Task 38583285
| Name | PFKFB3_A28_A07_r0_4-QUICO_ATM_GAFF2_LOMAP_PFKFB3-3-5-RND2738_0 |
| Workunit | 31547443 |
| Created | 14 Dec 2025, 0:29:51 UTC |
| Sent | 14 Dec 2025, 0:29:56 UTC |
| Report deadline | 19 Dec 2025, 0:29:56 UTC |
| Received | 14 Dec 2025, 11:55:07 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 648044 |
| Run time | 1 hours 44 min 45 sec |
| CPU time | 1 hours 44 min 45 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 82,582.58 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 688.21 MB |
| Peak swap size | 12.98 GB |
| Peak disk usage | 3.50 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2025-12-14 01:30:35 (5659): wrapper (8.1.26018): starting
2025-12-14 01:30:51 (5659): wrapper: running bin/python (bin/conda-unpack)
2025-12-14 01:30:51 (5659): wrapper: created child process 5661
2025-12-14 01:30:52 (5659): bin/python exited; CPU time 0.068233
2025-12-14 01:30:52 (5659): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-14 01:30:52 (5659): wrapper: created child process 5662
2025-12-14 01:30:53 (5659): bin/tar exited; CPU time 0.905533
2025-12-14 01:30:53 (5659): wrapper: running bin/bash (run.sh)
2025-12-14 01:30:53 (5659): wrapper: created child process 5664
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/michael/slots/0/bin
+++ dirname /home/michael/slots/0/bin
++ local full_path_env=/home/michael/slots/0
+++ basename /home/michael/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/michael/slots/0
++ CONDA_PREFIX=/home/michael/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/michael/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/michael/slots/0/etc/conda/activate.d
++ '[' -d /home/michael/slots/0/etc/conda/activate.d ']'
+ export PATH=/home/michael/slots/0:/home/michael/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/michael/slots/0:/home/michael/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/michael/slots/0/tmp
+ TMP=/home/michael/slots/0/tmp
+ mkdir -p /home/michael/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/michael/slots/0/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
+ python -m pip install --no-dependencies atom-openmm -v
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A28_A07_input.yaml
+ python bin/rbfe_production QB_A28_A07_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/home/michael/slots/0/lib/python3.11/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 3 leaked semaphore objects to clean up at shutdown
warnings.warn('resource_tracker: There appear to be %d '
2025-12-14 11:10:45 (93): wrapper (8.1.26018): starting
2025-12-14 11:10:45 (93): wrapper: running bin/bash (run.sh)
2025-12-14 11:10:45 (93): wrapper: created child process 96
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/michael/slots/0/bin
+++ dirname /home/michael/slots/0/bin
++ local full_path_env=/home/michael/slots/0
+++ basename /home/michael/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/michael/slots/0
++ CONDA_PREFIX=/home/michael/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/michael/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/michael/slots/0/etc/conda/activate.d
++ '[' -d /home/michael/slots/0/etc/conda/activate.d ']'
+ export PATH=/home/michael/slots/0:/home/michael/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/michael/slots/0:/home/michael/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/michael/slots/0/tmp
+ TMP=/home/michael/slots/0/tmp
+ mkdir -p /home/michael/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/michael/slots/0/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A28_A07_input.yaml
+ python bin/rbfe_production QB_A28_A07_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/home/michael/slots/0/bin/rbfe_production", line 8, in <module>
sys.exit(rbfe_production())
^^^^^^^^^^^^^^^^^
File "/home/michael/slots/0/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 33, in rbfe_production
rx.scheduleJobs()
File "/home/michael/slots/0/lib/python3.11/site-packages/atom_openmm/async_re.py", line 321, in scheduleJobs
self.transport.ProcessJobQueue(min_time,cycle_time)
File "/home/michael/slots/0/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 186, in ProcessJobQueue
self.isDone(repl,0)
File "/home/michael/slots/0/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 287, in isDone
retcode = self._update_replica(job)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/michael/slots/0/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 212, in _update_replica
pot = job['openmm_worker'].get_energy()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/michael/slots/0/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 451, in get_energy
return self._worker_getenergy()
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/michael/slots/0/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 400, in _worker_getenergy
state = self.simulation.context.getState(getEnergy = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/michael/slots/0/lib/python3.11/site-packages/openmm/openmm.py", line 15506, in getState
state = _openmm.Context_getState(self, types, enforcePeriodicBox, groups_mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Particle coordinate is NaN. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan
2025-12-14 12:53:14 (93): bin/bash exited; CPU time 6101.385272
2025-12-14 12:53:14 (93): app exit status: 0x1
2025-12-14 12:53:14 (93): called boinc_finish(195)
</stderr_txt>
]]>
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