Task 38583152
| Name | JNK1_A10_A05_r3_1-QUICO_ATM_GAFF2_LOMAP_JNK1-0-5-RND3327_5 |
| Workunit | 31545009 |
| Created | 13 Dec 2025, 20:50:17 UTC |
| Sent | 13 Dec 2025, 20:50:20 UTC |
| Report deadline | 18 Dec 2025, 20:50:20 UTC |
| Received | 13 Dec 2025, 20:53:04 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 628374 |
| Run time | 36 sec |
| CPU time | 2 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 84,054.54 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 594.98 MB |
| Peak swap size | 31.22 GB |
| Peak disk usage | 2.76 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2025-12-13 21:50:30 (75101): wrapper (8.1.26018): starting
2025-12-13 21:50:44 (75101): wrapper: running bin/python (bin/conda-unpack)
2025-12-13 21:50:44 (75101): wrapper: created child process 75130
2025-12-13 21:50:45 (75101): bin/python exited; CPU time 0.055298
2025-12-13 21:50:45 (75101): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-13 21:50:45 (75101): wrapper: created child process 75131
2025-12-13 21:50:46 (75101): bin/tar exited; CPU time 0.736440
2025-12-13 21:50:46 (75101): wrapper: running bin/bash (run.sh)
2025-12-13 21:50:46 (75101): wrapper: created child process 75142
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/maciek/BOINC/40000/slots/1/bin
+++ dirname /home/maciek/BOINC/40000/slots/1/bin
++ local full_path_env=/home/maciek/BOINC/40000/slots/1
+++ basename /home/maciek/BOINC/40000/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/maciek/BOINC/40000/slots/1
++ CONDA_PREFIX=/home/maciek/BOINC/40000/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/maciek/BOINC/40000/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/maciek/BOINC/40000/slots/1/etc/conda/activate.d
++ '[' -d /home/maciek/BOINC/40000/slots/1/etc/conda/activate.d ']'
+ export PATH=/home/maciek/BOINC/40000/slots/1:/home/maciek/BOINC/40000/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/maciek/BOINC/40000/slots/1:/home/maciek/BOINC/40000/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/maciek/BOINC/40000/slots/1/tmp
+ TMP=/home/maciek/BOINC/40000/slots/1/tmp
+ mkdir -p /home/maciek/BOINC/40000/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/maciek/BOINC/40000/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample does not exist.'
+ echo 'Install ATM and deps'
+ python -m pip list
+ python -m pip install pyaml -v
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
+ python -m pip install --no-dependencies git+https://github.com/Acellera/atm.git -v
Running command git version
git version 2.47.0
Running command git clone --filter=blob:none https://github.com/Acellera/atm.git /home/maciek/BOINC/40000/slots/1/tmp/pip-req-build-_6ngd4hc
Cloning into '/home/maciek/BOINC/40000/slots/1/tmp/pip-req-build-_6ngd4hc'...
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Running command git rev-parse HEAD
fb3bd66350c574830c3fc01598222448ed865c00
Running command git rev-parse HEAD
fb3bd66350c574830c3fc01598222448ed865c00
Running command pip subprocess to install build dependencies
Using pip 24.3.1 from /home/maciek/BOINC/40000/slots/1/lib/python3.11/site-packages/pip (python 3.11)
Collecting setuptools
Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl.metadata
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Collecting setuptools-scm>=8
Obtaining dependency information for setuptools-scm>=8 from https://files.pythonhosted.org/packages/3d/ea/ac2bf868899d0d2e82ef72d350d97a846110c709bacf2d968431576ca915/setuptools_scm-9.2.2-py3-none-any.whl.metadata
Using cached setuptools_scm-9.2.2-py3-none-any.whl.metadata (7.7 kB)
Collecting packaging>=20 (from setuptools-scm>=8)
Obtaining dependency information for packaging>=20 from https://files.pythonhosted.org/packages/20/12/38679034af332785aac8774540895e234f4d07f7545804097de4b666afd8/packaging-25.0-py3-none-any.whl.metadata
Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Using cached setuptools_scm-9.2.2-py3-none-any.whl (62 kB)
Using cached packaging-25.0-py3-none-any.whl (66 kB)
Installing collected packages: setuptools, packaging, setuptools-scm
Creating /home/maciek/BOINC/40000/slots/1/tmp/pip-build-env-hk0auh7n/overlay/bin
changing mode of /home/maciek/BOINC/40000/slots/1/tmp/pip-build-env-hk0auh7n/overlay/bin/setuptools-scm to 755
Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
Running command Getting requirements to build wheel
running egg_info
creating acellera_atm.egg-info
writing acellera_atm.egg-info/PKG-INFO
writing dependency_links to acellera_atm.egg-info/dependency_links.txt
writing entry points to acellera_atm.egg-info/entry_points.txt
writing top-level names to acellera_atm.egg-info/top_level.txt
writing manifest file 'acellera_atm.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'manifest.json' under directory 'atm/apps'
warning: manifest_maker: MANIFEST.in, line 3: 'prune' expects a single <dir_pattern>
adding license file 'LICENSE'
writing manifest file 'acellera_atm.egg-info/SOURCES.txt'
Running command Preparing metadata (pyproject.toml)
running dist_info
creating /home/maciek/BOINC/40000/slots/1/tmp/pip-modern-metadata-hf1chyoq/acellera_atm.egg-info
writing /home/maciek/BOINC/40000/slots/1/tmp/pip-modern-metadata-hf1chyoq/acellera_atm.egg-info/PKG-INFO
writing dependency_links to /home/maciek/BOINC/40000/slots/1/tmp/pip-modern-metadata-hf1chyoq/acellera_atm.egg-info/dependency_links.txt
writing entry points to /home/maciek/BOINC/40000/slots/1/tmp/pip-modern-metadata-hf1chyoq/acellera_atm.egg-info/entry_points.txt
writing top-level names to /home/maciek/BOINC/40000/slots/1/tmp/pip-modern-metadata-hf1chyoq/acellera_atm.egg-info/top_level.txt
writing manifest file '/home/maciek/BOINC/40000/slots/1/tmp/pip-modern-metadata-hf1chyoq/acellera_atm.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'manifest.json' under directory 'atm/apps'
warning: manifest_maker: MANIFEST.in, line 3: 'prune' expects a single <dir_pattern>
adding license file 'LICENSE'
writing manifest file '/home/maciek/BOINC/40000/slots/1/tmp/pip-modern-metadata-hf1chyoq/acellera_atm.egg-info/SOURCES.txt'
creating '/home/maciek/BOINC/40000/slots/1/tmp/pip-modern-metadata-hf1chyoq/acellera_atm-0.1.2.dev2+gfb3bd6635.dist-info'
Running command Building wheel for acellera-atm (pyproject.toml)
running bdist_wheel
running build
running build_py
creating build/lib/atm
copying atm/utils.py -> build/lib/atm
copying atm/rbfe_structprep.py -> build/lib/atm
copying atm/atom_nnp_wrapper.py -> build/lib/atm
copying atm/atomutils.py -> build/lib/atm
copying atm/uwham.py -> build/lib/atm
copying atm/worker.py -> build/lib/atm
copying atm/rbfe_production.py -> build/lib/atm
copying atm/ommsystem.py -> build/lib/atm
copying atm/__init__.py -> build/lib/atm
copying atm/ommreplica.py -> build/lib/atm
running egg_info
writing acellera_atm.egg-info/PKG-INFO
writing dependency_links to acellera_atm.egg-info/dependency_links.txt
writing entry points to acellera_atm.egg-info/entry_points.txt
writing top-level names to acellera_atm.egg-info/top_level.txt
reading manifest template 'MANIFEST.in'
warning: no files found matching 'manifest.json' under directory 'atm/apps'
warning: manifest_maker: MANIFEST.in, line 3: 'prune' expects a single <dir_pattern>
adding license file 'LICENSE'
writing manifest file 'acellera_atm.egg-info/SOURCES.txt'
copying atm/logging.ini -> build/lib/atm
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/atm
copying build/lib/atm/utils.py -> build/bdist.linux-x86_64/wheel/./atm
copying build/lib/atm/rbfe_structprep.py -> build/bdist.linux-x86_64/wheel/./atm
copying build/lib/atm/atom_nnp_wrapper.py -> build/bdist.linux-x86_64/wheel/./atm
copying build/lib/atm/atomutils.py -> build/bdist.linux-x86_64/wheel/./atm
copying build/lib/atm/uwham.py -> build/bdist.linux-x86_64/wheel/./atm
copying build/lib/atm/worker.py -> build/bdist.linux-x86_64/wheel/./atm
copying build/lib/atm/rbfe_production.py -> build/bdist.linux-x86_64/wheel/./atm
copying build/lib/atm/ommsystem.py -> build/bdist.linux-x86_64/wheel/./atm
copying build/lib/atm/__init__.py -> build/bdist.linux-x86_64/wheel/./atm
copying build/lib/atm/ommreplica.py -> build/bdist.linux-x86_64/wheel/./atm
copying build/lib/atm/logging.ini -> build/bdist.linux-x86_64/wheel/./atm
running install_egg_info
Copying acellera_atm.egg-info to build/bdist.linux-x86_64/wheel/./acellera_atm-0.1.2.dev2+gfb3bd6635-py3.11.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/acellera_atm-0.1.2.dev2+gfb3bd6635.dist-info/WHEEL
creating '/home/maciek/BOINC/40000/slots/1/tmp/pip-wheel-40_foiba/.tmp-2iww6255/acellera_atm-0.1.2.dev2+gfb3bd6635-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'acellera_atm-0.1.2.dev2+gfb3bd6635.dist-info/licenses/LICENSE'
adding 'atm/__init__.py'
adding 'atm/atom_nnp_wrapper.py'
adding 'atm/atomutils.py'
adding 'atm/logging.ini'
adding 'atm/ommreplica.py'
adding 'atm/ommsystem.py'
adding 'atm/rbfe_production.py'
adding 'atm/rbfe_structprep.py'
adding 'atm/utils.py'
adding 'atm/uwham.py'
adding 'atm/worker.py'
adding 'acellera_atm-0.1.2.dev2+gfb3bd6635.dist-info/METADATA'
adding 'acellera_atm-0.1.2.dev2+gfb3bd6635.dist-info/WHEEL'
adding 'acellera_atm-0.1.2.dev2+gfb3bd6635.dist-info/entry_points.txt'
adding 'acellera_atm-0.1.2.dev2+gfb3bd6635.dist-info/top_level.txt'
adding 'acellera_atm-0.1.2.dev2+gfb3bd6635.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A10_A05_input.yaml
+ python bin/rbfe_production QB_A10_A05_input.yaml
2025-12-13 21:50:56,205 - atm.rbfe_production - INFO - Configuration:
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - ACORE: 0.0625
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - ALIGN_KF_SEP: 2.5
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - ALIGN_K_PSI: 50.0
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - ALIGN_K_THETA: 50.0
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - ALIGN_LIGAND1_REF_ATOMS: [9, 21, 14]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - ALIGN_LIGAND2_REF_ATOMS: [9, 21, 14]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - ALPHA: [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - ANNEALING_STEPS: 250000
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - BASENAME: QB_A10_A05
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - CHECKPOINT_FILE: checkpoint.xml
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - CHECKPOINT_FREQUENCY: 30
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - CHECKPOINT_TIME: 30
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - CM_KF: 0.0
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - CM_TOL: 5.0
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - CYCLE_TIME: 60
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - DIRECTION: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - DISPLACEMENT: [21.0, 21.0, 21.0]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - EQUILIBRATION_STEPS: 150000
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - FRICTION_COEFF: 0.1
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - HMASS: 4.0
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - INTEGRATOR: LangevinMiddle
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - INTERMEDIATE: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - JOB_TRANSPORT: LOCAL_OPENMM
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - LAMBDA1: [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - LAMBDA2: [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - LAMBDAS: [0.0, 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, 1.0]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - LIGAND1_ATOMS: [6011, 6012, 6013, 6014, 6015, 6016, 6017, 6018, 6019, 6020, 6021, 6022, 6023, 6024, 6025, 6026, 6027, 6028, 6029, 6030, 6031, 6032, 6033, 6034, 6035, 6036, 6037, 6038, 6039, 6040, 6041, 6042, 6043, 6044, 6045, 6046, 6047, 6048, 6049, 6050, 6051, 6052, 6053, 6054, 6055, 6056, 6057, 6058, 6059, 6060]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - LIGAND1_CM_ATOMS: [6020]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - LIGAND2_ATOMS: [6061, 6062, 6063, 6064, 6065, 6066, 6067, 6068, 6069, 6070, 6071, 6072, 6073, 6074, 6075, 6076, 6077, 6078, 6079, 6080, 6081, 6082, 6083, 6084, 6085, 6086, 6087, 6088, 6089, 6090, 6091, 6092, 6093, 6094, 6095, 6096, 6097, 6098, 6099, 6100, 6101, 6102, 6103, 6104, 6105, 6106, 6107]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - LIGAND2_CM_ATOMS: [6070]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - MAX_SAMPLES: +120
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - MIN_TIME: 0
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - NODEFILE: nodefile
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - OPENMM_PLATFORM: CUDA
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - OVERRIDE_SAFECHECKPOINT: True
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - POSRE_FORCE_CONSTANT: 25.0
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - POSRE_TOLERANCE: 1.5
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - POS_RESTRAINED_ATOMS: [8, 22, 36, 56, 77, 88, 104, 119, 138, 145, 157, 168, 182, 202, 216, 232, 251, 273, 297, 318, 335, 349, 368, 398, 404, 423, 430, 441, 448, 458, 475, 482, 501, 517, 528, 538, 548, 569, 581, 591, 610, 629, 644, 668, 682, 698, 708, 727, 749, 771, 790, 801, 833, 839, 859, 876, 890, 907, 921, 938, 948, 970, 994, 1004, 1025, 1049, 1064, 1083, 1099, 1118, 1135, 1157, 1168, 1184, 1198, 1215, 1237, 1251, 1270, 1289, 1296, 1315, 1334, 1348, 1364, 1384, 1406, 1412, 1429, 1451, 1462, 1481, 1496, 1511, 1531, 1548, 1560, 1576, 1597, 1616, 1632, 1649, 1664, 1683, 1700, 1712, 1722, 1736, 1755, 1766, 1783, 1799, 1818, 1835, 1852, 1867, 1886, 1898, 1915, 1930, 1954, 1971, 1982, 2003, 2022, 2041, 2062, 2079, 2096, 2115, 2126, 2133, 2152, 2174, 2191, 2210, 2228, 2239, 2249, 2256, 2275, 2294, 2312, 2336, 2348, 2367, 2397, 2403, 2414, 2428, 2447, 2463, 2479, 2501, 2512, 2524, 2535, 2549, 2568, 2590, 2609, 2628, 2640, 2660, 2667, 2686, 2696, 2720, 2734, 2744, 2751, 2765, 2776, 2796, 2813, 2830, 2853, 2859, 2874, 2890, 2906, 2920, 2944, 2965, 2986, 3010, 3028, 3034, 3049, 3065, 3084, 3103, 3110, 3127, 3134, 3155, 3177, 3192, 3206, 3222, 3234, 3253, 3277, 3288, 3304, 3311, 3322, 3341, 3358, 3365, 3380, 3397, 3413, 3424, 3441, 3463, 3482, 3501, 3529, 3535, 3542, 3566, 3578, 3599, 3618, 3630, 3647, 3671, 3685, 3707, 3723, 3742, 3757, 3774, 3793, 3800, 3822, 3828, 3847, 3853, 3868, 3888, 3905, 3927, 3949, 3968, 3993, 3999, 4013, 4029, 4053, 4067, 4088, 4104, 4119, 4133, 4165, 4171, 4193, 4214, 4224, 4231, 4252, 4263, 4283, 4298, 4320, 4339, 4367, 4373, 4385, 4401, 4420, 4448, 4454, 4464, 4476, 4487, 4502, 4519, 4533, 4555, 4574, 4596, 4606, 4617, 4634, 4644, 4668, 4680, 4699, 4718, 4729, 4751, 4768, 4787, 4803, 4822, 4834, 4844, 4855, 4877, 4901, 4920, 4931, 4947, 4959, 4974, 4984, 5003, 5020, 5046, 5052, 5073, 5092, 5106, 5122, 5146, 5167, 5187, 5193, 5204, 5219, 5229, 5244, 5262, 5276, 5290, 5296, 5318, 5345, 5351, 5363, 5385, 5402, 5421, 5433, 5448, 5472, 5487, 5504, 5518, 5537, 5552, 5567, 5591, 5613, 5628, 5647, 5666, 5687, 5709, 5724, 5740, 5757, 5769, 5788, 5803, 5841, 5847, 5869, 5901, 5907, 5921, 5935, 5954, 5968, 5987]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - PRNT_FREQUENCY: 2000
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - PRODUCTION_STEPS: 2000
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - RCPT_CM_ATOMS: [404, 423, 430, 441, 448, 501, 528, 698, 727, 1270, 1632, 1649, 1664, 1683, 1700, 1712, 1722, 2403, 2414, 2447, 2609, 2628]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - RE_MODE: sync
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - STEPS_PER_CYCLE: 5000
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - TEMPERATURES: [298]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - THERMALIZATION_STEPS: 150000
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - TIME_STEP: 0.004
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - TRJ_FREQUENCY: 2000
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - U0: [110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0, 110.0]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - UBCORE: 100.0
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - UMAX: 200.0
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - VERBOSE: False
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - W0COEFF: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - WALL_TIME: 9999
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - SUBJOBS_BUFFER_SIZE: 0
2025-12-13 21:50:56,213 - atm.rbfe_production - INFO - State parameters
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.0, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.0, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.05, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.1, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.1, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.2, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.15, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.3, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.2, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.4, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.25, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.3, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.1, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.35, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.2, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.4, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.3, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.45, 'atmdirection': 1.0, 'atmintermediate': 0.0, 'lambda1': 0.4, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.5, 'atmdirection': 1.0, 'atmintermediate': 1.0, 'lambda1': 0.5, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.5, 'atmdirection': -1.0, 'atmintermediate': 1.0, 'lambda1': 0.5, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.55, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.4, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.6, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.3, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.65, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.2, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.7, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.1, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.75, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.5, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.8, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.4, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.85, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.3, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.9, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.2, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 0.95, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.1, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - State: {'lambda': 1.0, 'atmdirection': -1.0, 'atmintermediate': 0.0, 'lambda1': 0.0, 'lambda2': 0.0, 'alpha': Quantity(value=0.1, unit=mole/kilocalorie), 'uh': Quantity(value=110.0, unit=kilocalorie/mole), 'Umax': Quantity(value=200.0, unit=kilocalorie/mole), 'Ubcore': Quantity(value=100.0, unit=kilocalorie/mole), 'Acore': 0.0625, 'w0': Quantity(value=0.0, unit=kilocalorie/mole), 'temperature': Quantity(value=298.0, unit=kelvin)}
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - Started: ATM setup
2025-12-13 21:50:56,214 - atm.rbfe_production - INFO - Started: create system
2025-12-13 21:50:57,164 - atm.rbfe_production - INFO - Integrator: LangevinMiddle
2025-12-13 21:50:57,164 - atm.rbfe_production - INFO - Temperature: 300.0 K
2025-12-13 21:50:57,164 - atm.rbfe_production - INFO - Friction: 0.1 /ps
2025-12-13 21:50:57,164 - atm.rbfe_production - INFO - Step size: 0.004 ps
2025-12-13 21:50:57,164 - atm.rbfe_production - INFO - Constraint tolerance: 1e-05
2025-12-13 21:50:57,164 - atm.rbfe_production - INFO - Finished: create system (duration: 0.9506107029992563 s)
2025-12-13 21:50:57,164 - atm.rbfe_production - INFO - Started: create worker
2025-12-13 21:50:57,165 - atm.rbfe_production - INFO - Platform: CUDA {'DeviceIndex': '0', 'Precision': 'mixed'}
Traceback (most recent call last):
File "/home/maciek/BOINC/40000/slots/1/bin/rbfe_production", line 8, in <module>
sys.exit(rbfe_production())
^^^^^^^^^^^^^^^^^
File "/home/maciek/BOINC/40000/slots/1/lib/python3.11/site-packages/atm/rbfe_production.py", line 331, in rbfe_production
rx.setupJob()
File "/home/maciek/BOINC/40000/slots/1/lib/python3.11/site-packages/atm/rbfe_production.py", line 97, in setupJob
self.worker = OMMWorkerATM(ommsystem, self.config, self.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/maciek/BOINC/40000/slots/1/lib/python3.11/site-packages/atm/worker.py", line 50, in __init__
self.simulation.loadState(basename + "_0.xml")
File "/home/maciek/BOINC/40000/slots/1/lib/python3.11/site-packages/openmm/app/simulation.py", line 363, in loadState
self.context.setState(mm.XmlSerializer.deserialize(xml))
File "/home/maciek/BOINC/40000/slots/1/lib/python3.11/site-packages/openmm/openmm.py", line 15222, in setState
return _openmm.Context_setState(self, state)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Called setParameter() with invalid parameter name: UOffset
2025-12-13 21:51:04 (75101): bin/bash exited; CPU time 11.999461
2025-12-13 21:51:04 (75101): app exit status: 0x1
2025-12-13 21:51:04 (75101): called boinc_finish(195)
</stderr_txt>
]]>
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