Task 38598733

Stderr output

<core_client_version>8.2.4</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
07:47:50 (10204): wrapper (7.9.26016): starting
07:47:50 (10204): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A17_A21_0.pdb
QB_A17_A21_0.xml
QB_A17_A21.inpcrd
QB_A17_A21_input.yaml
QB_A17_A21.pdb
QB_A17_A21.prmtop
QB_A17_A21_sys.xml
run.bat
run.sh
07:47:51 (10204): Library/usr/bin/tar.exe exited; CPU time 0.000000
07:47:51 (10204): 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\24\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\24\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) : {3835111} normal block at 0x00000239A605E4A0, 8 bytes long.
 Data: <    9   > 00 00 FE A5 39 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833962} normal block at 0x00000239A7D076B0, 1080 bytes long.
 Data: <h               > 68 81 00 00 CD CD CD CD 04 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {313} normal block at 0x00000239A6055BC0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
09:05:32 (2396): wrapper (7.9.26016): starting
09:05:32 (2396): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x0000024C217F64F0, 8 bytes long.
 Data: <  w!L   > 00 00 77 21 4C 02 00 00 
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x0000024C217F7060, 1080 bytes long.
 Data: < ~              > D8 7E 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
09:59:51 (33684): wrapper (7.9.26016): starting
09:59:51 (33684): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x000001D533B25B40, 8 bytes long.
 Data: <   3    > 00 00 A9 33 D5 01 00 00 
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x000001D533B26660, 1080 bytes long.
 Data: < }              > 04 7D 00 00 CD CD CD CD B0 01 00 00 00 00 00 00 
Object dump complete.
10:45:09 (29760): wrapper (7.9.26016): starting
10:45:09 (29760): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x00000173648F55A0, 8 bytes long.
 Data: <   ds   > 00 00 CC 64 73 01 00 00 
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x00000173648F6660, 1080 bytes long.
 Data: <<j              > 3C 6A 00 00 CD CD CD CD AC 01 00 00 00 00 00 00 
Object dump complete.
11:38:05 (12740): wrapper (7.9.26016): starting
11:38:05 (12740): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x000002096C955EB0, 8 bytes long.
 Data: <   l    > 00 00 92 6C 09 02 00 00 
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x000002096C9566B0, 1080 bytes long.
 Data: <x               > 78 7F 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
14:09:39 (25368): wrapper (7.9.26016): starting
14:09:39 (25368): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x0000020953565130, 8 bytes long.
 Data: <   S    > 00 00 AE 53 09 02 00 00 
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x0000020953565C20, 1080 bytes long.
 Data: < K              > D8 4B 00 00 CD CD CD CD C4 00 00 00 00 00 00 00 
Object dump complete.
15:40:47 (26376): wrapper (7.9.26016): starting
15:40:47 (26376): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x000002389F1358B0, 8 bytes long.
 Data: <  u 8   > 00 00 75 9F 38 02 00 00 
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x000002389F136330, 1080 bytes long.
 Data: < &              > C0 26 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
17:22:55 (27812): wrapper (7.9.26016): starting
17:22:55 (27812): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x000002653BFA5D20, 8 bytes long.
 Data: <  f<e   > 00 00 66 3C 65 02 00 00 
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x000002653BFA66B0, 1080 bytes long.
 Data: < [              > EC 5B 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
17:55:53 (16140): wrapper (7.9.26016): starting
17:55:53 (16140): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x0000012651A05870, 8 bytes long.
 Data: <  GS&   > 00 00 47 53 26 01 00 00 
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x0000012651A06660, 1080 bytes long.
 Data: <(B              > 28 42 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
19:04:28 (31404): wrapper (7.9.26016): starting
19:04:28 (31404): 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\24\tmp already exists.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x00000284D1A05640, 8 bytes long.
 Data: <        > 00 00 EB D1 84 02 00 00 
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x00000284D1A06660, 1080 bytes long.
 Data: < p              > 98 70 00 00 CD CD CD CD 1C 00 00 00 00 00 00 00 
Object dump complete.
20:02:05 (30048): wrapper (7.9.26016): starting
20:02:05 (30048): 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\24\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\24\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\24\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\24\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\24\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\24\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\24\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\24\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\24\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\24\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
20:32:42 (30048): C:/Windows/system32/cmd.exe exited; CPU time 1787.750000
20:32:42 (30048): app exit status: 0x16
20:32:42 (30048): 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: 32270039 bytes.
Dumping objects ->
{1543} normal block at 0x00000186A27B4880, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1532} normal block at 0x00000186A27B47A0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1521} normal block at 0x00000186A27B4DC0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1510} normal block at 0x00000186A27B4B90, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1499} normal block at 0x00000186A27B4960, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1468} normal block at 0x00000186A27A06D0, 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) : {1455} normal block at 0x00000186A27B57D0, 8 bytes long.
 Data: <        > 00 00 15 A4 86 01 00 00 
{307} normal block at 0x00000186A27B56E0, 8 bytes long.
 Data: < f{     > B0 66 7B A2 86 01 00 00 
{298} normal block at 0x00000186A27A1CE0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{297} normal block at 0x00000186A27B5DC0, 16 bytes long.
 Data: < e{             > B8 65 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x00000186A27B5D70, 16 bytes long.
 Data: < e{             > 90 65 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x00000186A27B07E0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{294} normal block at 0x00000186A27B55F0, 16 bytes long.
 Data: <he{             > 68 65 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x00000186A27B5B90, 16 bytes long.
 Data: <@e{             > 40 65 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x00000186A27B5B40, 16 bytes long.
 Data: < e{             > 18 65 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x00000186A27B53C0, 16 bytes long.
 Data: < d{             > F0 64 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x00000186A27B4D50, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{289} normal block at 0x00000186A27B5AA0, 16 bytes long.
 Data: <  y             > A8 F1 79 A2 86 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x00000186A27B10E0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{287} normal block at 0x00000186A27B5A00, 16 bytes long.
 Data: <  y             > 80 F1 79 A2 86 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x00000186A27B59B0, 16 bytes long.
 Data: <X y             > 58 F1 79 A2 86 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000186A27B6180, 16 bytes long.
 Data: <0 y             > 30 F1 79 A2 86 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x00000186A27B5C80, 16 bytes long.
 Data: <  y             > 08 F1 79 A2 86 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x00000186A27B6040, 16 bytes long.
 Data: <  y             > E0 F0 79 A2 86 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000186A27B5FF0, 16 bytes long.
 Data: <  y             > B8 F0 79 A2 86 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000186A27B0780, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{279} normal block at 0x00000186A27B5D20, 16 bytes long.
 Data: <  y             > 90 F0 79 A2 86 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000186A279F090, 320 bytes long.
 Data: < ]{       {     > 20 5D 7B A2 86 01 00 00 80 07 7B A2 86 01 00 00 
{277} normal block at 0x00000186A27B54B0, 16 bytes long.
 Data: < d{             > D0 64 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x00000186A27B5500, 16 bytes long.
 Data: < d{             > A8 64 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x00000186A27B0AE0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{274} normal block at 0x00000186A27B5FA0, 16 bytes long.
 Data: < d{             > 80 64 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x00000186A27B06C0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{272} normal block at 0x00000186A27B5910, 16 bytes long.
 Data: < c{             > C8 63 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x00000186A27B58C0, 16 bytes long.
 Data: < c{             > A0 63 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x00000186A27B5870, 16 bytes long.
 Data: <xc{             > 78 63 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000186A27B5460, 16 bytes long.
 Data: <Pc{             > 50 63 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000186A27B5CD0, 16 bytes long.
 Data: <(c{             > 28 63 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000186A27B52D0, 16 bytes long.
 Data: < c{             > 00 63 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x00000186A27B5410, 16 bytes long.
 Data: < H{             > F0 48 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000186A27B48F0, 40 bytes long.
 Data: < T{       z     > 10 54 7B A2 86 01 00 00 D0 06 7A A2 86 01 00 00 
{263} normal block at 0x00000186A27B5820, 16 bytes long.
 Data: < b{             > E0 62 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x00000186A27B5370, 16 bytes long.
 Data: < b{             > B8 62 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000186A27B0DE0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{260} normal block at 0x00000186A27B5780, 16 bytes long.
 Data: < b{             > 90 62 7B A2 86 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x00000186A27B6290, 992 bytes long.
 Data: < W{       {     > 80 57 7B A2 86 01 00 00 E0 0D 7B A2 86 01 00 00 
{95} normal block at 0x00000186A27B14A0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{94} normal block at 0x00000186A27AD3D0, 16 bytes long.
 Data: <  y             > 10 DA 79 A2 86 01 00 00 00 00 00 00 00 00 00 00 
{93} normal block at 0x00000186A279DA10, 40 bytes long.
 Data: <  z       {     > D0 D3 7A A2 86 01 00 00 A0 14 7B A2 86 01 00 00 
{72} normal block at 0x00000186A27AD1A0, 16 bytes long.
 Data: <   7            > 80 EA A2 37 F7 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x00000186A27AD240, 16 bytes long.
 Data: <@  7            > 40 E9 A2 37 F7 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x00000186A27ADBF0, 16 bytes long.
 Data: < W 7            > F8 57 9F 37 F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x00000186A27ACFC0, 16 bytes long.
 Data: < W 7            > D8 57 9F 37 F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x00000186A27AD510, 16 bytes long.
 Data: <P  7            > 50 04 9F 37 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000186A27AD4C0, 16 bytes long.
 Data: <0  7            > 30 04 9F 37 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x00000186A27AD2E0, 16 bytes long.
 Data: <   7            > E0 02 9F 37 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x00000186A27AD150, 16 bytes long.
 Data: <   7            > 10 04 9F 37 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x00000186A27AD970, 16 bytes long.
 Data: <p  7            > 70 04 9F 37 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x00000186A27ACF20, 16 bytes long.
 Data: <   7            > 18 C0 9D 37 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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