Task 38600708

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>
01:21:52 (11720): wrapper (7.9.26016): starting
01:21:52 (11720): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A01_A27_0.pdb
QB_A01_A27_0.xml
QB_A01_A27.inpcrd
QB_A01_A27_input.yaml
QB_A01_A27.pdb
QB_A01_A27.prmtop
QB_A01_A27_sys.xml
run.bat
run.sh
01:21:53 (11720): Library/usr/bin/tar.exe exited; CPU time 0.015625
01:21:53 (11720): 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:\Data\BOINC\slots\2\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:\Data\BOINC\slots\2\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) : {3835433} normal block at 0x00000147C71DC660, 8 bytes long.
 Data: <  i G   > 00 00 69 C7 47 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833958} normal block at 0x00000147C9D5A2D0, 1080 bytes long.
 Data: <8               > 38 18 00 00 CD CD CD CD B0 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {311} normal block at 0x00000147C71D33A0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
02:41:19 (50316): wrapper (7.9.26016): starting
02:41:19 (50316): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\Data\BOINC\slots\2\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:\Data\BOINC\slots\2\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\Data\BOINC\slots\2\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\Data\BOINC\slots\2\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\Data\BOINC\slots\2\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\Data\BOINC\slots\2\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Data\BOINC\slots\2\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Data\BOINC\slots\2\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Data\BOINC\slots\2\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Data\BOINC\slots\2\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
04:04:37 (50316): C:/Windows/system32/cmd.exe exited; CPU time 5033.421875
04:04:37 (50316): app exit status: 0x16
04:04:37 (50316): called boinc_finish(195)
0 bytes in 0 Free Blocks.
176 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: 100580795 bytes.
Dumping objects ->
{1867} normal block at 0x000001B4243269E0, 48 bytes long.
 Data: <PATH=C:\Data\BOI> 50 41 54 48 3D 43 3A 5C 44 61 74 61 5C 42 4F 49 
{1856} normal block at 0x000001B424322690, 32 bytes long.
 Data: <HOME=C:\Data\BOI> 48 4F 4D 45 3D 43 3A 5C 44 61 74 61 5C 42 4F 49 
{1845} normal block at 0x000001B4243223F0, 32 bytes long.
 Data: <TMP=C:\Data\BOIN> 54 4D 50 3D 43 3A 5C 44 61 74 61 5C 42 4F 49 4E 
{1834} normal block at 0x000001B424322210, 32 bytes long.
 Data: <TEMP=C:\Data\BOI> 54 45 4D 50 3D 43 3A 5C 44 61 74 61 5C 42 4F 49 
{1823} normal block at 0x000001B424321CD0, 32 bytes long.
 Data: <TMPDIR=C:\Data\B> 54 4D 50 44 49 52 3D 43 3A 5C 44 61 74 61 5C 42 
{1792} normal block at 0x000001B424326D60, 48 bytes long.
 Data: <PATH=C:\Data\BOI> 50 41 54 48 3D 43 3A 5C 44 61 74 61 5C 42 4F 49 
..\api\boinc_api.cpp(309) : {1779} normal block at 0x000001B424327B00, 8 bytes long.
 Data: <   $    > 00 00 A6 24 B4 01 00 00 
{305} normal block at 0x000001B4243277E0, 8 bytes long.
 Data: <  2$    > D0 85 32 24 B4 01 00 00 
{296} normal block at 0x000001B424314B50, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{295} normal block at 0x000001B4243280A0, 16 bytes long.
 Data: <  2$            > D8 84 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x000001B424328000, 16 bytes long.
 Data: <  2$            > B0 84 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000001B424321F70, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{292} normal block at 0x000001B4243273D0, 16 bytes long.
 Data: <  2$            > 88 84 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000001B424328050, 16 bytes long.
 Data: <` 2$            > 60 84 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000001B424327E70, 16 bytes long.
 Data: <8 2$            > 38 84 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000001B424327920, 16 bytes long.
 Data: <  2$            > 10 84 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000001B424326C80, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{287} normal block at 0x000001B424327E20, 16 bytes long.
 Data: <x;1$            > 78 3B 31 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000001B424321D30, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{285} normal block at 0x000001B424327AB0, 16 bytes long.
 Data: <P;1$            > 50 3B 31 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000001B424327F60, 16 bytes long.
 Data: <(;1$            > 28 3B 31 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000001B424327D80, 16 bytes long.
 Data: < ;1$            > 00 3B 31 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000001B424327510, 16 bytes long.
 Data: < :1$            > D8 3A 31 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001B424327650, 16 bytes long.
 Data: < :1$            > B0 3A 31 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001B424327600, 16 bytes long.
 Data: < :1$            > 88 3A 31 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001B4243220F0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{277} normal block at 0x000001B424327330, 16 bytes long.
 Data: <`:1$            > 60 3A 31 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000001B424313A60, 320 bytes long.
 Data: <0s2$      2$    > 30 73 32 24 B4 01 00 00 F0 20 32 24 B4 01 00 00 
{275} normal block at 0x000001B424327420, 16 bytes long.
 Data: <  2$            > F0 83 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000001B4243272E0, 16 bytes long.
 Data: <  2$            > C8 83 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001B424322090, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{272} normal block at 0x000001B424327F10, 16 bytes long.
 Data: <  2$            > A0 83 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001B424322030, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{270} normal block at 0x000001B424327EC0, 16 bytes long.
 Data: <  2$            > E8 82 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000001B424327470, 16 bytes long.
 Data: <  2$            > C0 82 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000001B424327D30, 16 bytes long.
 Data: <  2$            > 98 82 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001B424327290, 16 bytes long.
 Data: <p 2$            > 70 82 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001B424327CE0, 16 bytes long.
 Data: <H 2$            > 48 82 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000001B4243276A0, 16 bytes long.
 Data: <  2$            > 20 82 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000001B424327C90, 16 bytes long.
 Data: < l2$            > F0 6C 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000001B424326CF0, 40 bytes long.
 Data: < |2$    `m2$    > 90 7C 32 24 B4 01 00 00 60 6D 32 24 B4 01 00 00 
{261} normal block at 0x000001B424327C40, 16 bytes long.
 Data: <  2$            > 00 82 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000001B424327240, 16 bytes long.
 Data: <  2$            > D8 81 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x000001B424321A90, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{258} normal block at 0x000001B424327BF0, 16 bytes long.
 Data: <  2$            > B0 81 32 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x000001B4243281B0, 992 bytes long.
 Data: < {2$      2$    > F0 7B 32 24 B4 01 00 00 90 1A 32 24 B4 01 00 00 
{93} normal block at 0x000001B4243225D0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{92} normal block at 0x000001B42431CD40, 16 bytes long.
 Data: <  1$            > 00 00 31 24 B4 01 00 00 00 00 00 00 00 00 00 00 
{91} normal block at 0x000001B424310000, 40 bytes long.
 Data: <@ 1$     %2$    > 40 CD 31 24 B4 01 00 00 D0 25 32 24 B4 01 00 00 
{70} normal block at 0x000001B42431CA70, 16 bytes long.
 Data: <  8             > 80 EA 38 C6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000001B42431C1B0, 16 bytes long.
 Data: <@ 8             > 40 E9 38 C6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001B42431CB60, 16 bytes long.
 Data: < W5             > F8 57 35 C6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001B42431CA20, 16 bytes long.
 Data: < W5             > D8 57 35 C6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001B42431CE30, 16 bytes long.
 Data: <P 5             > 50 04 35 C6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001B42431C200, 16 bytes long.
 Data: <0 5             > 30 04 35 C6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001B42431C9D0, 16 bytes long.
 Data: <  5             > E0 02 35 C6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001B42431C840, 16 bytes long.
 Data: <  5             > 10 04 35 C6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001B42431CCA0, 16 bytes long.
 Data: <p 5             > 70 04 35 C6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001B42431CC50, 16 bytes long.
 Data: <  3             > 18 C0 33 C6 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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