Task 38581289
| Name | PFKFB3_A41_A40_r0_5-QUICO_ATM_GAFF2_LOMAP_PFKFB3-0-5-RND3087_0 |
| Workunit | 31545815 |
| Created | 12 Dec 2025, 10:42:33 UTC |
| Sent | 12 Dec 2025, 10:42:36 UTC |
| Report deadline | 17 Dec 2025, 10:42:36 UTC |
| Received | 13 Dec 2025, 7:23:32 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 569442 |
| Run time | 57 sec |
| CPU time | 15 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 3,094.53 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 382.08 MB |
| Peak swap size | 10.63 GB |
| Peak disk usage | 1.37 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2025-12-12 22:36:45 (91793): wrapper (8.1.26018): starting
2025-12-12 22:37:11 (91793): wrapper: running bin/python (bin/conda-unpack)
2025-12-12 22:37:11 (91793): wrapper: created child process 91799
2025-12-12 22:37:12 (91793): bin/python exited; CPU time 0.263819
2025-12-12 22:37:12 (91793): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-12 22:37:12 (91793): wrapper: created child process 91800
2025-12-12 22:37:15 (91793): bin/tar exited; CPU time 2.696680
2025-12-12 22:37:15 (91793): wrapper: running bin/bash (run.sh)
2025-12-12 22:37:15 (91793): wrapper: created child process 91802
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/2/bin
+++ dirname /var/lib/boinc-client/slots/2/bin
++ local full_path_env=/var/lib/boinc-client/slots/2
+++ basename /var/lib/boinc-client/slots/2
++ local env_name=2
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/2
++ CONDA_PREFIX=/var/lib/boinc-client/slots/2
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(2) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/2/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/2/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/2:/var/lib/boinc-client/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/2:/var/lib/boinc-client/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/2/tmp
+ TMP=/var/lib/boinc-client/slots/2/tmp
+ mkdir -p /var/lib/boinc-client/slots/2/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/2/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_A41_A40_input.yaml
+ python bin/rbfe_production QB_A41_A40_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2025-12-13 07:21:39 (2644): wrapper (8.1.26018): starting
2025-12-13 07:21:39 (2644): wrapper: running bin/bash (run.sh)
2025-12-13 07:21:39 (2644): wrapper: created child process 2665
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/2/bin
+++ dirname /var/lib/boinc-client/slots/2/bin
++ local full_path_env=/var/lib/boinc-client/slots/2
+++ basename /var/lib/boinc-client/slots/2
++ local env_name=2
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/2
++ CONDA_PREFIX=/var/lib/boinc-client/slots/2
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(2) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/2/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/2/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/2:/var/lib/boinc-client/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/2:/var/lib/boinc-client/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/2/tmp
+ TMP=/var/lib/boinc-client/slots/2/tmp
+ mkdir -p /var/lib/boinc-client/slots/2/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/2/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A41_A40_input.yaml
+ python bin/rbfe_production QB_A41_A40_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/var/lib/boinc-client/slots/2/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 432, in __init__
replica = OMMReplicaATM(i, self.basename, self.service_worker, self.logger, self.keywords)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/2/lib/python3.11/site-packages/atom_openmm/ommreplica.py", line 42, in __init__
self.open_xtc()
File "/var/lib/boinc-client/slots/2/lib/python3.11/site-packages/atom_openmm/ommreplica.py", line 99, in open_xtc
self.xtc = XTCFile(self.xtcfile, self.worker.topology, self.ommsystem.MDstepsize, interval=interval, append=append)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/2/lib/python3.11/site-packages/openmm/app/xtcfile.py", line 57, in __init__
self._modelCount = get_xtc_nframes(self._filename.encode("utf-8"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "openmm/app/internal/xtc_utils/xtc.pyx", line 43, in openmm.app.internal.xtc_utils.get_xtc_nframes
RuntimeError: xtc_read(): XTC file is corrupt
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/var/lib/boinc-client/slots/2/bin/rbfe_production", line 8, in <module>
sys.exit(rbfe_production())
^^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/2/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 29, in rbfe_production
rx = openmm_job_RBFE(
^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/2/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 434, in __init__
self._exit("Error when creating replica.")
File "/var/lib/boinc-client/slots/2/lib/python3.11/site-packages/atom_openmm/async_re.py", line 69, in _exit
self.checkpointJob()
File "/var/lib/boinc-client/slots/2/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 48, in checkpointJob
self.update_state_of_replica(repl)
File "/var/lib/boinc-client/slots/2/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 86, in update_state_of_replica
stateid = self.status[repl]['stateid_current']
^^^^^^^^^^^
File "/var/lib/boinc-client/slots/2/lib/python3.11/site-packages/atom_openmm/async_re.py", line 131, in __getattribute__
return object.__getattribute__(self,name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'openmm_job_RBFE' object has no attribute 'status'
2025-12-13 07:22:03 (2644): bin/bash exited; CPU time 15.217801
2025-12-13 07:22:03 (2644): app exit status: 0x1
2025-12-13 07:22:03 (2644): called boinc_finish(195)
</stderr_txt>
]]>
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