Task 38593247
| Name | shp2_A20_A19_r0_2-QUICO_ATM_GAFF2_LOMAP_SHP2-1-6-RND8360_9 |
| Workunit | 31550466 |
| Created | 24 Jan 2026, 4:55:09 UTC |
| Sent | 24 Jan 2026, 4:55:15 UTC |
| Report deadline | 29 Jan 2026, 4:55:15 UTC |
| Received | 28 Jan 2026, 8:53:35 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 641403 |
| Run time | 6 hours 15 min 34 sec |
| CPU time | 6 hours 15 min 34 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 9,524.94 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 845.00 MB |
| Peak swap size | 15.89 GB |
| Peak disk usage | 3.39 GB |
Stderr output
<core_client_version>8.2.4</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2026-01-24 12:35:35 (2194): wrapper (8.1.26018): starting
2026-01-24 12:36:12 (2194): wrapper: running bin/python (bin/conda-unpack)
2026-01-24 12:36:12 (2194): wrapper: created child process 2258
2026-01-24 12:36:13 (2194): bin/python exited; CPU time 0.422858
2026-01-24 12:36:13 (2194): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-01-24 12:36:13 (2194): wrapper: created child process 2259
2026-01-24 12:36:18 (2194): bin/tar exited; CPU time 4.185606
2026-01-24 12:36:18 (2194): wrapper: running bin/bash (run.sh)
2026-01-24 12:36:18 (2194): wrapper: created child process 2397
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/5/bin
+++ dirname /var/lib/boinc/slots/5/bin
++ local full_path_env=/var/lib/boinc/slots/5
+++ basename /var/lib/boinc/slots/5
++ local env_name=5
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/5
++ CONDA_PREFIX=/var/lib/boinc/slots/5
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(5) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/5/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/5/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/5:/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/5:/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/5/tmp
+ TMP=/var/lib/boinc/slots/5/tmp
+ mkdir -p /var/lib/boinc/slots/5/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/5/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_A20_A19_input.yaml
+ python bin/rbfe_production QB_A20_A19_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
SIGSEGV: segmentation violation
Stack trace (13 frames):
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x42c050]
/lib64/libc.so.6(+0x40fd0)[0x7f3a96d52fd0]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x463138]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x45f5d5]
/lib64/libc.so.6(+0x40fd0)[0x7f3a96d52fd0]
/lib64/libc.so.6(clock_nanosleep+0x63)[0x7f3a96df64d3]
/lib64/libc.so.6(nanosleep+0x17)[0x7f3a96e025c7]
/lib64/libc.so.6(usleep+0x4a)[0x7f3a96e2da9a]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x4398c2]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x40b2e5]
/lib64/libc.so.6(+0x2a088)[0x7f3a96d3c088]
/lib64/libc.so.6(__libc_start_main+0x8b)[0x7f3a96d3c14b]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x407cc5]
Exiting...
/var/lib/boinc/slots/5/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 '
2026-01-25 09:01:56 (1601): wrapper (8.1.26018): starting
2026-01-25 09:01:56 (1601): wrapper: running bin/bash (run.sh)
2026-01-25 09:01:56 (1601): wrapper: created child process 1603
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/5/bin
+++ dirname /var/lib/boinc/slots/5/bin
++ local full_path_env=/var/lib/boinc/slots/5
+++ basename /var/lib/boinc/slots/5
++ local env_name=5
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/5
++ CONDA_PREFIX=/var/lib/boinc/slots/5
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(5) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/5/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/5/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/5:/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/5:/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/5/tmp
+ TMP=/var/lib/boinc/slots/5/tmp
+ mkdir -p /var/lib/boinc/slots/5/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/5/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A20_A19_input.yaml
+ python bin/rbfe_production QB_A20_A19_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc/slots/5/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 '
2026-01-26 09:01:57 (1599): wrapper (8.1.26018): starting
2026-01-26 09:01:57 (1599): wrapper: running bin/bash (run.sh)
2026-01-26 09:01:57 (1599): wrapper: created child process 1601
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/5/bin
+++ dirname /var/lib/boinc/slots/5/bin
++ local full_path_env=/var/lib/boinc/slots/5
+++ basename /var/lib/boinc/slots/5
++ local env_name=5
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/5
++ CONDA_PREFIX=/var/lib/boinc/slots/5
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(5) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/5/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/5/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/5:/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/5:/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/5/tmp
+ TMP=/var/lib/boinc/slots/5/tmp
+ mkdir -p /var/lib/boinc/slots/5/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/5/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A20_A19_input.yaml
+ python bin/rbfe_production QB_A20_A19_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc/slots/5/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 '
2026-01-27 09:01:55 (1589): wrapper (8.1.26018): starting
2026-01-27 09:01:55 (1589): wrapper: running bin/bash (run.sh)
2026-01-27 09:01:55 (1589): wrapper: created child process 1591
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/5/bin
+++ dirname /var/lib/boinc/slots/5/bin
++ local full_path_env=/var/lib/boinc/slots/5
+++ basename /var/lib/boinc/slots/5
++ local env_name=5
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/5
++ CONDA_PREFIX=/var/lib/boinc/slots/5
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(5) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/5/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/5/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/5:/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/5:/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/5/tmp
+ TMP=/var/lib/boinc/slots/5/tmp
+ mkdir -p /var/lib/boinc/slots/5/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/5/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A20_A19_input.yaml
+ python bin/rbfe_production QB_A20_A19_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc/slots/5/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 '
2026-01-28 09:01:57 (1593): wrapper (8.1.26018): starting
2026-01-28 09:01:57 (1593): wrapper: running bin/bash (run.sh)
2026-01-28 09:01:57 (1593): wrapper: created child process 1597
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/5/bin
+++ dirname /var/lib/boinc/slots/5/bin
++ local full_path_env=/var/lib/boinc/slots/5
+++ basename /var/lib/boinc/slots/5
++ local env_name=5
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/5
++ CONDA_PREFIX=/var/lib/boinc/slots/5
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(5) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/5/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/5/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/5:/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/5:/var/lib/boinc/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/5/tmp
+ TMP=/var/lib/boinc/slots/5/tmp
+ mkdir -p /var/lib/boinc/slots/5/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/5/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A20_A19_input.yaml
+ python bin/rbfe_production QB_A20_A19_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/var/lib/boinc/slots/5/bin/rbfe_production", line 8, in <module>
sys.exit(rbfe_production())
^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/5/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 33, in rbfe_production
rx.scheduleJobs()
File "/var/lib/boinc/slots/5/lib/python3.11/site-packages/atom_openmm/async_re.py", line 321, in scheduleJobs
self.transport.ProcessJobQueue(min_time,cycle_time)
File "/var/lib/boinc/slots/5/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 186, in ProcessJobQueue
self.isDone(repl,0)
File "/var/lib/boinc/slots/5/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 287, in isDone
retcode = self._update_replica(job)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/5/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 212, in _update_replica
pot = job['openmm_worker'].get_energy()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/5/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 451, in get_energy
return self._worker_getenergy()
^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/5/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 400, in _worker_getenergy
state = self.simulation.context.getState(getEnergy = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/5/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
2026-01-28 15:52:28 (1593): bin/bash exited; CPU time 22495.483380
2026-01-28 15:52:28 (1593): app exit status: 0x1
2026-01-28 15:52:28 (1593): called boinc_finish(195)
</stderr_txt>
]]>
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