Task 38643768

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
12:02:12 (5596): wrapper (7.9.26016): starting
12:02:12 (5596): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A04_A02_0.pdb
QB_A04_A02_0.xml
QB_A04_A02.inpcrd
QB_A04_A02_input.yaml
QB_A04_A02.pdb
QB_A04_A02.prmtop
QB_A04_A02_sys.xml
run.bat
run.sh
12:02:13 (5596): Library/usr/bin/tar.exe exited; CPU time 0.015625
12:02:13 (5596): 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\4\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\4\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) : {3835419} normal block at 0x000001EC44A5AED0, 8 bytes long.
 Data: <   D    > 00 00 F0 44 EC 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833972} normal block at 0x000001EC4689E6F0, 1080 bytes long.
 Data: <        <       > BC DF 00 00 CD CD CD CD 3C 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {318} normal block at 0x000001EC44A61350, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
12:58:42 (58920): wrapper (7.9.26016): starting
12:58:42 (58920): 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\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1758} normal block at 0x00000207110B6C50, 8 bytes long.
 Data: <  i     > 00 00 69 11 07 02 00 00 
..\lib\diagnostics_win.cpp(417) : {311} normal block at 0x00000207110B74A0, 1080 bytes long.
 Data: <Li      H       > 4C 69 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
13:30:32 (56068): wrapper (7.9.26016): starting
13:30:32 (56068): 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\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1758} normal block at 0x00000199AE8C6520, 8 bytes long.
 Data: <  /     > 00 00 2F B0 99 01 00 00 
..\lib\diagnostics_win.cpp(417) : {311} normal block at 0x00000199AE8C7040, 1080 bytes long.
 Data: <4       H       > 34 E5 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
13:43:08 (56292): wrapper (7.9.26016): starting
13:43:08 (56292): 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\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1758} normal block at 0x0000022A90EF5E90, 8 bytes long.
 Data: <  ? *   > 00 00 3F 91 2A 02 00 00 
..\lib\diagnostics_win.cpp(417) : {311} normal block at 0x0000022A90EF7040, 1080 bytes long.
 Data: <        H       > B0 DE 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
15:07:13 (58324): wrapper (7.9.26016): starting
15:07:13 (58324): 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\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1758} normal block at 0x0000023474996AA0, 8 bytes long.
 Data: <   t4   > 00 00 EB 74 34 02 00 00 
..\lib\diagnostics_win.cpp(417) : {311} normal block at 0x0000023474997070, 1080 bytes long.
 Data: <        `       > 90 C6 00 00 CD CD CD CD 60 01 00 00 00 00 00 00 
Object dump complete.
15:39:18 (63472): wrapper (7.9.26016): starting
15:39:18 (63472): 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\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1758} normal block at 0x0000015CD39B6DC0, 8 bytes long.
 Data: <    \   > 00 00 F3 D3 5C 01 00 00 
..\lib\diagnostics_win.cpp(417) : {311} normal block at 0x0000015CD39B72A0, 1080 bytes long.
 Data: <x       L       > 78 A8 00 00 CD CD CD CD 4C 01 00 00 00 00 00 00 
Object dump complete.
16:30:18 (29416): wrapper (7.9.26016): starting
16:30:18 (29416): 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\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1758} normal block at 0x0000027650A26670, 8 bytes long.
 Data: <   Pv   > 00 00 9A 50 76 02 00 00 
..\lib\diagnostics_win.cpp(417) : {311} normal block at 0x0000027650A26DD0, 1080 bytes long.
 Data: <        H       > CC F4 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
16:41:28 (59748): wrapper (7.9.26016): starting
16:41:28 (59748): 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\4\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\4\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\4\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\4\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\4\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
17:05:35 (59748): C:/Windows/system32/cmd.exe exited; CPU time 1348.437500
17:05:35 (59748): app exit status: 0x16
17:05:35 (59748): 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: 39361548 bytes.
Dumping objects ->
{1846} normal block at 0x0000019980805340, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1835} normal block at 0x00000199808052D0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1824} normal block at 0x00000199808053B0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1813} normal block at 0x0000019980805180, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1802} normal block at 0x00000199808051F0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1771} normal block at 0x0000019980805BC0, 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) : {1758} normal block at 0x0000019980805D30, 8 bytes long.
 Data: <  x     > 00 00 78 80 99 01 00 00 
{312} normal block at 0x0000019980805D80, 8 bytes long.
 Data: <pp      > 70 70 80 80 99 01 00 00 
{303} normal block at 0x00000199807F6970, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{302} normal block at 0x0000019980806A00, 16 bytes long.
 Data: <xo              > 78 6F 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{301} normal block at 0x0000019980806BE0, 16 bytes long.
 Data: <Po              > 50 6F 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{300} normal block at 0x00000199807FEFF0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{299} normal block at 0x0000019980806780, 16 bytes long.
 Data: <(o              > 28 6F 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{298} normal block at 0x00000199808068C0, 16 bytes long.
 Data: < o              > 00 6F 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{297} normal block at 0x00000199808067D0, 16 bytes long.
 Data: < n              > D8 6E 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x0000019980806B90, 16 bytes long.
 Data: < n              > B0 6E 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x0000019980805110, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{294} normal block at 0x0000019980806370, 16 bytes long.
 Data: < Y              > F8 59 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x00000199807FEC30, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{292} normal block at 0x0000019980806320, 16 bytes long.
 Data: < Y              > D0 59 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x00000199808061E0, 16 bytes long.
 Data: < Y              > A8 59 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000019980805E20, 16 bytes long.
 Data: < Y              > 80 59 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000019980806AA0, 16 bytes long.
 Data: <XY              > 58 59 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000019980806190, 16 bytes long.
 Data: <0Y              > 30 59 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000019980806050, 16 bytes long.
 Data: < Y              > 08 59 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x00000199807FF470, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{284} normal block at 0x00000199808066E0, 16 bytes long.
 Data: < X              > E0 58 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x00000199808058E0, 320 bytes long.
 Data: < f      p       > E0 66 80 80 99 01 00 00 70 F4 7F 80 99 01 00 00 
{282} normal block at 0x00000199808064B0, 16 bytes long.
 Data: < n              > 90 6E 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000019980806730, 16 bytes long.
 Data: <hn              > 68 6E 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000199807FF830, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{279} normal block at 0x0000019980806B40, 16 bytes long.
 Data: <@n              > 40 6E 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000199807FF2F0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{277} normal block at 0x0000019980806500, 16 bytes long.
 Data: < m              > 88 6D 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x00000199808062D0, 16 bytes long.
 Data: <`m              > 60 6D 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000019980806690, 16 bytes long.
 Data: <8m              > 38 6D 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000019980806640, 16 bytes long.
 Data: < m              > 10 6D 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000019980805EC0, 16 bytes long.
 Data: < l              > E8 6C 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000019980806AF0, 16 bytes long.
 Data: < l              > C0 6C 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x00000199808060A0, 16 bytes long.
 Data: <`R              > 60 52 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000019980805260, 40 bytes long.
 Data: < `       [      > A0 60 80 80 99 01 00 00 C0 5B 80 80 99 01 00 00 
{268} normal block at 0x0000019980806910, 16 bytes long.
 Data: < l              > A0 6C 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000019980806A50, 16 bytes long.
 Data: <xl              > 78 6C 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x00000199807FECF0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{265} normal block at 0x0000019980805FB0, 16 bytes long.
 Data: <Pl              > 50 6C 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000019980806C50, 992 bytes long.
 Data: < _              > B0 5F 80 80 99 01 00 00 F0 EC 7F 80 99 01 00 00 
{100} normal block at 0x00000199807FEB70, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{99} normal block at 0x00000199807FB4A0, 16 bytes long.
 Data: <0P              > 30 50 80 80 99 01 00 00 00 00 00 00 00 00 00 00 
{98} normal block at 0x0000019980805030, 40 bytes long.
 Data: <        p       > A0 B4 7F 80 99 01 00 00 70 EB 7F 80 99 01 00 00 
{77} normal block at 0x00000199807FAC80, 16 bytes long.
 Data: <                > 80 EA C4 B2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{76} normal block at 0x00000199807FAFA0, 16 bytes long.
 Data: <@               > 40 E9 C4 B2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{75} normal block at 0x00000199807FAAF0, 16 bytes long.
 Data: < W              > F8 57 C1 B2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x00000199807FAAA0, 16 bytes long.
 Data: < W              > D8 57 C1 B2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x00000199807FAE10, 16 bytes long.
 Data: <P               > 50 04 C1 B2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x00000199807FB090, 16 bytes long.
 Data: <0               > 30 04 C1 B2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x00000199807FAB40, 16 bytes long.
 Data: <                > E0 02 C1 B2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x00000199807FB4F0, 16 bytes long.
 Data: <                > 10 04 C1 B2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x00000199807FB860, 16 bytes long.
 Data: <p               > 70 04 C1 B2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x00000199807FB0E0, 16 bytes long.
 Data: <                > 18 C0 BF B2 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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