Task 38618244

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>
10:27:25 (472): wrapper (7.9.26016): starting
10:27:25 (472): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A03_A01_0.pdb
QB_A03_A01_0.xml
QB_A03_A01.inpcrd
QB_A03_A01_input.yaml
QB_A03_A01.pdb
QB_A03_A01.prmtop
QB_A03_A01_sys.xml
run.bat
run.sh
10:27:27 (472): Library/usr/bin/tar.exe exited; CPU time 0.000000
10:27:27 (472): 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\17\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\17\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) : {3835105} normal block at 0x00000000005FDC80, 8 bytes long.
 Data: <        > 00 00 82 00 00 00 00 00 
..\lib\diagnostics_win.cpp(417) : {3833954} normal block at 0x000000000269D840, 1080 bytes long.
 Data: <8               > 38 1A 00 00 CD CD CD CD 98 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x00000000005F07A0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
13:46:11 (19092): wrapper (7.9.26016): starting
13:46:11 (19092): 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\17\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1453} normal block at 0x0000000000435AE0, 8 bytes long.
 Data: <        > 00 00 D0 00 00 00 00 00 
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x0000000000436A60, 1080 bytes long.
 Data: <`F              > 60 46 00 00 CD CD CD CD AC 01 00 00 00 00 00 00 
Object dump complete.
18:00:58 (5656): wrapper (7.9.26016): starting
18:00:58 (5656): 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\17\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\17\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\17\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\17\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\17\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\17\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\17\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\17\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\17\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\17\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
21:23:40 (5656): C:/Windows/system32/cmd.exe exited; CPU time 12080.562500
21:23:40 (5656): app exit status: 0x16
21:23:40 (5656): 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: 176289211 bytes.
Dumping objects ->
{1541} normal block at 0x00000000004D08F0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1530} normal block at 0x00000000004D03B0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1519} normal block at 0x00000000004D0730, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1508} normal block at 0x00000000004D0340, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1497} normal block at 0x00000000004D0880, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1466} normal block at 0x00000000004BFF00, 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) : {1453} normal block at 0x00000000004D5770, 8 bytes long.
 Data: <  I     > 00 00 49 00 00 00 00 00 
{303} normal block at 0x00000000004D5C20, 8 bytes long.
 Data: <`jM     > 60 6A 4D 00 00 00 00 00 
{294} normal block at 0x00000000004C1EC0, 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 0x00000000004D6530, 16 bytes long.
 Data: <hiM             > 68 69 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x00000000004D6490, 16 bytes long.
 Data: <@iM             > 40 69 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x00000000004D16A0, 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 0x00000000004D5BD0, 16 bytes long.
 Data: < iM             > 18 69 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x00000000004D5720, 16 bytes long.
 Data: < hM             > F0 68 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x00000000004D5900, 16 bytes long.
 Data: < hM             > C8 68 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x00000000004D5D60, 16 bytes long.
 Data: < hM             > A0 68 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x00000000004D0810, 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 0x00000000004D5680, 16 bytes long.
 Data: <  K             > F8 F2 4B 00 00 00 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000000004D12E0, 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 0x00000000004D65D0, 16 bytes long.
 Data: <  K             > D0 F2 4B 00 00 00 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000000004D5B80, 16 bytes long.
 Data: <  K             > A8 F2 4B 00 00 00 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000000004D5D10, 16 bytes long.
 Data: <  K             > 80 F2 4B 00 00 00 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x00000000004D63A0, 16 bytes long.
 Data: <X K             > 58 F2 4B 00 00 00 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000000004D6440, 16 bytes long.
 Data: <0 K             > 30 F2 4B 00 00 00 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x00000000004D6300, 16 bytes long.
 Data: <  K             > 08 F2 4B 00 00 00 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x00000000004D1940, 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 0x00000000004D58B0, 16 bytes long.
 Data: <  K             > E0 F1 4B 00 00 00 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000000004BF1E0, 320 bytes long.
 Data: < XM     @ M     > B0 58 4D 00 00 00 00 00 40 19 4D 00 00 00 00 00 
{273} normal block at 0x00000000004D5E50, 16 bytes long.
 Data: < hM             > 80 68 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x00000000004D5860, 16 bytes long.
 Data: <XhM             > 58 68 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x00000000004D0CE0, 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 0x00000000004D5A40, 16 bytes long.
 Data: <0hM             > 30 68 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000000004D18E0, 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 0x00000000004D6120, 16 bytes long.
 Data: <xgM             > 78 67 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000000004D56D0, 16 bytes long.
 Data: <PgM             > 50 67 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x00000000004D57C0, 16 bytes long.
 Data: <(gM             > 28 67 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x00000000004D5AE0, 16 bytes long.
 Data: < gM             > 00 67 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000000004D6580, 16 bytes long.
 Data: < fM             > D8 66 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x00000000004D6260, 16 bytes long.
 Data: < fM             > B0 66 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000000004D63F0, 16 bytes long.
 Data: <  M             > C0 06 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x00000000004D06C0, 40 bytes long.
 Data: < cM       K     > F0 63 4D 00 00 00 00 00 00 FF 4B 00 00 00 00 00 
{259} normal block at 0x00000000004D64E0, 16 bytes long.
 Data: < fM             > 90 66 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x00000000004D6170, 16 bytes long.
 Data: <hfM             > 68 66 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x00000000004D1400, 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 0x00000000004D5B30, 16 bytes long.
 Data: <@fM             > 40 66 4D 00 00 00 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x00000000004D6640, 992 bytes long.
 Data: <0[M       M     > 30 5B 4D 00 00 00 00 00 00 14 4D 00 00 00 00 00 
{91} normal block at 0x00000000004D1700, 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 0x00000000004CDB50, 16 bytes long.
 Data: <  K             > E0 EE 4B 00 00 00 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x00000000004BEEE0, 40 bytes long.
 Data: <P L       M     > 50 DB 4C 00 00 00 00 00 00 17 4D 00 00 00 00 00 
{68} normal block at 0x00000000004CD380, 16 bytes long.
 Data: <                > 80 EA C2 FE F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000000004CD560, 16 bytes long.
 Data: <@               > 40 E9 C2 FE F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x00000000004CD510, 16 bytes long.
 Data: < W              > F8 57 BF FE F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x00000000004CDBA0, 16 bytes long.
 Data: < W              > D8 57 BF FE F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x00000000004CD740, 16 bytes long.
 Data: <P               > 50 04 BF FE F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x00000000004CD6F0, 16 bytes long.
 Data: <0               > 30 04 BF FE F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x00000000004CDCE0, 16 bytes long.
 Data: <                > E0 02 BF FE F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x00000000004CD4C0, 16 bytes long.
 Data: <                > 10 04 BF FE F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x00000000004CDB00, 16 bytes long.
 Data: <p               > 70 04 BF FE F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x00000000004CD970, 16 bytes long.
 Data: <                > 18 C0 BD FE F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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