Task 38584156

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
System operacyjny nie mo�e uruchomi� (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
15:28:44 (12420): wrapper (7.9.26016): starting
15:28:44 (12420): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A16_A10_0.pdb
QB_A16_A10_0.xml
QB_A16_A10_equil.pdb
QB_A16_A10.inpcrd
QB_A16_A10_input.yaml
QB_A16_A10_mdlambda.pdb
QB_A16_A10_min.pdb
QB_A16_A10_npt.pdb
QB_A16_A10_out_merged_nowater.pdb
QB_A16_A10.pdb
QB_A16_A10.prmtop
QB_A16_A10_sys.xml
QB_A16_A10_therm.pdb
run.bat
run.sh
15:28:48 (12420): Library/usr/bin/tar.exe exited; CPU time 0.000000
15:28:48 (12420): 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 'D:\ProgramData\BOINC\slots\1\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 'D:\ProgramData\BOINC\slots\1\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) : {3835150} normal block at 0x000002464D60D900, 8 bytes long.
 Data: <   MF   > 00 00 A4 4D 46 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833954} normal block at 0x000002464D5FD590, 1080 bytes long.
 Data: <P4              > 50 34 00 00 CD CD CD CD FC 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x000002464D600980, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
02:43:06 (16724): wrapper (7.9.26016): starting
02:43:06 (16724): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\ProgramData\BOINC\slots\1\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1498} normal block at 0x000001FD8DA185B0, 8 bytes long.
 Data: <        > 00 00 9D 8D FD 01 00 00 
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x000001FD8DA18F10, 1080 bytes long.
 Data: < C              > D4 43 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
07:46:28 (16000): wrapper (7.9.26016): starting
07:46:28 (16000): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\ProgramData\BOINC\slots\1\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 "D:\ProgramData\BOINC\slots\1\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "D:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "D:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "D:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "D:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\ProgramData\BOINC\slots\1\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
15:47:49 (16000): C:/Windows/system32/cmd.exe exited; CPU time 10953.859375
15:47:49 (16000): app exit status: 0x16
15:47:49 (16000): called boinc_finish(195)
0 bytes in 0 Free Blocks.
256 bytes in 6 Normal Blocks.
2288 bytes in 2 CRT Blocks.
0 bytes in 0 Ignore Blocks.
0 bytes in 0 Client Blocks.
Largest number used: 0 bytes.
Total allocations: 467900472 bytes.
Dumping objects ->
{1586} normal block at 0x000002526AA74980, 48 bytes long.
 Data: <PATH=D:\ProgramD> 50 41 54 48 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1575} normal block at 0x000002526AA74D70, 48 bytes long.
 Data: <HOME=D:\ProgramD> 48 4F 4D 45 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1564} normal block at 0x000002526AA747C0, 48 bytes long.
 Data: <TMP=D:\ProgramDa> 54 4D 50 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1553} normal block at 0x000002526AA74D00, 48 bytes long.
 Data: <TEMP=D:\ProgramD> 54 45 4D 50 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1542} normal block at 0x000002526AA74750, 48 bytes long.
 Data: <TMPDIR=D:\Progra> 54 4D 50 44 49 52 3D 44 3A 5C 50 72 6F 67 72 61 
{1511} normal block at 0x000002526AA60610, 64 bytes long.
 Data: <PATH=D:\ProgramD> 50 41 54 48 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
..\api\boinc_api.cpp(309) : {1498} normal block at 0x000002526AA75CA0, 8 bytes long.
 Data: <   jR   > 00 00 A3 6A 52 02 00 00 
{303} normal block at 0x000002526AA75700, 8 bytes long.
 Data: < f jR   > D0 66 A7 6A 52 02 00 00 
{294} normal block at 0x000002526AA61950, 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 0x000002526AA75D40, 16 bytes long.
 Data: < e jR           > D8 65 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000002526AA75AC0, 16 bytes long.
 Data: < e jR           > B0 65 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000002526AA71360, 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 0x000002526AA75930, 16 bytes long.
 Data: < e jR           > 88 65 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000002526AA758E0, 16 bytes long.
 Data: <`e jR           > 60 65 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000002526AA75340, 16 bytes long.
 Data: <8e jR           > 38 65 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000002526AA75ED0, 16 bytes long.
 Data: < e jR           > 10 65 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000002526AA749F0, 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 0x000002526AA75890, 16 bytes long.
 Data: <H  jR           > 48 B3 A5 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000002526AA70F40, 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 0x000002526AA75E80, 16 bytes long.
 Data: <   jR           > 20 B3 A5 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000002526AA75DE0, 16 bytes long.
 Data: <   jR           > F8 B2 A5 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000002526AA757A0, 16 bytes long.
 Data: <   jR           > D0 B2 A5 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000002526AA753E0, 16 bytes long.
 Data: <   jR           > A8 B2 A5 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000002526AA75A20, 16 bytes long.
 Data: <   jR           > 80 B2 A5 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000002526AA75B60, 16 bytes long.
 Data: <X  jR           > 58 B2 A5 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000002526AA71300, 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 0x000002526AA75A70, 16 bytes long.
 Data: <0  jR           > 30 B2 A5 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000002526AA5B230, 320 bytes long.
 Data: <pZ jR      jR   > 70 5A A7 6A 52 02 00 00 00 13 A7 6A 52 02 00 00 
{273} normal block at 0x000002526AA761A0, 16 bytes long.
 Data: < d jR           > F0 64 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000002526AA76150, 16 bytes long.
 Data: < d jR           > C8 64 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000002526AA70EE0, 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 0x000002526AA75CF0, 16 bytes long.
 Data: < d jR           > A0 64 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000002526AA710C0, 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 0x000002526AA76100, 16 bytes long.
 Data: < c jR           > E8 63 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000002526AA756B0, 16 bytes long.
 Data: < c jR           > C0 63 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000002526AA75430, 16 bytes long.
 Data: < c jR           > 98 63 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000002526AA75FC0, 16 bytes long.
 Data: <pc jR           > 70 63 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000002526AA75C50, 16 bytes long.
 Data: <Hc jR           > 48 63 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000002526AA75D90, 16 bytes long.
 Data: < c jR           > 20 63 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000002526AA75840, 16 bytes long.
 Data: < K jR           > B0 4B A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000002526AA74BB0, 40 bytes long.
 Data: <@X jR      jR   > 40 58 A7 6A 52 02 00 00 10 06 A6 6A 52 02 00 00 
{259} normal block at 0x000002526AA75BB0, 16 bytes long.
 Data: < c jR           > 00 63 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000002526AA75F70, 16 bytes long.
 Data: < b jR           > D8 62 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x000002526AA70B80, 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 0x000002526AA761F0, 16 bytes long.
 Data: < b jR           > B0 62 A7 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x000002526AA762B0, 992 bytes long.
 Data: < a jR      jR   > F0 61 A7 6A 52 02 00 00 80 0B A7 6A 52 02 00 00 
{91} normal block at 0x000002526AA70FA0, 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 0x000002526AA6D620, 16 bytes long.
 Data: <   jR           > 00 C5 A5 6A 52 02 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x000002526AA5C500, 40 bytes long.
 Data: <   jR      jR   > 20 D6 A6 6A 52 02 00 00 A0 0F A7 6A 52 02 00 00 
{68} normal block at 0x000002526AA6CF40, 16 bytes long.
 Data: <   w            > 80 EA B9 77 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002526AA6DB20, 16 bytes long.
 Data: <@  w            > 40 E9 B9 77 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002526AA6D0D0, 16 bytes long.
 Data: < W w            > F8 57 B6 77 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000002526AA6D530, 16 bytes long.
 Data: < W w            > D8 57 B6 77 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002526AA6DC60, 16 bytes long.
 Data: <P  w            > 50 04 B6 77 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000002526AA6D260, 16 bytes long.
 Data: <0  w            > 30 04 B6 77 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000002526AA6D940, 16 bytes long.
 Data: <   w            > E0 02 B6 77 F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000002526AA6D3F0, 16 bytes long.
 Data: <   w            > 10 04 B6 77 F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000002526AA6D300, 16 bytes long.
 Data: <p  w            > 70 04 B6 77 F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000002526AA6DAD0, 16 bytes long.
 Data: <   w            > 18 C0 B4 77 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

©2025 Universitat Pompeu Fabra