Task 38681549

Stderr output

<core_client_version>8.2.4</core_client_version>
<![CDATA[
<stderr_txt>
17:54:40 (9592): wrapper (7.9.26016): starting
17:54:40 (9592): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A34_A12_0.pdb
QB_A34_A12_0.xml
QB_A34_A12_input.yaml
QB_A34_A12.pdb
QB_A34_A12.prmtop
QB_A34_A12_sys.xml
run.bat
run.sh
17:54:42 (9592): Library/usr/bin/tar.exe exited; CPU time 0.000000
17:54:42 (9592): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x0000022589978F90>: Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pyaml/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x0000022589A3CA90>: Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pyaml/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x0000022589A3D290>: Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pyaml/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x0000022589A3DB50>: Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pyaml/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x0000022589A3E410>: Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /simple/pyaml/
  WARNING: The script pyaml.exe is installed in 'C:\ProgramData\BOINC\slots\4\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\4\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) : {3835103} normal block at 0x000002B6C0276140, 8 bytes long.
 Data: <  %     > 00 00 25 C0 B6 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833950} normal block at 0x000002B6C1CB1CA0, 1080 bytes long.
 Data: < a              > 8C 61 00 00 CD CD CD CD 8C 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {307} normal block at 0x000002B6C0280660, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
20:34:23 (22980): wrapper (7.9.26016): starting
20:34:23 (22980): 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\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1453} normal block at 0x000001FCAF5E14E0, 8 bytes long.
 Data: <  Z     > 00 00 5A AF FC 01 00 00 
..\lib\diagnostics_win.cpp(417) : {300} normal block at 0x000001FCAF5E3C80, 1080 bytes long.
 Data: <        D       > CC 1B 00 00 CD CD CD CD 44 01 00 00 00 00 00 00 
Object dump complete.
21:13:22 (21588): wrapper (7.9.26016): starting
21:13:22 (21588): 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\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1453} normal block at 0x0000026FC7A62040, 8 bytes long.
 Data: <  6 o   > 00 00 36 C9 6F 02 00 00 
..\lib\diagnostics_win.cpp(417) : {300} normal block at 0x0000026FC7A63CA0, 1080 bytes long.
 Data: < b      D       > 98 62 00 00 CD CD CD CD 44 01 00 00 00 00 00 00 
Object dump complete.
21:26:37 (27928): wrapper (7.9.26016): starting
21:26:37 (27928): 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\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1453} normal block at 0x00000160E1AC1640, 8 bytes long.
 Data: <    `   > 00 00 A8 E1 60 01 00 00 
..\lib\diagnostics_win.cpp(417) : {300} normal block at 0x00000160E1AC3CA0, 1080 bytes long.
 Data: <        D       > A4 18 00 00 CD CD CD CD 44 01 00 00 00 00 00 00 
Object dump complete.
21:36:39 (20544): wrapper (7.9.26016): starting
21:36:39 (20544): 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\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
tar: run.log: file changed as we read it
tar: r*/*.dcd: Cannot stat: No such file or directory
tar: r*/*.xtc: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors
21:53:54 (20544): C:/Windows/system32/cmd.exe exited; CPU time 938.359375
21:53:54 (20544): called boinc_finish(0)
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: 18535294 bytes.
Dumping objects ->
{1541} normal block at 0x0000025E89BCD060, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1530} normal block at 0x0000025E89BCD300, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1519} normal block at 0x0000025E89BCCFF0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1508} normal block at 0x0000025E89BCD6F0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1497} normal block at 0x0000025E89BCD4C0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1466} normal block at 0x0000025E89BBB6D0, 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) : {1453} normal block at 0x0000025E89BD22D0, 8 bytes long.
 Data: <    ^   > 00 00 B4 89 5E 02 00 00 
{301} normal block at 0x0000025E89BD1740, 8 bytes long.
 Data: <`<  ^   > 60 3C BD 89 5E 02 00 00 
{292} normal block at 0x0000025E89BB6410, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{291} normal block at 0x0000025E89BD1E70, 16 bytes long.
 Data: <h;  ^           > 68 3B BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000025E89BD20A0, 16 bytes long.
 Data: <@;  ^           > 40 3B BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000025E89BCB950, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{288} normal block at 0x0000025E89BD1DD0, 16 bytes long.
 Data: < ;  ^           > 18 3B BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000025E89BD1C90, 16 bytes long.
 Data: < :  ^           > F0 3A BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000025E89BD1D80, 16 bytes long.
 Data: < :  ^           > C8 3A BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000025E89BD2230, 16 bytes long.
 Data: < :  ^           > A0 3A BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000025E89BCD680, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{283} normal block at 0x0000025E89BD1FB0, 16 bytes long.
 Data: < c  ^           > A8 63 BB 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000025E89BCB9B0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{281} normal block at 0x0000025E89BD1790, 16 bytes long.
 Data: < c  ^           > 80 63 BB 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000025E89BD16A0, 16 bytes long.
 Data: <Xc  ^           > 58 63 BB 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000025E89BD15B0, 16 bytes long.
 Data: <0c  ^           > 30 63 BB 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000025E89BD1EC0, 16 bytes long.
 Data: < c  ^           > 08 63 BB 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000025E89BD1B50, 16 bytes long.
 Data: < b  ^           > E0 62 BB 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000025E89BD21E0, 16 bytes long.
 Data: < b  ^           > B8 62 BB 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000025E89BCAE70, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{273} normal block at 0x0000025E89BD2280, 16 bytes long.
 Data: < b  ^           > 90 62 BB 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000025E89BB6290, 320 bytes long.
 Data: < "  ^   p   ^   > 80 22 BD 89 5E 02 00 00 70 AE BC 89 5E 02 00 00 
{271} normal block at 0x0000025E89BD1BF0, 16 bytes long.
 Data: < :  ^           > 80 3A BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000025E89BD1CE0, 16 bytes long.
 Data: <X:  ^           > 58 3A BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000025E89BCB530, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{268} normal block at 0x0000025E89BD1510, 16 bytes long.
 Data: <0:  ^           > 30 3A BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000025E89BCB5F0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{266} normal block at 0x0000025E89BD1D30, 16 bytes long.
 Data: <x9  ^           > 78 39 BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000025E89BD1B00, 16 bytes long.
 Data: <P9  ^           > 50 39 BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000025E89BD1AB0, 16 bytes long.
 Data: <(9  ^           > 28 39 BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000025E89BD23C0, 16 bytes long.
 Data: < 9  ^           > 00 39 BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000025E89BD1E20, 16 bytes long.
 Data: < 8  ^           > D8 38 BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000025E89BD2190, 16 bytes long.
 Data: < 8  ^           > B0 38 BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000025E89BD1560, 16 bytes long.
 Data: <    ^           > D0 D0 BC 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x0000025E89BCD0D0, 40 bytes long.
 Data: <`   ^       ^   > 60 15 BD 89 5E 02 00 00 D0 B6 BB 89 5E 02 00 00 
{257} normal block at 0x0000025E89BD1970, 16 bytes long.
 Data: < 8  ^           > 90 38 BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x0000025E89BD1920, 16 bytes long.
 Data: <h8  ^           > 68 38 BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x0000025E89BCB110, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{254} normal block at 0x0000025E89BD1F10, 16 bytes long.
 Data: <@8  ^           > 40 38 BD 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{253} normal block at 0x0000025E89BD3840, 992 bytes long.
 Data: <    ^       ^   > 10 1F BD 89 5E 02 00 00 10 B1 BC 89 5E 02 00 00 
{89} normal block at 0x0000025E89BCAD50, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{88} normal block at 0x0000025E89BC62D0, 16 bytes long.
 Data: <    ^           > 10 D6 BC 89 5E 02 00 00 00 00 00 00 00 00 00 00 
{87} normal block at 0x0000025E89BCD610, 40 bytes long.
 Data: < b  ^   P   ^   > D0 62 BC 89 5E 02 00 00 50 AD BC 89 5E 02 00 00 
{66} normal block at 0x0000025E89BC66E0, 16 bytes long.
 Data: <   W            > 80 EA BA 57 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000025E89BC6000, 16 bytes long.
 Data: <@  W            > 40 E9 BA 57 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000025E89BC60F0, 16 bytes long.
 Data: < W W            > F8 57 B7 57 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000025E89BC5FB0, 16 bytes long.
 Data: < W W            > D8 57 B7 57 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000025E89BC5E70, 16 bytes long.
 Data: <P  W            > 50 04 B7 57 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000025E89BC6370, 16 bytes long.
 Data: <0  W            > 30 04 B7 57 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x0000025E89BC61E0, 16 bytes long.
 Data: <   W            > E0 02 B7 57 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x0000025E89BC6C30, 16 bytes long.
 Data: <   W            > 10 04 B7 57 F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x0000025E89BC65F0, 16 bytes long.
 Data: <p  W            > 70 04 B7 57 F7 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x0000025E89BC5D80, 16 bytes long.
 Data: <   W            > 18 C0 B5 57 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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