Task 38596021

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
���ϵͳ�޷����� (null)��
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
19:01:53 (12836): wrapper (7.9.26016): starting
19:01:53 (12836): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A04_A02_0.pdb
QB_A04_A02_0.xml
QB_A04_A02.inpcrd
QB_A04_A02_input.yaml
QB_A04_A02.pdb
QB_A04_A02.prmtop
QB_A04_A02_sys.xml
run.bat
run.sh
19:01:57 (12836): Library/usr/bin/tar.exe exited; CPU time 0.015625
19:01:57 (12836): 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:\BOINC\Data\slots\20\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:\BOINC\Data\slots\20\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.
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:\BOINC\Data\slots\20\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "D:\BOINC\Data\slots\20\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "D:\BOINC\Data\slots\20\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "D:\BOINC\Data\slots\20\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "D:\BOINC\Data\slots\20\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BOINC\Data\slots\20\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BOINC\Data\slots\20\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BOINC\Data\slots\20\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BOINC\Data\slots\20\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
19:04:15 (12836): C:/Windows/system32/cmd.exe exited; CPU time 91.906250
19:04:15 (12836): app exit status: 0x16
19:04:15 (12836): 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: 2045169 bytes.
Dumping objects ->
{3835307} normal block at 0x0000015DE877C370, 48 bytes long.
 Data: <PATH=D:\BOINC\Da> 50 41 54 48 3D 44 3A 5C 42 4F 49 4E 43 5C 44 61 
{3835296} normal block at 0x0000015DEA686860, 32 bytes long.
 Data: <HOME=D:\BOINC\Da> 48 4F 4D 45 3D 44 3A 5C 42 4F 49 4E 43 5C 44 61 
{3835285} normal block at 0x0000015DEA686A40, 32 bytes long.
 Data: <TMP=D:\BOINC\Dat> 54 4D 50 3D 44 3A 5C 42 4F 49 4E 43 5C 44 61 74 
{3835274} normal block at 0x0000015DEA6869E0, 32 bytes long.
 Data: <TEMP=D:\BOINC\Da> 54 45 4D 50 3D 44 3A 5C 42 4F 49 4E 43 5C 44 61 
{3835263} normal block at 0x0000015DEA6864A0, 32 bytes long.
 Data: <TMPDIR=D:\BOINC\> 54 4D 50 44 49 52 3D 44 3A 5C 42 4F 49 4E 43 5C 
{3835232} normal block at 0x0000015DE877C300, 48 bytes long.
 Data: <PATH=D:\BOINC\Da> 50 41 54 48 3D 44 3A 5C 42 4F 49 4E 43 5C 44 61 
..\api\boinc_api.cpp(309) : {3835219} normal block at 0x0000015DE8781A90, 8 bytes long.
 Data: <  t ]   > 00 00 74 E8 5D 01 00 00 
{3834027} normal block at 0x0000015DE8781D10, 8 bytes long.
 Data: <  z ]   > D0 97 7A E8 5D 01 00 00 
..\zip\boinc_zip.cpp(122) : {305} normal block at 0x0000015DE8782380, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000015DE8765B60, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{289} normal block at 0x0000015DE8777810, 16 bytes long.
 Data: < 5x ]           > A8 35 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000015DE8777D60, 16 bytes long.
 Data: < 5x ]           > 80 35 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000015DE877D5D0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{286} normal block at 0x0000015DE8778080, 16 bytes long.
 Data: <X5x ]           > 58 35 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000015DE87783A0, 16 bytes long.
 Data: <05x ]           > 30 35 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000015DE8777720, 16 bytes long.
 Data: < 5x ]           > 08 35 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000015DE8778440, 16 bytes long.
 Data: < 4x ]           > E0 34 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000015DE877C680, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{281} normal block at 0x0000015DE8777EF0, 16 bytes long.
 Data: < Zv ]           > F8 5A 76 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000015DE877DF90, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{279} normal block at 0x0000015DE8778030, 16 bytes long.
 Data: < Zv ]           > D0 5A 76 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000015DE8777C20, 16 bytes long.
 Data: < Zv ]           > A8 5A 76 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000015DE87777C0, 16 bytes long.
 Data: < Zv ]           > 80 5A 76 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000015DE8778260, 16 bytes long.
 Data: <XZv ]           > 58 5A 76 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000015DE8781A40, 16 bytes long.
 Data: <0Zv ]           > 30 5A 76 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000015DE8781BD0, 16 bytes long.
 Data: < Zv ]           > 08 5A 76 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000015DE877E2F0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{271} normal block at 0x0000015DE87819F0, 16 bytes long.
 Data: < Yv ]           > E0 59 76 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000015DE87659E0, 320 bytes long.
 Data: <  x ]     w ]   > F0 19 78 E8 5D 01 00 00 F0 E2 77 E8 5D 01 00 00 
{269} normal block at 0x0000015DE8781C20, 16 bytes long.
 Data: < 4x ]           > C0 34 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000015DE8781B80, 16 bytes long.
 Data: < 4x ]           > 98 34 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000015DE877DE10, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{266} normal block at 0x0000015DE87819A0, 16 bytes long.
 Data: <p4x ]           > 70 34 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000015DE877D930, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{264} normal block at 0x0000015DE87817C0, 16 bytes long.
 Data: < 3x ]           > B8 33 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000015DE8781AE0, 16 bytes long.
 Data: < 3x ]           > 90 33 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000015DE8781950, 16 bytes long.
 Data: <h3x ]           > 68 33 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000015DE8781770, 16 bytes long.
 Data: <@3x ]           > 40 33 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000015DE8781720, 16 bytes long.
 Data: < 3x ]           > 18 33 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000015DE8781900, 16 bytes long.
 Data: < 2x ]           > F0 32 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000015DE87816D0, 16 bytes long.
 Data: <` w ]           > 60 C7 77 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x0000015DE877C760, 40 bytes long.
 Data: <  x ]     w ]   > D0 16 78 E8 5D 01 00 00 00 C3 77 E8 5D 01 00 00 
{255} normal block at 0x0000015DE8781B30, 16 bytes long.
 Data: < 2x ]           > D0 32 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{254} normal block at 0x0000015DE87818B0, 16 bytes long.
 Data: < 2x ]           > A8 32 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{253} normal block at 0x0000015DE877E0B0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{252} normal block at 0x0000015DE8781680, 16 bytes long.
 Data: < 2x ]           > 80 32 78 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{251} normal block at 0x0000015DE8783280, 992 bytes long.
 Data: <  x ]     w ]   > 80 16 78 E8 5D 01 00 00 B0 E0 77 E8 5D 01 00 00 
{87} normal block at 0x0000015DE877DC30, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{86} normal block at 0x0000015DE8777A90, 16 bytes long.
 Data: <P w ]           > 50 C4 77 E8 5D 01 00 00 00 00 00 00 00 00 00 00 
{85} normal block at 0x0000015DE877C450, 40 bytes long.
 Data: < zw ]   0 w ]   > 90 7A 77 E8 5D 01 00 00 30 DC 77 E8 5D 01 00 00 
{62} normal block at 0x0000015DE8777B30, 16 bytes long.
 Data: <  +o            > 80 EA 2B 6F F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000015DE8778170, 16 bytes long.
 Data: <@ +o            > 40 E9 2B 6F F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x0000015DE8777AE0, 16 bytes long.
 Data: < W(o            > F8 57 28 6F F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x0000015DE8777A40, 16 bytes long.
 Data: < W(o            > D8 57 28 6F F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x0000015DE8778300, 16 bytes long.
 Data: <P (o            > 50 04 28 6F F7 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x0000015DE87779A0, 16 bytes long.
 Data: <0 (o            > 30 04 28 6F F7 7F 00 00 00 00 00 00 00 00 00 00 
{56} normal block at 0x0000015DE8777B80, 16 bytes long.
 Data: <  (o            > E0 02 28 6F F7 7F 00 00 00 00 00 00 00 00 00 00 
{55} normal block at 0x0000015DE8777E00, 16 bytes long.
 Data: <  (o            > 10 04 28 6F F7 7F 00 00 00 00 00 00 00 00 00 00 
{54} normal block at 0x0000015DE8778120, 16 bytes long.
 Data: <p (o            > 70 04 28 6F F7 7F 00 00 00 00 00 00 00 00 00 00 
{53} normal block at 0x0000015DE8778350, 16 bytes long.
 Data: <  &o            > 18 C0 26 6F F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

©2026 Universitat Pompeu Fabra