Task 38645138

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
�@�~�t�εL�k���� (null)�C
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
13:42:10 (17672): wrapper (7.9.26016): starting
13:42:10 (17672): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A26_A17_0.pdb
QB_A26_A17_0.xml
QB_A26_A17.inpcrd
QB_A26_A17_input.yaml
QB_A26_A17.pdb
QB_A26_A17.prmtop
QB_A26_A17_sys.xml
run.bat
run.sh
13:42:12 (17672): Library/usr/bin/tar.exe exited; CPU time 0.000000
13:42:12 (17672): 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 'E:\BOINC_DATA\slots\14\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 'E:\BOINC_DATA\slots\14\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 "E:\BOINC_DATA\slots\14\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "E:\BOINC_DATA\slots\14\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "E:\BOINC_DATA\slots\14\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "E:\BOINC_DATA\slots\14\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "E:\BOINC_DATA\slots\14\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "E:\BOINC_DATA\slots\14\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "E:\BOINC_DATA\slots\14\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "E:\BOINC_DATA\slots\14\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "E:\BOINC_DATA\slots\14\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
14:41:02 (17672): C:/Windows/system32/cmd.exe exited; CPU time 3668.906250
14:41:02 (17672): app exit status: 0x16
14:41:02 (17672): called boinc_finish(195)
0 bytes in 0 Free Blocks.
346 bytes in 8 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: 76195230 bytes.
Dumping objects ->
{3835666} normal block at 0x000001EE2B7D7600, 48 bytes long.
 Data: <PATH=E:\BOINC_DA> 50 41 54 48 3D 45 3A 5C 42 4F 49 4E 43 5F 44 41 
{3835655} normal block at 0x000001EE2D763750, 32 bytes long.
 Data: <HOME=E:\BOINC_DA> 48 4F 4D 45 3D 45 3A 5C 42 4F 49 4E 43 5F 44 41 
{3835644} normal block at 0x000001EE2D7648F0, 32 bytes long.
 Data: <TMP=E:\BOINC_DAT> 54 4D 50 3D 45 3A 5C 42 4F 49 4E 43 5F 44 41 54 
{3835633} normal block at 0x000001EE2D7636F0, 32 bytes long.
 Data: <TEMP=E:\BOINC_DA> 54 45 4D 50 3D 45 3A 5C 42 4F 49 4E 43 5F 44 41 
{3835622} normal block at 0x000001EE2D7641D0, 32 bytes long.
 Data: <TMPDIR=E:\BOINC_> 54 4D 50 44 49 52 3D 45 3A 5C 42 4F 49 4E 43 5F 
{3835591} normal block at 0x000001EE2B7D71A0, 48 bytes long.
 Data: <PATH=E:\BOINC_DA> 50 41 54 48 3D 45 3A 5C 42 4F 49 4E 43 5F 44 41 
{3835580} normal block at 0x000001EE2D6CD9D0, 85 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
..\api\boinc_api.cpp(309) : {3835577} normal block at 0x000001EE2B7A8140, 8 bytes long.
 Data: <   -    > 00 00 11 2D EE 01 00 00 
{3834808} normal block at 0x000001EE2D6CE6F0, 85 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{3834075} normal block at 0x000001EE2B7A80A0, 8 bytes long.
 Data: <p b-    > 70 E8 62 2D EE 01 00 00 
..\zip\boinc_zip.cpp(122) : {316} normal block at 0x000001EE2B7B2920, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{301} normal block at 0x000001EE2B7AE8A0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{300} normal block at 0x000001EE2B7B3EB0, 16 bytes long.
 Data: < N{+            > 18 4E 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{299} normal block at 0x000001EE2B7B3E60, 16 bytes long.
 Data: < M{+            > F0 4D 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{298} normal block at 0x000001EE2B7ACB80, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{297} normal block at 0x000001EE2B7B4590, 16 bytes long.
 Data: < M{+            > C8 4D 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x000001EE2B7B4270, 16 bytes long.
 Data: < M{+            > A0 4D 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x000001EE2B7B3B90, 16 bytes long.
 Data: <xM{+            > 78 4D 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x000001EE2B7B41D0, 16 bytes long.
 Data: <PM{+            > 50 4D 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000001EE2B7AC790, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{292} normal block at 0x000001EE2B7B3D20, 16 bytes long.
 Data: <8 z+            > 38 E8 7A 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000001EE2B7AD120, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{290} normal block at 0x000001EE2B7B3960, 16 bytes long.
 Data: <  z+            > 10 E8 7A 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000001EE2B7B3820, 16 bytes long.
 Data: <  z+            > E8 E7 7A 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001EE2B7B4180, 16 bytes long.
 Data: <  z+            > C0 E7 7A 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000001EE2B7B3E10, 16 bytes long.
 Data: <  z+            > 98 E7 7A 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000001EE2B7B3910, 16 bytes long.
 Data: <p z+            > 70 E7 7A 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000001EE2B7B3AA0, 16 bytes long.
 Data: <H z+            > 48 E7 7A 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000001EE2B7ACE80, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{282} normal block at 0x000001EE2B7B4450, 16 bytes long.
 Data: <  z+            > 20 E7 7A 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000001EE2B7AE720, 320 bytes long.
 Data: <PD{+      z+    > 50 44 7B 2B EE 01 00 00 80 CE 7A 2B EE 01 00 00 
{280} normal block at 0x000001EE2B7B4090, 16 bytes long.
 Data: <0M{+            > 30 4D 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001EE2B7B4040, 16 bytes long.
 Data: < M{+            > 08 4D 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001EE2B7AD660, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{277} normal block at 0x000001EE2B7B37D0, 16 bytes long.
 Data: < L{+            > E0 4C 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000001EE2B7ACB20, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{275} normal block at 0x000001EE2B7B40E0, 16 bytes long.
 Data: <(L{+            > 28 4C 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000001EE2B7B38C0, 16 bytes long.
 Data: < L{+            > 00 4C 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001EE2B7B3780, 16 bytes long.
 Data: < K{+            > D8 4B 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001EE2B7B3730, 16 bytes long.
 Data: < K{+            > B0 4B 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001EE2B7B44F0, 16 bytes long.
 Data: < K{+            > 88 4B 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000001EE2B7B4220, 16 bytes long.
 Data: <`K{+            > 60 4B 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000001EE2B7B4130, 16 bytes long.
 Data: <` z+            > 60 C5 7A 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001EE2B7AC560, 40 bytes long.
 Data: <0A{+     q}+    > 30 41 7B 2B EE 01 00 00 A0 71 7D 2B EE 01 00 00 
{266} normal block at 0x000001EE2B7B44A0, 16 bytes long.
 Data: <@K{+            > 40 4B 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000001EE2B7B3CD0, 16 bytes long.
 Data: < K{+            > 18 4B 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001EE2B7ACCA0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{263} normal block at 0x000001EE2B7B3870, 16 bytes long.
 Data: < J{+            > F0 4A 7B 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000001EE2B7B4AF0, 992 bytes long.
 Data: <p8{+      z+    > 70 38 7B 2B EE 01 00 00 A0 CC 7A 2B EE 01 00 00 
{98} normal block at 0x000001EE2B7AD540, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{97} normal block at 0x000001EE2B7A82D0, 16 bytes long.
 Data: <  z+            > A0 C3 7A 2B EE 01 00 00 00 00 00 00 00 00 00 00 
{96} normal block at 0x000001EE2B7AC3A0, 40 bytes long.
 Data: <  z+    @ z+    > D0 82 7A 2B EE 01 00 00 40 D5 7A 2B EE 01 00 00 
{73} normal block at 0x000001EE2B7A7E20, 16 bytes long.
 Data: <  &|            > 80 EA 26 7C F7 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x000001EE2B7A7DD0, 16 bytes long.
 Data: <@ &|            > 40 E9 26 7C F7 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000001EE2B7A7D30, 16 bytes long.
 Data: < W#|            > F8 57 23 7C F7 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000001EE2B7A7F10, 16 bytes long.
 Data: < W#|            > D8 57 23 7C F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000001EE2B7A7C90, 16 bytes long.
 Data: <P #|            > 50 04 23 7C F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001EE2B7A7C40, 16 bytes long.
 Data: <0 #|            > 30 04 23 7C F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001EE2B7A78D0, 16 bytes long.
 Data: <  #|            > E0 02 23 7C F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001EE2B7A8370, 16 bytes long.
 Data: <  #|            > 10 04 23 7C F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001EE2B7A7880, 16 bytes long.
 Data: <p #|            > 70 04 23 7C F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001EE2B7A7510, 16 bytes long.
 Data: <  !|            > 18 C0 21 7C F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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