Task 38583528

Stderr output

<core_client_version>8.0.4</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2025-12-14 21:48:28 (31763): wrapper (8.1.26018): starting
2025-12-14 21:48:48 (31763): wrapper: running bin/python (bin/conda-unpack)
2025-12-14 21:48:48 (31763): wrapper: created child process 31772
2025-12-14 21:48:49 (31763): bin/python exited; CPU time 0.080687
2025-12-14 21:48:49 (31763): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-14 21:48:49 (31763): wrapper: created child process 31777
2025-12-14 21:48:51 (31763): bin/tar exited; CPU time 1.043248
2025-12-14 21:48:51 (31763): wrapper: running bin/bash (run.sh)
2025-12-14 21:48:51 (31763): wrapper: created child process 31780
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/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
+ python -m pip install --no-dependencies atom-openmm -v
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='pypi.org', port=443): Read timed out. (read timeout=15)")': /simple/atom-openmm/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='pypi.org', port=443): Read timed out. (read timeout=15)")': /simple/atom-openmm/
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A04_A37_input.yaml
+ python bin/rbfe_production QB_A04_A37_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]
/lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x717790c45330]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x463138]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x45f5d5]
/lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x717790c45330]
/lib/x86_64-linux-gnu/libc.so.6(clock_nanosleep+0xbf)[0x717790cecadf]
/lib/x86_64-linux-gnu/libc.so.6(nanosleep+0x17)[0x717790cf9a27]
/lib/x86_64-linux-gnu/libc.so.6(usleep+0x4c)[0x717790d2975c]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x4398c2]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x40b2e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x717790c2a1ca]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x717790c2a28b]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x407cc5]

Exiting...
/var/lib/boinc-client/slots/1/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 22:29:52 (5091): wrapper (8.1.26018): starting
2025-12-14 22:30:12 (5091): wrapper: running bin/bash (run.sh)
2025-12-14 22:30:12 (5091): wrapper: created child process 5112
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A04_A37_input.yaml
+ python bin/rbfe_production QB_A04_A37_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "/var/lib/boinc-client/slots/1/bin/rbfe_production", line 8, in <module>
    sys.exit(rbfe_production())
             ^^^^^^^^^^^^^^^^^
  File "/var/lib/boinc-client/slots/1/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/1/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 443, in __init__
    self.openmm_workers.append(ommworkercls(self.basename, ommsys, self.keywords, node_info = node, compute = True, logger = self.logger))
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 53, in __init__
    self.start_worker()
  File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 444, in start_worker
    self._openmm_worker_makecontext()
  File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 229, in _openmm_worker_makecontext
    self.platform = Platform.getPlatformByName(self.platform_name)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/openmm/openmm.py", line 9567, in getPlatformByName
    return _openmm.Platform_getPlatformByName(name)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: There is no registered Platform called "CUDA"
2025-12-14 22:30:26 (5091): bin/bash exited; CPU time 13.675682
2025-12-14 22:30:26 (5091): app exit status: 0x1
2025-12-14 22:30:26 (5091): called boinc_finish(195)

</stderr_txt>
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