX /home/benchmark/prefix/fdbft
Install for MiniConda is detected, skipping installation procedure...
Updating conda base...
unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/linux/conda/bin/activate && conda update --all --yes
Channels:
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): - \ | / done
Solving environment: \ | done
# All requested packages already installed.
Setting up Conda for Python-2.7 virtual environment...
cd /home/benchmark/working_dir && unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/linux/conda/bin/activate && ( conda create --quiet --yes --prefix /home/benchmark/working_dir/.conda-python-2.7 python=2.7 || ( conda clean --yes && conda create --quiet --yes --prefix /home/benchmark/working_dir/.conda-python-2.7 python=2.7 ) )
Channels:
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/benchmark/working_dir/.conda-python-2.7
added / updated specs:
- python=2.7
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
ca-certificates pkgs/main/linux-64::ca-certificates-2024.12.31-h06a4308_0
certifi pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
libffi pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1
libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
ncurses pkgs/main/linux-64::ncurses-6.4-h6a678d5_0
pip pkgs/main/linux-64::pip-19.3.1-py27_0
python pkgs/main/linux-64::python-2.7.18-h42bf7aa_3
readline pkgs/main/linux-64::readline-8.2-h5eee18b_0
setuptools pkgs/main/linux-64::setuptools-44.0.0-py27_0
sqlite pkgs/main/linux-64::sqlite-3.45.3-h5eee18b_0
tk pkgs/main/linux-64::tk-8.6.14-h39e8969_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
zlib pkgs/main/linux-64::zlib-1.2.13-h5eee18b_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Getting python configuration info...
unset __PYVENV_LAUNCHER__ && cd /home/benchmark/working_dir/.conda-python-2.7/bin && PATH=.:$PATH && /home/benchmark/working_dir/.conda-python-2.7/bin/python2.7 /home/benchmark/working_dir/.conda-python-2.7/bin/python2.7-config --prefix --includes
/home/benchmark/working_dir/.conda-python-2.7
-I/home/benchmark/working_dir/.conda-python-2.7/include/python2.7 -I/home/benchmark/working_dir/.conda-python-2.7/include/python2.7
Adding extra extra channel bioconda...
unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/linux/conda/bin/activate && conda activate /home/benchmark/working_dir/.conda-python-2.7 && conda config --env --add channels bioconda
Adding extra extra channel compbiocore...
unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/linux/conda/bin/activate && conda activate /home/benchmark/working_dir/.conda-python-2.7 && conda config --env --add channels compbiocore
Setting up extra packages perl perl-if perl-parallel-forkmanager perl-switch perl-text-balanced perl-json...
unset __PYVENV_LAUNCHER__ && unset PYTHONHOME && unset PYTHONPATH && . /home/benchmark/prefix/nobu-5/linux/conda/bin/activate && conda activate /home/benchmark/working_dir/.conda-python-2.7 && conda install --quiet --yes perl perl-if perl-parallel-forkmanager perl-switch perl-text-balanced perl-json
Channels:
- compbiocore
- bioconda
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/benchmark/working_dir/.conda-python-2.7
added / updated specs:
- perl
- perl-if
- perl-json
- perl-parallel-forkmanager
- perl-switch
- perl-text-balanced
The following NEW packages will be INSTALLED:
perl pkgs/main/linux-64::perl-5.38.2-0_h5eee18b_perl5
perl-common-sense compbiocore/linux-64::perl-common-sense-3.74-pl526_1
perl-if compbiocore/linux-64::perl-if-0.0608-pl526_1
perl-json compbiocore/linux-64::perl-json-2.90-pl526_1
perl-json-xs compbiocore/linux-64::perl-json-xs-2.34-pl526_1
perl-parallel-for~ compbiocore/linux-64::perl-parallel-forkmanager-1.17-pl526_1
perl-switch compbiocore/linux-64::perl-switch-2.17-pl526_1
perl-text-balanced compbiocore/linux-64::perl-text-balanced-2.03-pl526_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Traceback (most recent call last):
File "/home/benchmark/prefix/nobu-5/linux/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib/python3.8/urllib/request.py", line 1561, in ftp_open
host = socket.gethostbyname(host)
socket.gaierror: [Errno -2] Name or service not known
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "1.submit.py", line 118, in <module>
with closing(request.urlopen("ftp://ftp.rcsb.org/pub/pdb/derived_data/pdb_seqres.txt")) as r:
File "/home/benchmark/prefix/nobu-5/linux/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib/python3.8/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/home/benchmark/prefix/nobu-5/linux/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib/python3.8/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/home/benchmark/prefix/nobu-5/linux/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib/python3.8/urllib/request.py", line 542, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/home/benchmark/prefix/nobu-5/linux/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib/python3.8/urllib/request.py", line 502, in _call_chain
result = func(*args)
File "/home/benchmark/prefix/nobu-5/linux/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib/python3.8/urllib/request.py", line 1563, in ftp_open
raise URLError(msg)
urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>