Task 38638374

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>
06:52:57 (31924): wrapper (7.9.26016): starting
06:52:57 (31924): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A21_A06_0.pdb
QB_A21_A06_0.xml
QB_A21_A06.inpcrd
QB_A21_A06_input.yaml
QB_A21_A06.pdb
QB_A21_A06.prmtop
QB_A21_A06_sys.xml
run.bat
run.sh
06:52:58 (31924): Library/usr/bin/tar.exe exited; CPU time 0.015625
06:52:58 (31924): 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\12\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\12\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) : {3835488} normal block at 0x000001DB8D18E370, 8 bytes long.
 Data: <        > 00 00 10 8D DB 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833960} normal block at 0x000001DB8D17DBC0, 1080 bytes long.
 Data: < 8      X       > 84 38 00 00 CD CD CD CD 58 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {312} normal block at 0x000001DB8D181380, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
11:21:40 (5948): wrapper (7.9.26016): starting
11:21:40 (5948): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1833} normal block at 0x000001E060136460, 8 bytes long.
 Data: <   `    > 00 00 0D 60 E0 01 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x000001E060137520, 1080 bytes long.
 Data: <                > B8 AA 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
12:08:50 (27672): wrapper (7.9.26016): starting
12:08:50 (27672): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1833} normal block at 0x0000021AC9346730, 8 bytes long.
 Data: <        > 00 00 81 C9 1A 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x0000021AC9347520, 1080 bytes long.
 Data: <                > E8 80 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
12:15:05 (40156): wrapper (7.9.26016): starting
12:15:05 (40156): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1833} normal block at 0x0000019E32E86870, 8 bytes long.
 Data: <  43    > 00 00 34 33 9E 01 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x0000019E32E87520, 1080 bytes long.
 Data: <                > D8 A8 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
12:35:49 (12008): wrapper (7.9.26016): starting
12:35:49 (12008): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1833} normal block at 0x0000018025296170, 8 bytes long.
 Data: <  "%    > 00 00 22 25 80 01 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x0000018025296CE0, 1080 bytes long.
 Data: < q              > DC 71 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
12:44:10 (39424): wrapper (7.9.26016): starting
12:44:10 (39424): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1833} normal block at 0x00000255927F6D70, 8 bytes long.
 Data: <  . U   > 00 00 2E 94 55 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x00000255927F7520, 1080 bytes long.
 Data: <                > E0 99 00 00 CD CD CD CD B0 01 00 00 00 00 00 00 
Object dump complete.
13:13:56 (3100): wrapper (7.9.26016): starting
13:13:56 (3100): 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\12\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\12\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\12\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\12\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\12\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
13:53:58 (3100): C:/Windows/system32/cmd.exe exited; CPU time 2137.312500
13:53:58 (3100): app exit status: 0x16
13:53:58 (3100): called boinc_finish(195)
0 bytes in 0 Free Blocks.
256 bytes in 6 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: 48978833 bytes.
Dumping objects ->
{1921} normal block at 0x000002A47C6D5840, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1910} normal block at 0x000002A47C6D5610, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1899} normal block at 0x000002A47C6D5BC0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1888} normal block at 0x000002A47C6D5AE0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1877} normal block at 0x000002A47C6D5A70, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1846} normal block at 0x000002A47C6C0C50, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
..\api\boinc_api.cpp(309) : {1833} normal block at 0x000002A47C6D65A0, 8 bytes long.
 Data: <  d|    > 00 00 64 7C A4 02 00 00 
{306} normal block at 0x000002A47C6D6D70, 8 bytes long.
 Data: < um|    > 20 75 6D 7C A4 02 00 00 
{297} normal block at 0x000002A47C6C2020, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{296} normal block at 0x000002A47C6D63C0, 16 bytes long.
 Data: <(tm|            > 28 74 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x000002A47C6D6E60, 16 bytes long.
 Data: < tm|            > 00 74 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x000002A47C6CFB60, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{293} normal block at 0x000002A47C6D6AA0, 16 bytes long.
 Data: < sm|            > D8 73 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000002A47C6D6D20, 16 bytes long.
 Data: < sm|            > B0 73 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000002A47C6D6C80, 16 bytes long.
 Data: < sm|            > 88 73 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000002A47C6D6820, 16 bytes long.
 Data: <`sm|            > 60 73 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000002A47C6D55A0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{288} normal block at 0x000002A47C6D7040, 16 bytes long.
 Data: <( k|            > 28 F7 6B 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000002A47C6D0280, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{286} normal block at 0x000002A47C6D6780, 16 bytes long.
 Data: <  k|            > 00 F7 6B 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000002A47C6D6C30, 16 bytes long.
 Data: <  k|            > D8 F6 6B 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000002A47C6D6A50, 16 bytes long.
 Data: <  k|            > B0 F6 6B 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000002A47C6D6BE0, 16 bytes long.
 Data: <  k|            > 88 F6 6B 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000002A47C6D6AF0, 16 bytes long.
 Data: <` k|            > 60 F6 6B 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000002A47C6D6B40, 16 bytes long.
 Data: <8 k|            > 38 F6 6B 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000002A47C6D07C0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{278} normal block at 0x000002A47C6D6690, 16 bytes long.
 Data: <  k|            > 10 F6 6B 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000002A47C6BF610, 320 bytes long.
 Data: < fm|      m|    > 90 66 6D 7C A4 02 00 00 C0 07 6D 7C A4 02 00 00 
{276} normal block at 0x000002A47C6D67D0, 16 bytes long.
 Data: <@sm|            > 40 73 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000002A47C6D6280, 16 bytes long.
 Data: < sm|            > 18 73 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000002A47C6D0640, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{273} normal block at 0x000002A47C6D6730, 16 bytes long.
 Data: < rm|            > F0 72 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000002A47C6CFAA0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{271} normal block at 0x000002A47C6D65F0, 16 bytes long.
 Data: <8rm|            > 38 72 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000002A47C6D6CD0, 16 bytes long.
 Data: < rm|            > 10 72 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000002A47C6D6370, 16 bytes long.
 Data: < qm|            > E8 71 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000002A47C6D66E0, 16 bytes long.
 Data: < qm|            > C0 71 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000002A47C6D6640, 16 bytes long.
 Data: < qm|            > 98 71 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000002A47C6D6320, 16 bytes long.
 Data: <pqm|            > 70 71 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000002A47C6D6140, 16 bytes long.
 Data: <0\m|            > 30 5C 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000002A47C6D5C30, 40 bytes long.
 Data: <@am|    P l|    > 40 61 6D 7C A4 02 00 00 50 0C 6C 7C A4 02 00 00 
{262} normal block at 0x000002A47C6D6500, 16 bytes long.
 Data: <Pqm|            > 50 71 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000002A47C6D6550, 16 bytes long.
 Data: <(qm|            > 28 71 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000002A47C6D0100, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{259} normal block at 0x000002A47C6D6230, 16 bytes long.
 Data: < qm|            > 00 71 6D 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000002A47C6D7100, 992 bytes long.
 Data: <0bm|      m|    > 30 62 6D 7C A4 02 00 00 00 01 6D 7C A4 02 00 00 
{94} normal block at 0x000002A47C6D00A0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{93} normal block at 0x000002A47C6CD880, 16 bytes long.
 Data: <  k|            > C0 E9 6B 7C A4 02 00 00 00 00 00 00 00 00 00 00 
{92} normal block at 0x000002A47C6BE9C0, 40 bytes long.
 Data: <  l|      m|    > 80 D8 6C 7C A4 02 00 00 A0 00 6D 7C A4 02 00 00 
{71} normal block at 0x000002A47C6CE4B0, 16 bytes long.
 Data: <  %             > 80 EA 25 80 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000002A47C6CE3C0, 16 bytes long.
 Data: <@ %             > 40 E9 25 80 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000002A47C6CDF10, 16 bytes long.
 Data: < W"             > F8 57 22 80 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000002A47C6CE460, 16 bytes long.
 Data: < W"             > D8 57 22 80 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002A47C6CE320, 16 bytes long.
 Data: <P "             > 50 04 22 80 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002A47C6CD830, 16 bytes long.
 Data: <0 "             > 30 04 22 80 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000002A47C6CE000, 16 bytes long.
 Data: <  "             > E0 02 22 80 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002A47C6CDFB0, 16 bytes long.
 Data: <  "             > 10 04 22 80 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000002A47C6CDEC0, 16 bytes long.
 Data: <p "             > 70 04 22 80 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000002A47C6CDE70, 16 bytes long.
 Data: <                > 18 C0 20 80 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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