Task 38686092

Stderr output

<core_client_version>8.2.11</core_client_version>
<![CDATA[
<stderr_txt>
10:46:12 (50140): wrapper (7.9.26016): starting
10:46:12 (50140): 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
10:46:13 (50140): Library/usr/bin/tar.exe exited; CPU time 0.015625
10:46:13 (50140): 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 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x0000023DD335B750>, 'Connection to pypi.org timed out. (connect timeout=15)')': /simple/pyaml/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x0000023DD3504950>, 'Connection to pypi.org timed out. (connect timeout=15)')': /simple/pyaml/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x0000023DD3505290>, 'Connection to pypi.org timed out. (connect timeout=15)')': /simple/pyaml/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x0000023DD3505B90>, 'Connection to pypi.org timed out. (connect timeout=15)')': /simple/pyaml/
WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x0000023DD3506410>, 'Connection to pypi.org timed out. (connect timeout=15)')': /simple/pyaml/
ERROR: Could not find a version that satisfies the requirement pyaml==26.2.1 (from versions: none)
ERROR: No matching distribution found for pyaml==26.2.1
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x00000263C952D950>, 'Connection to pypi.org timed out. (connect timeout=15)')': /simple/atom-openmm/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x00000263C952E7D0>, 'Connection to pypi.org timed out. (connect timeout=15)')': /simple/atom-openmm/
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x00000263C952F190>, 'Connection to pypi.org timed out. (connect timeout=15)')': /simple/atom-openmm/
WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x00000263C952FE90>, 'Connection to pypi.org timed out. (connect timeout=15)')': /simple/atom-openmm/
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835490} normal block at 0x0000026C245EDC10, 8 bytes long.
 Data: <   $l   > 00 00 9E 24 6C 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833958} normal block at 0x0000026C246CE950, 1080 bytes long.
 Data: <                > 0C 0B 00 00 CD CD CD CD D8 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {311} normal block at 0x0000026C245F2330, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
11:12:24 (4916): wrapper (7.9.26016): starting
11:12:24 (4916): 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\6\tmp already exists.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1836} normal block at 0x0000020F3E3C7ED0, 8 bytes long.
 Data: <  4>    > 00 00 34 3E 0F 02 00 00 
..\lib\diagnostics_win.cpp(417) : {304} normal block at 0x0000020F3E3C8400, 1080 bytes long.
 Data: <\       H       > 5C 90 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
11:17:27 (50724): wrapper (7.9.26016): starting
11:17:27 (50724): 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\6\tmp already exists.
  WARNING: The script pyaml.exe is installed in 'C:\ProgramData\BOINC\slots\6\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\6\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.
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
11:43:25 (50724): C:/Windows/system32/cmd.exe exited; CPU time 1532.984375
11:43:25 (50724): 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: 39596812 bytes.
Dumping objects ->
{1924} normal block at 0x000001756F4D0850, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1913} normal block at 0x000001756F4D09A0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1902} normal block at 0x000001756F4D0D20, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1891} normal block at 0x000001756F4D0620, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1880} normal block at 0x000001756F4D0930, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1849} normal block at 0x000001756F4C95A0, 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) : {1836} normal block at 0x000001756F4D5EA0, 8 bytes long.
 Data: <   ou   > 00 00 AE 6F 75 01 00 00 
{305} normal block at 0x000001756F4D6C10, 8 bytes long.
 Data: < qMou   > 90 71 4D 6F 75 01 00 00 
{296} normal block at 0x000001756F4C6C70, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{295} normal block at 0x000001756F4D5E50, 16 bytes long.
 Data: < pMou           > 98 70 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x000001756F4D6A30, 16 bytes long.
 Data: <ppMou           > 70 70 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000001756F4CFFD0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{292} normal block at 0x000001756F4D6710, 16 bytes long.
 Data: <HpMou           > 48 70 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000001756F4D68A0, 16 bytes long.
 Data: < pMou           > 20 70 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000001756F4D66C0, 16 bytes long.
 Data: < oMou           > F8 6F 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000001756F4D64E0, 16 bytes long.
 Data: < oMou           > D0 6F 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000001756F4D0B60, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{287} normal block at 0x000001756F4D6CB0, 16 bytes long.
 Data: <  Kou           > A8 F7 4B 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000001756F4CFD90, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{285} normal block at 0x000001756F4D5DB0, 16 bytes long.
 Data: <  Kou           > 80 F7 4B 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000001756F4D6210, 16 bytes long.
 Data: <X Kou           > 58 F7 4B 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000001756F4D6440, 16 bytes long.
 Data: <0 Kou           > 30 F7 4B 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000001756F4D61C0, 16 bytes long.
 Data: <  Kou           > 08 F7 4B 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001756F4D6620, 16 bytes long.
 Data: <  Kou           > E0 F6 4B 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001756F4D63A0, 16 bytes long.
 Data: <  Kou           > B8 F6 4B 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001756F4D0510, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{277} normal block at 0x000001756F4D6490, 16 bytes long.
 Data: <  Kou           > 90 F6 4B 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000001756F4BF690, 320 bytes long.
 Data: < dMou     Mou   > 90 64 4D 6F 75 01 00 00 10 05 4D 6F 75 01 00 00 
{275} normal block at 0x000001756F4D6580, 16 bytes long.
 Data: < oMou           > B0 6F 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000001756F4D6800, 16 bytes long.
 Data: < oMou           > 88 6F 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001756F4D0450, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{272} normal block at 0x000001756F4D6BC0, 16 bytes long.
 Data: <`oMou           > 60 6F 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001756F4CFCD0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{270} normal block at 0x000001756F4D6170, 16 bytes long.
 Data: < nMou           > A8 6E 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000001756F4D6C60, 16 bytes long.
 Data: < nMou           > 80 6E 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000001756F4D63F0, 16 bytes long.
 Data: <XnMou           > 58 6E 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001756F4D6D00, 16 bytes long.
 Data: <0nMou           > 30 6E 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001756F4D6120, 16 bytes long.
 Data: < nMou           > 08 6E 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000001756F4D6530, 16 bytes long.
 Data: < mMou           > E0 6D 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000001756F4D6940, 16 bytes long.
 Data: <  Mou           > E0 07 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000001756F4D07E0, 40 bytes long.
 Data: <@iMou     Lou   > 40 69 4D 6F 75 01 00 00 A0 95 4C 6F 75 01 00 00 
{261} normal block at 0x000001756F4D5E00, 16 bytes long.
 Data: < mMou           > C0 6D 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000001756F4D67B0, 16 bytes long.
 Data: < mMou           > 98 6D 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x000001756F4D02D0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{258} normal block at 0x000001756F4D6080, 16 bytes long.
 Data: <pmMou           > 70 6D 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x000001756F4D6D70, 992 bytes long.
 Data: < `Mou     Mou   > 80 60 4D 6F 75 01 00 00 D0 02 4D 6F 75 01 00 00 
{93} normal block at 0x000001756F4CFBB0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{92} normal block at 0x000001756F4CD930, 16 bytes long.
 Data: <  Mou           > F0 0A 4D 6F 75 01 00 00 00 00 00 00 00 00 00 00 
{91} normal block at 0x000001756F4D0AF0, 40 bytes long.
 Data: <0 Lou     Lou   > 30 D9 4C 6F 75 01 00 00 B0 FB 4C 6F 75 01 00 00 
{70} normal block at 0x000001756F4CE5B0, 16 bytes long.
 Data: <   \            > 80 EA A8 5C F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000001756F4CE4C0, 16 bytes long.
 Data: <@  \            > 40 E9 A8 5C F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001756F4CE0B0, 16 bytes long.
 Data: < W \            > F8 57 A5 5C F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001756F4CE600, 16 bytes long.
 Data: < W \            > D8 57 A5 5C F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001756F4CD7A0, 16 bytes long.
 Data: <P  \            > 50 04 A5 5C F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001756F4CDED0, 16 bytes long.
 Data: <0  \            > 30 04 A5 5C F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001756F4CDA20, 16 bytes long.
 Data: <   \            > E0 02 A5 5C F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001756F4CDE30, 16 bytes long.
 Data: <   \            > 10 04 A5 5C F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001756F4CDDE0, 16 bytes long.
 Data: <p  \            > 70 04 A5 5C F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001756F4CDC00, 16 bytes long.
 Data: <   \            > 18 C0 A3 5C F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
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