Task 38643225

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>
06:58:37 (7548): wrapper (7.9.26016): starting
06:58:37 (7548): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A08_A13_0.pdb
QB_A08_A13_0.xml
QB_A08_A13.inpcrd
QB_A08_A13_input.yaml
QB_A08_A13.pdb
QB_A08_A13.prmtop
QB_A08_A13_sys.xml
run.bat
run.sh
06:58:49 (7548): Library/usr/bin/tar.exe exited; CPU time 0.187500
06:58:49 (7548): 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\6\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\6\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) : {3835122} normal block at 0x00000268DBB3DB80, 8 bytes long.
 Data: <    h   > 00 00 01 DC 68 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833970} normal block at 0x00000268DD8F4520, 1080 bytes long.
 Data: <H1              > 48 31 00 00 CD CD CD CD 94 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {317} normal block at 0x00000268DBB428A0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
07:14:21 (14644): wrapper (7.9.26016): starting
07:14:21 (14644): 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\6\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1462} normal block at 0x000001AA74346570, 8 bytes long.
 Data: <   t    > 00 00 87 74 AA 01 00 00 
..\lib\diagnostics_win.cpp(417) : {310} normal block at 0x000001AA74345D60, 1080 bytes long.
 Data: < Y      H       > C4 59 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
07:35:59 (26928): wrapper (7.9.26016): starting
07:35:59 (26928): 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\6\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1462} normal block at 0x000002157B9D6F70, 8 bytes long.
 Data: <   {    > 00 00 E5 7B 15 02 00 00 
..\lib\diagnostics_win.cpp(417) : {310} normal block at 0x000002157B9D5D60, 1080 bytes long.
 Data: < B              > 18 42 00 00 CD CD CD CD B4 00 00 00 00 00 00 00 
Object dump complete.
07:40:41 (6548): wrapper (7.9.26016): starting
07:40:41 (6548): 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\6\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1462} normal block at 0x0000023461996D90, 8 bytes long.
 Data: <   a4   > 00 00 DE 61 34 02 00 00 
..\lib\diagnostics_win.cpp(417) : {310} normal block at 0x0000023461995D60, 1080 bytes long.
 Data: < R      H       > 84 52 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
07:51:44 (17172): wrapper (7.9.26016): starting
07:51:44 (17172): 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\6\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1462} normal block at 0x000001CDC2A97060, 8 bytes long.
 Data: <  S     > 00 00 53 C4 CD 01 00 00 
..\lib\diagnostics_win.cpp(417) : {310} normal block at 0x000001CDC2A95D60, 1080 bytes long.
 Data: < q      ,       > EC 71 00 00 CD CD CD CD 2C 01 00 00 00 00 00 00 
Object dump complete.
07:57:16 (24496): wrapper (7.9.26016): starting
07:57:16 (24496): 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\6\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1462} normal block at 0x0000020DABBE6570, 8 bytes long.
 Data: <        > 00 00 B9 AB 0D 02 00 00 
..\lib\diagnostics_win.cpp(417) : {310} normal block at 0x0000020DABBE5D60, 1080 bytes long.
 Data: < i      H       > C4 69 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
08:05:18 (25084): wrapper (7.9.26016): starting
08:05:18 (25084): 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\6\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1462} normal block at 0x00000222096B69D0, 8 bytes long.
 Data: <  b "   > 00 00 62 09 22 02 00 00 
..\lib\diagnostics_win.cpp(417) : {310} normal block at 0x00000222096B5D60, 1080 bytes long.
 Data: < G      H       > A8 47 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
08:15:28 (23776): wrapper (7.9.26016): starting
08:15:28 (23776): 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\6\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\6\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\6\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\6\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\6\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
08:34:55 (23776): C:/Windows/system32/cmd.exe exited; CPU time 1117.187500
08:34:55 (23776): app exit status: 0x16
08:34:55 (23776): 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: 18868596 bytes.
Dumping objects ->
{1550} normal block at 0x000002621DCC1240, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1539} normal block at 0x000002621DCC1320, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1528} normal block at 0x000002621DCC1080, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1517} normal block at 0x000002621DCC0C90, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1506} normal block at 0x000002621DCC0F30, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1475} normal block at 0x000002621DCAEF30, 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) : {1462} normal block at 0x000002621DCC6A00, 8 bytes long.
 Data: <    b   > 00 00 C2 1D 62 02 00 00 
{311} normal block at 0x000002621DCC6EB0, 8 bytes long.
 Data: <pu  b   > 70 75 CC 1D 62 02 00 00 
{302} normal block at 0x000002621DCB7280, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{301} normal block at 0x000002621DCC6D70, 16 bytes long.
 Data: <xt  b           > 78 74 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{300} normal block at 0x000002621DCC6E60, 16 bytes long.
 Data: <Pt  b           > 50 74 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{299} normal block at 0x000002621DCC0100, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{298} normal block at 0x000002621DCC6910, 16 bytes long.
 Data: <(t  b           > 28 74 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{297} normal block at 0x000002621DCC70E0, 16 bytes long.
 Data: < t  b           > 00 74 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x000002621DCC6FA0, 16 bytes long.
 Data: < s  b           > D8 73 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x000002621DCC6640, 16 bytes long.
 Data: < s  b           > B0 73 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x000002621DCC0EC0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{293} normal block at 0x000002621DCC6690, 16 bytes long.
 Data: <    b           > C8 EE CA 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000002621DCC00A0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{291} normal block at 0x000002621DCC6550, 16 bytes long.
 Data: <    b           > A0 EE CA 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000002621DCC6F50, 16 bytes long.
 Data: <x   b           > 78 EE CA 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000002621DCC6870, 16 bytes long.
 Data: <P   b           > 50 EE CA 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000002621DCC67D0, 16 bytes long.
 Data: <(   b           > 28 EE CA 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000002621DCC6500, 16 bytes long.
 Data: <    b           > 00 EE CA 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000002621DCC66E0, 16 bytes long.
 Data: <    b           > D8 ED CA 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000002621DCC0A60, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{283} normal block at 0x000002621DCC6410, 16 bytes long.
 Data: <    b           > B0 ED CA 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000002621DCAEDB0, 320 bytes long.
 Data: < d  b   `   b   > 10 64 CC 1D 62 02 00 00 60 0A CC 1D 62 02 00 00 
{281} normal block at 0x000002621DCC6AF0, 16 bytes long.
 Data: < s  b           > 90 73 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000002621DCC6FF0, 16 bytes long.
 Data: <hs  b           > 68 73 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000002621DCC0940, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{278} normal block at 0x000002621DCC6960, 16 bytes long.
 Data: <@s  b           > 40 73 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000002621DCC0340, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{276} normal block at 0x000002621DCC6D20, 16 bytes long.
 Data: < r  b           > 88 72 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000002621DCC69B0, 16 bytes long.
 Data: <`r  b           > 60 72 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000002621DCC64B0, 16 bytes long.
 Data: <8r  b           > 38 72 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000002621DCC63C0, 16 bytes long.
 Data: < r  b           > 10 72 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000002621DCC6F00, 16 bytes long.
 Data: < q  b           > E8 71 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000002621DCC6370, 16 bytes long.
 Data: < q  b           > C0 71 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000002621DCC65F0, 16 bytes long.
 Data: <    b           > E0 0D CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000002621DCC0DE0, 40 bytes long.
 Data: < e  b   0   b   > F0 65 CC 1D 62 02 00 00 30 EF CA 1D 62 02 00 00 
{267} normal block at 0x000002621DCC6CD0, 16 bytes long.
 Data: < q  b           > A0 71 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000002621DCC65A0, 16 bytes long.
 Data: <xq  b           > 78 71 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000002621DCC0820, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{264} normal block at 0x000002621DCC62D0, 16 bytes long.
 Data: <Pq  b           > 50 71 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000002621DCC7150, 992 bytes long.
 Data: < b  b       b   > D0 62 CC 1D 62 02 00 00 20 08 CC 1D 62 02 00 00 
{99} normal block at 0x000002621DCC03A0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{98} normal block at 0x000002621DCBDAE0, 16 bytes long.
 Data: <    b           > B0 12 CC 1D 62 02 00 00 00 00 00 00 00 00 00 00 
{97} normal block at 0x000002621DCC12B0, 40 bytes long.
 Data: <    b       b   > E0 DA CB 1D 62 02 00 00 A0 03 CC 1D 62 02 00 00 
{76} normal block at 0x000002621DCBDB30, 16 bytes long.
 Data: <                > 80 EA C3 CA F6 7F 00 00 00 00 00 00 00 00 00 00 
{75} normal block at 0x000002621DCBE620, 16 bytes long.
 Data: <@               > 40 E9 C3 CA F6 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x000002621DCBE6C0, 16 bytes long.
 Data: < W              > F8 57 C0 CA F6 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x000002621DCBE8A0, 16 bytes long.
 Data: < W              > D8 57 C0 CA F6 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x000002621DCBE530, 16 bytes long.
 Data: <P               > 50 04 C0 CA F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000002621DCBE850, 16 bytes long.
 Data: <0               > 30 04 C0 CA F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000002621DCBDBD0, 16 bytes long.
 Data: <                > E0 02 C0 CA F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000002621DCBE120, 16 bytes long.
 Data: <                > 10 04 C0 CA F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000002621DCBDF90, 16 bytes long.
 Data: <p               > 70 04 C0 CA F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002621DCBDF40, 16 bytes long.
 Data: <                > 18 C0 BE CA F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

©2026 Universitat Pompeu Fabra