Task 38643569

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>
17:46:00 (16304): wrapper (7.9.26016): starting
17:46:00 (16304): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A16_A13_0.pdb
QB_A16_A13_0.xml
QB_A16_A13.inpcrd
QB_A16_A13_input.yaml
QB_A16_A13.pdb
QB_A16_A13.prmtop
QB_A16_A13_sys.xml
run.bat
run.sh
17:46:02 (16304): Library/usr/bin/tar.exe exited; CPU time 0.031250
17:46:02 (16304): 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\24\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\24\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) : {3835337} normal block at 0x000001534B79F540, 8 bytes long.
 Data: <   KS   > 00 00 E2 4B 53 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833952} normal block at 0x000001534D6046D0, 1080 bytes long.
 Data: <,W              > 2C 57 00 00 CD CD CD CD B4 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {308} normal block at 0x000001534B795C50, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
21:10:35 (6068): wrapper (7.9.26016): starting
21:10:35 (6068): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1686} normal block at 0x000001ED63A466E0, 8 bytes long.
 Data: <   c    > 00 00 A1 63 ED 01 00 00 
..\lib\diagnostics_win.cpp(417) : {301} normal block at 0x000001ED63A46E90, 1080 bytes long.
 Data: < Y      ,       > EC 59 00 00 CD CD CD CD 2C 01 00 00 00 00 00 00 
Object dump complete.
06:45:25 (24744): wrapper (7.9.26016): starting
06:45:25 (24744): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1686} normal block at 0x00000206C7685C40, 8 bytes long.
 Data: <  _     > 00 00 5F C7 06 02 00 00 
..\lib\diagnostics_win.cpp(417) : {301} normal block at 0x00000206C7686850, 1080 bytes long.
 Data: <                > B0 06 00 00 CD CD CD CD B4 00 00 00 00 00 00 00 
Object dump complete.
06:52:18 (16216): wrapper (7.9.26016): starting
06:52:18 (16216): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1686} normal block at 0x00000224507654B0, 8 bytes long.
 Data: <  oP$   > 00 00 6F 50 24 02 00 00 
..\lib\diagnostics_win.cpp(417) : {301} normal block at 0x0000022450766660, 1080 bytes long.
 Data: <,W              > 2C 57 00 00 CD CD CD CD CC 00 00 00 00 00 00 00 
Object dump complete.
08:58:27 (14492): wrapper (7.9.26016): starting
08:58:27 (14492): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1686} normal block at 0x000001C6F7BD54E0, 8 bytes long.
 Data: <        > 00 00 FC F7 C6 01 00 00 
..\lib\diagnostics_win.cpp(417) : {301} normal block at 0x000001C6F7BD6730, 1080 bytes long.
 Data: <P       H       > 50 09 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
11:40:33 (18608): wrapper (7.9.26016): starting
11:40:33 (18608): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1686} normal block at 0x000001AF53045D50, 8 bytes long.
 Data: <   R    > 00 00 FC 52 AF 01 00 00 
..\lib\diagnostics_win.cpp(417) : {301} normal block at 0x000001AF53046870, 1080 bytes long.
 Data: < +      H       > E4 2B 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
12:06:56 (552): wrapper (7.9.26016): starting
12:06:56 (552): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1686} normal block at 0x000001AE41555CC0, 8 bytes long.
 Data: <  MA    > 00 00 4D 41 AE 01 00 00 
..\lib\diagnostics_win.cpp(417) : {301} normal block at 0x000001AE41556600, 1080 bytes long.
 Data: < c      L       > B0 63 00 00 CD CD CD CD 4C 01 00 00 00 00 00 00 
Object dump complete.
12:21:15 (15268): wrapper (7.9.26016): starting
12:21:15 (15268): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1686} normal block at 0x0000023F718C5C70, 8 bytes long.
 Data: <   q?   > 00 00 DA 71 3F 02 00 00 
..\lib\diagnostics_win.cpp(417) : {301} normal block at 0x0000023F718C66A0, 1080 bytes long.
 Data: <X2      P       > 58 32 00 00 CD CD CD CD 50 01 00 00 00 00 00 00 
Object dump complete.
13:03:19 (14764): wrapper (7.9.26016): starting
13:03:19 (14764): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1686} normal block at 0x000001941FBC6FE0, 8 bytes long.
 Data: <        > 00 00 B9 1F 94 01 00 00 
..\lib\diagnostics_win.cpp(417) : {301} normal block at 0x000001941FBC7880, 1080 bytes long.
 Data: < (      H       > FC 28 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
16:10:00 (15640): wrapper (7.9.26016): starting
16:10:00 (15640): 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\24\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1686} normal block at 0x000002CEFC825BE0, 8 bytes long.
 Data: <        > 00 00 EC FC CE 02 00 00 
..\lib\diagnostics_win.cpp(417) : {301} normal block at 0x000002CEFC826840, 1080 bytes long.
 Data: < @      P       > A4 40 00 00 CD CD CD CD 50 01 00 00 00 00 00 00 
Object dump complete.
17:03:02 (21608): wrapper (7.9.26016): starting
17:03:02 (21608): 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\24\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\24\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\24\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\24\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\24\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\24\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\24\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\24\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\24\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\24\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
17:47:43 (21608): C:/Windows/system32/cmd.exe exited; CPU time 1606.578125
17:47:43 (21608): app exit status: 0x16
17:47:43 (21608): 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: 14673285 bytes.
Dumping objects ->
{1774} normal block at 0x0000026015F04820, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1763} normal block at 0x0000026015F047B0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1752} normal block at 0x0000026015F04890, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1741} normal block at 0x0000026015F049E0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1730} normal block at 0x0000026015F04CF0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1699} normal block at 0x0000026015EF05F0, 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) : {1686} normal block at 0x0000026015F05DF0, 8 bytes long.
 Data: <    `   > 00 00 ED 15 60 02 00 00 
{302} normal block at 0x0000026015F056C0, 8 bytes long.
 Data: <0g  `   > 30 67 F0 15 60 02 00 00 
{293} normal block at 0x0000026015EF0010, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{292} normal block at 0x0000026015F06160, 16 bytes long.
 Data: <8f  `           > 38 66 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000026015F05670, 16 bytes long.
 Data: < f  `           > 10 66 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000026015F00E80, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{289} normal block at 0x0000026015F05C60, 16 bytes long.
 Data: < e  `           > E8 65 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000026015F055D0, 16 bytes long.
 Data: < e  `           > C0 65 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000026015F053A0, 16 bytes long.
 Data: < e  `           > 98 65 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000026015F058F0, 16 bytes long.
 Data: <pe  `           > 70 65 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000026015F04E40, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{284} normal block at 0x0000026015F05D00, 16 bytes long.
 Data: <    `           > A8 F2 EF 15 60 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000026015F00DC0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{282} normal block at 0x0000026015F05990, 16 bytes long.
 Data: <    `           > 80 F2 EF 15 60 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000026015F05350, 16 bytes long.
 Data: <X   `           > 58 F2 EF 15 60 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000026015F053F0, 16 bytes long.
 Data: <0   `           > 30 F2 EF 15 60 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000026015F05D50, 16 bytes long.
 Data: <    `           > 08 F2 EF 15 60 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000026015F054E0, 16 bytes long.
 Data: <    `           > E0 F1 EF 15 60 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000026015F05490, 16 bytes long.
 Data: <    `           > B8 F1 EF 15 60 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000026015F012A0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{274} normal block at 0x0000026015F05CB0, 16 bytes long.
 Data: <    `           > 90 F1 EF 15 60 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000026015EFF190, 320 bytes long.
 Data: < \  `       `   > B0 5C F0 15 60 02 00 00 A0 12 F0 15 60 02 00 00 
{272} normal block at 0x0000026015F060C0, 16 bytes long.
 Data: <Pe  `           > 50 65 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000026015F05F80, 16 bytes long.
 Data: <(e  `           > 28 65 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000026015F01060, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{269} normal block at 0x0000026015F059E0, 16 bytes long.
 Data: < e  `           > 00 65 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000026015F00D60, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{267} normal block at 0x0000026015F05BC0, 16 bytes long.
 Data: <Hd  `           > 48 64 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000026015F05580, 16 bytes long.
 Data: < d  `           > 20 64 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000026015F05940, 16 bytes long.
 Data: < c  `           > F8 63 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000026015F05620, 16 bytes long.
 Data: < c  `           > D0 63 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000026015F05F30, 16 bytes long.
 Data: < c  `           > A8 63 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000026015F05440, 16 bytes long.
 Data: < c  `           > 80 63 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000026015F06200, 16 bytes long.
 Data: < L  `           > 80 4C F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000026015F04C80, 40 bytes long.
 Data: < b  `       `   > 00 62 F0 15 60 02 00 00 F0 05 EF 15 60 02 00 00 
{258} normal block at 0x0000026015F05530, 16 bytes long.
 Data: <`c  `           > 60 63 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000026015F062A0, 16 bytes long.
 Data: <8c  `           > 38 63 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x0000026015F00580, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{255} normal block at 0x0000026015F05710, 16 bytes long.
 Data: < c  `           > 10 63 F0 15 60 02 00 00 00 00 00 00 00 00 00 00 
{254} normal block at 0x0000026015F06310, 992 bytes long.
 Data: < W  `       `   > 10 57 F0 15 60 02 00 00 80 05 F0 15 60 02 00 00 
{90} normal block at 0x0000026015F009A0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{89} normal block at 0x0000026015EFF930, 16 bytes long.
 Data: <    `           > 20 E1 EE 15 60 02 00 00 00 00 00 00 00 00 00 00 
{88} normal block at 0x0000026015EEE120, 40 bytes long.
 Data: <0   `       `   > 30 F9 EF 15 60 02 00 00 A0 09 F0 15 60 02 00 00 
{67} normal block at 0x0000026015F000B0, 16 bytes long.
 Data: <  3             > 80 EA 33 9C F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000026015EFFFC0, 16 bytes long.
 Data: <@ 3             > 40 E9 33 9C F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000026015EFFE30, 16 bytes long.
 Data: < W0             > F8 57 30 9C F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000026015EFF750, 16 bytes long.
 Data: < W0             > D8 57 30 9C F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000026015EFFC00, 16 bytes long.
 Data: <P 0             > 50 04 30 9C F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000026015EFF8E0, 16 bytes long.
 Data: <0 0             > 30 04 30 9C F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000026015EFFDE0, 16 bytes long.
 Data: <  0             > E0 02 30 9C F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x0000026015EFF7A0, 16 bytes long.
 Data: <  0             > 10 04 30 9C F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x0000026015EFF7F0, 16 bytes long.
 Data: <p 0             > 70 04 30 9C F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x0000026015EFFBB0, 16 bytes long.
 Data: <  .             > 18 C0 2E 9C F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

©2026 Universitat Pompeu Fabra