Task 38641081

Stderr output

<core_client_version>8.0.4</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2026-05-02 07:51:03 (2961): wrapper (8.1.26018): starting
2026-05-02 07:51:27 (2961): wrapper: running bin/python (bin/conda-unpack)
2026-05-02 07:51:27 (2961): wrapper: created child process 2972
2026-05-02 07:51:28 (2961): bin/python exited; CPU time 0.130881
2026-05-02 07:51:28 (2961): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-05-02 07:51:28 (2961): wrapper: created child process 2978
2026-05-02 07:51:30 (2961): bin/tar exited; CPU time 1.268611
2026-05-02 07:51:30 (2961): wrapper: running bin/bash (run.sh)
2026-05-02 07:51:30 (2961): wrapper: created child process 2980
+ 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
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A26_A19_input.yaml
+ python bin/rbfe_production QB_A26_A19_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
SIGSEGV: segmentation violation
Stack trace (15 frames):
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x42c050]
/lib/x86_64-linux-gnu/libc.so.6(+0x3fdf0) [0x7fdb19c55df0]
../../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(+0x3fdf0) [0x7fdb19c55df0]
/lib/x86_64-linux-gnu/libc.so.6(+0x9a9ee) [0x7fdb19cb09ee]
/lib/x86_64-linux-gnu/libc.so.6(+0x8f668) [0x7fdb19ca5668]
/lib/x86_64-linux-gnu/libc.so.6(clock_nanosleep+0x2a) [0x7fdb19cf1fba]
/lib/x86_64-linux-gnu/libc.so.6(nanosleep+0x13) [0x7fdb19cfd3d3]
/lib/x86_64-linux-gnu/libc.so.6(usleep+0x43) [0x7fdb19d263b3]
../../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(+0x29ca8) [0x7fdb19c3fca8]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x85) [0x7fdb19c3fd65]
../../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 '
2026-05-02 16:21:28 (1289): wrapper (8.1.26018): starting
2026-05-02 16:21:53 (1289): wrapper: running bin/bash (run.sh)
2026-05-02 16:21:53 (1289): wrapper: created child process 1624
+ 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_A26_A19_input.yaml
+ python bin/rbfe_production QB_A26_A19_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"
2026-05-02 16:22:26 (1289): bin/bash exited; CPU time 29.826473
2026-05-02 16:22:26 (1289): app exit status: 0x1
2026-05-02 16:22:26 (1289): called boinc_finish(195)

</stderr_txt>
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