We have the CCP4 environment loaded (but source before the build/setpath.sh) as it is needed for other dials/xia2 tests.
If I don't load the CCP4 environment then I get a different error:
$ libtbx.python $(libtbx.find_in_repositories iotbx/regression/tst_pdb_as_cif.py)
Converting tst_pdb_as_cif_1.pdb to mmCIF format.
Traceback (most recent call last):
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 106, in <module>
exercise_01()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 37, in exercise_01
logger=null_out(),
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program
task.run()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/programs/pdb_as_cif.py", line 37, in run
txt = model.model_as_mmcif()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif
if self.get_restraints_manager() is not None:
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager
self.setup_restraints_manager()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager
self._process_input_model()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model
use_neutron_distances = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances)
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/utils/__init__.py", line 994, in __init__
if(mon_lib_srv is None): self.mon_lib_srv = monomer_library.server.server()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 399, in __init__
list_cif = mon_lib_list_cif()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 72, in mon_lib_list_cif
strict=strict)
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 65, in __init__
+ ", ".join(mon_lib_env_vars))
mmtbx.monomer_library.server.MonomerLibraryServerError: Cannot find CCP4 monomer library. Please define one of these environment variables: MMTBX_CCP4_MONOMER_LIB, CLIBD_MON
Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078
Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE
________________________________
From: [email protected] on behalf of Nigel Moriarty
Sent: 19 December 2018 16:58:09
To: cctbx mailing list
Subject: Re: [cctbxbb] Broken iotbx/pdb/cif test
I think the best clue was in the origin email you sent me.
expected_type, looped_id.split(":",1)[0], val))
ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7
It's failing to parse a CIF loop. It can't convert "1,7" to a float. Are you pointing your environment to a different monomer library that Phenix?
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.govhttp://CCI.LBL.gov
On Wed, Dec 19, 2018 at 8:42 AM [email protected]mailto:[email protected] mailto:[email protected]> wrote:
Hi Nigel,
As I mentioned in my email, this issue also affects my local builds on both mac and linux. I don't think I am doing any thing particularly odd in my local environments, and the fact that Jenkins also thinks the test is broken suggests that the issue is with the test and not my environment. Graeme also confirmed it was failing for him.
Is there anything in the error message that would suggest the underlying issue?
$ libtbx.python $(libtbx.find_in_repositories iotbx/regression/tst_pdb_as_cif.py)
Converting tst_pdb_as_cif_1.pdb to mmCIF format.
Traceback (most recent call last):
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 106, in <module>
exercise_01()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 37, in exercise_01
logger=null_out(),
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program
task.run()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/programs/pdb_as_cif.py", line 37, in run
txt = model.model_as_mmcif()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif
if self.get_restraints_manager() is not None:
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager
self.setup_restraints_manager()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager
self._process_input_model()
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model
use_neutron_distances = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances)
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__
use_neutron_distances=use_neutron_distances,
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__
use_neutron_distances=use_neutron_distances,
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all
use_neutron_distances=use_neutron_distances,
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom
entry = cif_types.energy_lib_atom(**dict(row))
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__
raise_value_error("Floating-point")
File "/dls/mx-scratch/rjgildea/software/cctbx/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 39, in raise_value_error
expected_type, looped_id.split(":",1)[0], val))
ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7
Cheers,
Richard
Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078
Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE
________________________________
From: [email protected]mailto:[email protected] mailto:[email protected]> on behalf of Nigel Moriarty mailto:[email protected]>
Sent: 19 December 2018 16:29:10
To: cctbx mailing list
Subject: Re: [cctbxbb] Broken iotbx/pdb/cif test
These tests worked when I committed and they work for me now. Also works in BuildBot. Not sure what is the difference between my normal up-to-date Phenix environment, BuildBot and Jenkins that is causing the problems for you.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.govhttp://CCI.LBL.govhttp://CCI.LBL.gov
On Wed, Dec 19, 2018 at 1:11 AM [email protected]mailto:[email protected]mailto:[email protected]> mailto:[email protected]mailto:[email protected]>> wrote:
According to Jenkins these two tests have been broken for several days - does anyone know what the issue is and could a fix be applied? Both look like the same error.
iotbx/regression/tst_pdb_as_cif.py
iotbx/regression/tst_data_manager.py
These have been failing since this commit:
https://github.com/cctbx/cctbx_project/commit/2c119fcf012ca4cc60dfce231902c6...
The tests also fail locally for me (not just on Jenkins).
Cheers,
Richard
Traceback (most recent call last):
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 106, in <module>
exercise_01()
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_pdb_as_cif.py", line 37, in exercise_01
logger=null_out(),
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program
task.run()
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/programs/pdb_as_cif.py", line 37, in run
txt = model.model_as_mmcif()
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif
if self.get_restraints_manager() is not None:
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager
self.setup_restraints_manager()
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager
self._process_input_model()
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model
use_neutron_distances = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances)
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__
use_neutron_distances=use_neutron_distances,
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__
use_neutron_distances=use_neutron_distances,
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all
use_neutron_distances=use_neutron_distances,
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom
entry = cif_types.energy_lib_atom(**dict(row))
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__
raise_value_error("Floating-point")
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 39, in raise_value_error
expected_type, looped_id.split(":",1)[0], val))
ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7
Traceback (most recent call last):
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py", line 532, in <module>
test_model_datatype()
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/iotbx/regression/tst_data_manager.py", line 233, in test_model_datatype
dm.get_model().model_as_mmcif(), overwrite=True)
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 879, in model_as_mmcif
if self.get_restraints_manager() is not None:
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 622, in get_restraints_manager
self.setup_restraints_manager()
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 1042, in setup_restraints_manager
self._process_input_model()
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/model/model.py", line 959, in _process_input_model
use_neutron_distances = self._pdb_interpretation_params.pdb_interpretation.use_neutron_distances)
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/utils/__init__.py", line 998, in __init__
use_neutron_distances=use_neutron_distances,
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 675, in __init__
use_neutron_distances=use_neutron_distances,
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 689, in convert_all
use_neutron_distances=use_neutron_distances,
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/server.py", line 700, in convert_lib_atom
entry = cif_types.energy_lib_atom(**dict(row))
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 49, in __init__
raise_value_error("Floating-point")
File "/scratch/jenkins_slave/workspace/cctbx_tests/build_dials/modules/cctbx_project/mmtbx/monomer_library/cif_types.py", line 39, in raise_value_error
expected_type, looped_id.split(":",1)[0], val))
ValueError: Floating-point value expected in CIF file: _lib_atom.ion_radius 1,7
Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078
Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE
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