Task 38626627

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
17:29:50 (28084): wrapper (7.9.26016): starting
17:29:50 (28084): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A33_A07_0.pdb
QB_A33_A07_0.xml
QB_A33_A07.inpcrd
QB_A33_A07_input.yaml
QB_A33_A07.pdb
QB_A33_A07.prmtop
QB_A33_A07_sys.xml
run.bat
run.sh
17:29:52 (28084): Library/usr/bin/tar.exe exited; CPU time 0.015625
17:29:52 (28084): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
  WARNING: The script pyaml.exe is installed in 'C:\ProgramData\BOINC\slots\28\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts abfe_production.exe, abfe_structprep.exe, make_atm_system_from_amber.exe, make_atm_system_from_pdb.exe, make_atm_system_from_rcpt_lig.exe, rbfe_production.exe and rbfe_structprep.exe are installed in 'C:\ProgramData\BOINC\slots\28\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835543} normal block at 0x0000020AD191DB30, 8 bytes long.
 Data: <        > 00 00 DA D1 0A 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833954} normal block at 0x0000020AD190D930, 1080 bytes long.
 Data: < i              > 84 69 00 00 CD CD CD CD 9C 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x0000020AD1911860, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
19:11:57 (26484): wrapper (7.9.26016): starting
19:11:57 (26484): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\28\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1891} normal block at 0x000001D6B6206000, 8 bytes long.
 Data: <        > 00 00 1A B6 D6 01 00 00 
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x000001D6B6207020, 1080 bytes long.
 Data: < n              > E4 6E 00 00 CD CD CD CD B4 01 00 00 00 00 00 00 
Object dump complete.
19:13:04 (22568): wrapper (7.9.26016): starting
19:13:04 (22568): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\28\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1891} normal block at 0x000002281E1468C0, 8 bytes long.
 Data: <  b (   > 00 00 62 1E 28 02 00 00 
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x000002281E147020, 1080 bytes long.
 Data: < l              > D4 6C 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
21:13:12 (23680): wrapper (7.9.26016): starting
21:13:12 (23680): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\28\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1891} normal block at 0x0000022AA1E95D40, 8 bytes long.
 Data: <  + *   > 00 00 2B A2 2A 02 00 00 
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x0000022AA1E97030, 1080 bytes long.
 Data: <ti              > 74 69 00 00 CD CD CD CD C0 01 00 00 00 00 00 00 
Object dump complete.
22:10:56 (3400): wrapper (7.9.26016): starting
22:10:56 (3400): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\28\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1891} normal block at 0x000001AE84C57680, 8 bytes long.
 Data: <        > 00 00 08 85 AE 01 00 00 
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x000001AE84C57E80, 1080 bytes long.
 Data: <hk              > 68 6B 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
22:21:28 (24880): wrapper (7.9.26016): starting
22:21:28 (24880): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\28\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1891} normal block at 0x0000026D328867D0, 8 bytes long.
 Data: <   2m   > 00 00 DD 32 6D 02 00 00 
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x0000026D32887020, 1080 bytes long.
 Data: <`               > 60 11 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
22:55:30 (26616): wrapper (7.9.26016): starting
22:55:30 (26616): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\28\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1891} normal block at 0x000001E999C96B90, 8 bytes long.
 Data: <        > 00 00 11 9A E9 01 00 00 
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x000001E999C97020, 1080 bytes long.
 Data: < j              > C4 6A 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
22:55:58 (10436): wrapper (7.9.26016): starting
22:55:58 (10436): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\28\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1891} normal block at 0x0000020D54AD68D0, 8 bytes long.
 Data: <   T    > 00 00 F4 54 0D 02 00 00 
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x0000020D54AD7030, 1080 bytes long.
 Data: < D              > A8 44 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
00:14:36 (12452): wrapper (7.9.26016): starting
00:14:36 (12452): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\28\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1891} normal block at 0x0000020CB60D6280, 8 bytes long.
 Data: <  ]     > 00 00 5D B6 0C 02 00 00 
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x0000020CB60D7020, 1080 bytes long.
 Data: <                > B0 04 00 00 CD CD CD CD C4 01 00 00 00 00 00 00 
Object dump complete.
00:24:55 (27104): wrapper (7.9.26016): starting
00:24:55 (27104): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\28\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\ProgramData\BOINC\slots\28\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\28\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\28\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\28\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\28\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\28\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\28\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\28\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\28\Lib\site-packages\openmm\openmm.py", line 5022, 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
02:45:53 (27104): C:/Windows/system32/cmd.exe exited; CPU time 8505.171875
02:45:53 (27104): app exit status: 0x16
02:45:53 (27104): called boinc_finish(195)
0 bytes in 0 Free Blocks.
460 bytes in 8 Normal Blocks.
1144 bytes in 1 CRT Blocks.
0 bytes in 0 Ignore Blocks.
0 bytes in 0 Client Blocks.
Largest number used: 0 bytes.
Total allocations: 147056463 bytes.
Dumping objects ->
{1980} normal block at 0x000002D8A61059C0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1969} normal block at 0x000002D8A6105CD0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1958} normal block at 0x000002D8A6105F00, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1947} normal block at 0x000002D8A6105A30, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1936} normal block at 0x000002D8A6105D40, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1905} normal block at 0x000002D8A60EB750, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1894} normal block at 0x000002D8A60EC340, 102 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
..\api\boinc_api.cpp(309) : {1891} normal block at 0x000002D8A61065D0, 8 bytes long.
 Data: <  V     > 00 00 56 A6 D8 02 00 00 
{1076} normal block at 0x000002D8A61064A0, 102 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{303} normal block at 0x000002D8A6106CB0, 8 bytes long.
 Data: <`{      > 60 7B 10 A6 D8 02 00 00 
{294} normal block at 0x000002D8A60F2C40, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{293} normal block at 0x000002D8A6107020, 16 bytes long.
 Data: <hz              > 68 7A 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000002D8A6106B20, 16 bytes long.
 Data: <@z              > 40 7A 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000002D8A6100C00, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{290} normal block at 0x000002D8A6106850, 16 bytes long.
 Data: < z              > 18 7A 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000002D8A6106C60, 16 bytes long.
 Data: < y              > F0 79 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000002D8A6106BC0, 16 bytes long.
 Data: < y              > C8 79 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000002D8A61068A0, 16 bytes long.
 Data: < y              > A0 79 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000002D8A6105F70, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{285} normal block at 0x000002D8A61072A0, 16 bytes long.
 Data: <                > E8 B6 0E A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000002D8A6100AE0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{283} normal block at 0x000002D8A6106D00, 16 bytes long.
 Data: <                > C0 B6 0E A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000002D8A6107070, 16 bytes long.
 Data: <                > 98 B6 0E A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000002D8A6106FD0, 16 bytes long.
 Data: <p               > 70 B6 0E A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000002D8A6107480, 16 bytes long.
 Data: <H               > 48 B6 0E A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000002D8A6106760, 16 bytes long.
 Data: <                > 20 B6 0E A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000002D8A6107110, 16 bytes long.
 Data: <                > F8 B5 0E A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000002D8A61000C0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{275} normal block at 0x000002D8A6106C10, 16 bytes long.
 Data: <                > D0 B5 0E A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000002D8A60EB5D0, 320 bytes long.
 Data: < l              > 10 6C 10 A6 D8 02 00 00 C0 00 10 A6 D8 02 00 00 
{273} normal block at 0x000002D8A6106D50, 16 bytes long.
 Data: < y              > 80 79 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000002D8A6106B70, 16 bytes long.
 Data: <Xy              > 58 79 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000002D8A6100060, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{270} normal block at 0x000002D8A6106EE0, 16 bytes long.
 Data: <0y              > 30 79 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000002D8A61004E0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{268} normal block at 0x000002D8A61067B0, 16 bytes long.
 Data: <xx              > 78 78 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000002D8A6106620, 16 bytes long.
 Data: <Px              > 50 78 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000002D8A6106AD0, 16 bytes long.
 Data: <(x              > 28 78 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000002D8A6107250, 16 bytes long.
 Data: < x              > 00 78 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000002D8A6107430, 16 bytes long.
 Data: < w              > D8 77 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000002D8A6106A80, 16 bytes long.
 Data: < w              > B0 77 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000002D8A6106F80, 16 bytes long.
 Data: < Z              > A0 5A 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000002D8A6105AA0, 40 bytes long.
 Data: < o      P       > 80 6F 10 A6 D8 02 00 00 50 B7 0E A6 D8 02 00 00 
{259} normal block at 0x000002D8A6106990, 16 bytes long.
 Data: < w              > 90 77 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000002D8A6106710, 16 bytes long.
 Data: <hw              > 68 77 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x000002D8A60FFFA0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{256} normal block at 0x000002D8A6106DA0, 16 bytes long.
 Data: <@w              > 40 77 10 A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x000002D8A6107740, 992 bytes long.
 Data: < m              > A0 6D 10 A6 D8 02 00 00 A0 FF 0F A6 D8 02 00 00 
{91} normal block at 0x000002D8A6100900, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{90} normal block at 0x000002D8A60FEC00, 16 bytes long.
 Data: <                > D0 C2 0E A6 D8 02 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x000002D8A60EC2D0, 40 bytes long.
 Data: <                > 00 EC 0F A6 D8 02 00 00 00 09 10 A6 D8 02 00 00 
{68} normal block at 0x000002D8A60FEB10, 16 bytes long.
 Data: <                > 80 EA 8E 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002D8A60FDD00, 16 bytes long.
 Data: <@               > 40 E9 8E 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002D8A60FDE90, 16 bytes long.
 Data: < W              > F8 57 8B 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000002D8A60FE610, 16 bytes long.
 Data: < W              > D8 57 8B 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002D8A60FE480, 16 bytes long.
 Data: <P               > 50 04 8B 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000002D8A60FDCB0, 16 bytes long.
 Data: <0               > 30 04 8B 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000002D8A60FE250, 16 bytes long.
 Data: <                > E0 02 8B 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000002D8A60FE2A0, 16 bytes long.
 Data: <                > 10 04 8B 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000002D8A60FE110, 16 bytes long.
 Data: <p               > 70 04 8B 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000002D8A60FE7A0, 16 bytes long.
 Data: <                > 18 C0 89 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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