Rosetta 4.0+

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Jim1348

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Message 90684 - Posted: 17 Apr 2019, 14:43:48 UTC - in response to Message 90682.  

Your numbers look reasonable enough to me.
Peak working set size 	1,070.88 MB
Peak swap size 	1,466.38 MB
Peak disk usage 	502.06 MB

If it is just a case of increasing the PC memory, I would do that rather than reducing the size of the molecules, if that is the issue.

I usually provide 1 GB per core, and can add more if needed. That should work most of the time.
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Message 90714 - Posted: 24 Apr 2019, 9:50:07 UTC

rb_04_18_3131_3164__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_829580_212_0

Peak working set size: 473.97 MB
Peak swap size: 476.66 MB
(so not really much)

Std_err:
<core_client_version>7.12.1</core_client_version>
<![CDATA[
<message>
(unknown error) - exit code -1073741819 (0xc0000005)</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.07_windows_intelx86.exe -run:protocol jd2_scripting @flags_rb_04_18_3131_3164__t000__0_C1_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_04_18_3131_3164__t000__0_C1_robetta.zip -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 2622694
Starting watchdog...
Watchdog active.


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x016AC0E8 write attempt to address 0x00D5212C

Engaging BOINC Windows Runtime Debugger...



********************


BOINC Windows Runtime Debugger Version 7.9.0


Dump Timestamp    : 04/22/19 17:23:00
Install Directory : 
Data Directory    : C:\ProgramData\BOINC
Project Symstore  : http://boinc.bakerlab.org/rosetta/symstore
LoadLibraryA( C:\ProgramData\BOINC\dbghelp.dll ): GetLastError = 126
Loaded Library    : dbghelp.dll
LoadLibraryA( C:\ProgramData\BOINC\symsrv.dll ): GetLastError = 126
LoadLibraryA( symsrv.dll ): GetLastError = 126
LoadLibraryA( C:\ProgramData\BOINC\srcsrv.dll ): GetLastError = 126
LoadLibraryA( srcsrv.dll ): GetLastError = 126
LoadLibraryA( C:\ProgramData\BOINC\version.dll ): GetLastError = 126
Loaded Library    : version.dll
Debugger Engine   : 4.0.5.0
Symbol Search Path: C:\ProgramData\BOINC\slots\3;C:\ProgramData\BOINC\projects\boinc.bakerlab.org_rosetta;srv*C:\ProgramData\BOINC\projects\boinc.bakerlab.org_rosetta\symbols*http://msdl.microsoft.com/download/symbols;srv*C:\ProgramData\BOINC\projects\boinc.bakerlab.org_rosetta\symbols*http://boinc.bakerlab.org/rosetta/symstore


ModLoad: 00000000013c0000 0000000003413000 C:\ProgramData\BOINC\projects\boinc.bakerlab.org_rosetta\rosetta_4.07_windows_intelx86.exe (-exported- Symbols Loaded)
    Linked PDB Filename   : C:\cygwin\home\boinc\Rosetta_4.07\main\source\ide\VisualStudio\BoincRelease\rosetta_4.07_windows_intelx86.pdb

ModLoad: 0000000077350000 000000000019c000 C:\Windows\SYSTEM32\ntdll.dll (6.2.17763.404) (-exported- Symbols Loaded)
    Linked PDB Filename   : wntdll.pdb
    File Version          : 10.0.17763.470 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Betriebssystem Microsoft&#174; Windows&#174;
    Product Version       : 10.0.17763.470

ModLoad: 0000000077260000 00000000000e0000 C:\Windows\System32\KERNEL32.DLL (6.2.17763.437) (-exported- Symbols Loaded)
    Linked PDB Filename   : wkernel32.pdb
    File Version          : 10.0.17763.470 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Betriebssystem Microsoft&#174; Windows&#174;
    Product Version       : 10.0.17763.470

ModLoad: 00000000765e0000 00000000001fa000 C:\Windows\System32\KERNELBASE.dll (6.2.17763.404) (-exported- Symbols Loaded)
    Linked PDB Filename   : wkernelbase.pdb
    File Version          : 10.0.17763.470 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Betriebssystem Microsoft&#174; Windows&#174;
    Product Version       : 10.0.17763.470

ModLoad: 00000000749e0000 000000000005f000 C:\Windows\System32\WS2_32.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : ws2_32.pdb
    File Version          : 10.0.17763.470 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Betriebssystem Microsoft&#174; Windows&#174;
    Product Version       : 10.0.17763.470

ModLoad: 0000000076f10000 00000000000bf000 C:\Windows\System32\RPCRT4.dll (6.2.17763.379) (-exported- Symbols Loaded)
    Linked PDB Filename   : wrpcrt4.pdb
    File Version          : 10.0.17763.470 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Betriebssystem Microsoft&#174; Windows&#174;
    Product Version       : 10.0.17763.470

ModLoad: 00000000749c0000 0000000000020000 C:\Windows\System32\SspiCli.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : wsspicli.pdb
    File Version          : 10.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.1

ModLoad: 00000000749b0000 000000000000a000 C:\Windows\System32\CRYPTBASE.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : cryptbase.pdb
    File Version          : 10.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.1

ModLoad: 0000000075ed0000 0000000000062000 C:\Windows\System32\bcryptPrimitives.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : bcryptprimitives.pdb
    File Version          : 10.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.1

ModLoad: 0000000074bc0000 0000000000079000 C:\Windows\System32\sechost.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : sechost.pdb
    File Version          : 10.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.1

ModLoad: 0000000075d30000 0000000000199000 C:\Windows\System32\USER32.dll (6.2.17763.168) (-exported- Symbols Loaded)
    Linked PDB Filename   : wuser32.pdb
    File Version          : 10.0.17763.470 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Betriebssystem Microsoft&#174; Windows&#174;
    Product Version       : 10.0.17763.470

ModLoad: 0000000075d10000 0000000000017000 C:\Windows\System32\win32u.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : wwin32u.pdb
    File Version          : 10.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.1

ModLoad: 0000000074b90000 0000000000023000 C:\Windows\System32\GDI32.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : wgdi32.pdb
    File Version          : 10.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.1

ModLoad: 0000000076fd0000 0000000000167000 C:\Windows\System32\gdi32full.dll (6.2.17763.437) (-exported- Symbols Loaded)
    Linked PDB Filename   : wgdi32full.pdb
    File Version          : 10.0.17763.437 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.437

ModLoad: 0000000076800000 0000000000080000 C:\Windows\System32\msvcp_win.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : msvcp_win.pdb
    File Version          : 10.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.1

ModLoad: 0000000075b70000 0000000000122000 C:\Windows\System32\ucrtbase.dll (6.2.17763.404) (-exported- Symbols Loaded)
    Linked PDB Filename   : ucrtbase.pdb
    File Version          : 10.0.17763.404 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.404

ModLoad: 0000000075af0000 000000000007e000 C:\Windows\System32\ADVAPI32.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : advapi32.pdb
    File Version          : 10.0.17763.470 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Betriebssystem Microsoft&#174; Windows&#174;
    Product Version       : 10.0.17763.470

ModLoad: 0000000075890000 00000000000c0000 C:\Windows\System32\msvcrt.dll (7.0.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : msvcrt.pdb
    File Version          : 7.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 7.0.17763.1

ModLoad: 0000000076ee0000 0000000000025000 C:\Windows\System32\IMM32.DLL (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : wimm32.pdb
    File Version          : 10.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.1

ModLoad: 0000000074c40000 000000000000f000 C:\Windows\System32\kernel.appcore.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : Kernel.Appcore.pdb
    File Version          : 10.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.1

ModLoad: 0000000074410000 0000000000029000 C:\Windows\SYSTEM32\ntmarta.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : ntmarta.pdb
    File Version          : 10.0.17763.470 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Betriebssystem Microsoft&#174; Windows&#174;
    Product Version       : 10.0.17763.470

ModLoad: 0000000070740000 000000000018f000 C:\Windows\SYSTEM32\dbghelp.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : dbghelp.pdb
    File Version          : 10.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.1

ModLoad: 00000000748e0000 0000000000008000 C:\Windows\SYSTEM32\version.dll (6.2.17763.1) (-exported- Symbols Loaded)
    Linked PDB Filename   : version.pdb
    File Version          : 10.0.17763.1 (WinBuild.160101.0800)
    Company Name          : Microsoft Corporation
    Product Name          : Microsoft&#174; Windows&#174; Operating System
    Product Version       : 10.0.17763.1



*** Dump of the Process Statistics: ***

- I/O Operations Counters -
Read: 73133, Write: 0, Other 15390

- I/O Transfers Counters -
Read: 0, Write: 209154, Other 0

- Paged Pool Usage -
QuotaPagedPoolUsage: 247488, QuotaPeakPagedPoolUsage: 247616
QuotaNonPagedPoolUsage: 19368, QuotaPeakNonPagedPoolUsage: 19912

- Virtual Memory Usage -
VirtualSize: 1086783488, PeakVirtualSize: 1089437696

- Pagefile Usage -
PagefileUsage: 396963840, PeakPagefileUsage: 499814400

- Working Set Size -
WorkingSetSize: 222756864, PeakWorkingSetSize: 497000448, PageFaultCount: 7022426

*** Dump of thread ID 8232 (state: Waiting): ***

- Information -
Status: Wait Reason: UserRequest, , Kernel Time: 447500000.000000, User Time: 204253429760.000000, Wait Time: 55205536.000000

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x016AC0E8 write attempt to address 0x00D5212C

- Registers -
eax=0a73b865 ebx=00000000 ecx=00d5212c edx=0a73bd10 esi=0a73b8c8 edi=00d5212c
eip=016ac0e8 esp=0a73b86c ebp=0a73b86c
cs=0023  ss=002b  ds=002b  es=002b  fs=0053  gs=002b             efl=00010203

- Callstack -
ChildEBP RetAddr  Args to Child
0a73b86c 016ab277 00000065 0a73b8e0 0a73b8c8 016ab20d rosetta_4.07_windows_intelx86!xmlParserInputRead+0x0 
0a73bd24 016ac3f5 00000005 00000000 00d5212c ffffffff rosetta_4.07_windows_intelx86!xmlParserInputRead+0x0 
0a73bd48 016c72f4 00000005 00000000 00d5212c ffffffff rosetta_4.07_windows_intelx86!xmlParserInputRead+0x0 
0a73bd6c 016d6dae 00d5212c 03b4f36c 03b4f46c 00000421 rosetta_4.07_windows_intelx86!xmlParserInputRead+0x0 
0a73bd8c 016ad384 0000000b 00000000 00000000 00000000 rosetta_4.07_windows_intelx86!xmlParserInputRead+0x0 
0a73bdac 016a22ab c0000005 0a73bde0 016a1980 fffffffe rosetta_4.07_windows_intelx86!xmlParserInputRead+0x0 
0a73fca8 77280419 0071f000 77280400 0a73fd14 773b662d rosetta_4.07_windows_intelx86!xmlParserInputRead+0x0 
0a73fcb8 773b662d 0071f000 ad7daa5d 00000000 00000000 KERNEL32!BaseThreadInitThunk+0x0 
0a73fd14 773b65fd ffffffff 773d51bc 00000000 00000000 ntdll!RtlGetAppContainerNamedObjectPath+0x0 
0a73fd24 00000000 016a22dd 0071f000 00000000 00000000 ntdll!RtlGetAppContainerNamedObjectPath+0x0 

*** Dump of thread ID 5860 (state: Waiting): ***

- Information -
Status: Wait Reason: ExecutionDelay, , Kernel Time: 468750.000000, User Time: 156250.000000, Wait Time: 55205536.000000

- Registers -
eax=00000000 ebx=299cf62c ecx=00000000 edx=00000000 esi=00000000 edi=299cf62c
eip=773c07ec esp=299cf5ec ebp=299cf650
cs=0023  ss=002b  ds=002b  es=002b  fs=0053  gs=002b             efl=00000202

- Callstack -
ChildEBP RetAddr  Args to Child
299cf650 766edb6f 00000064 00000000 299cf88c 028ad11b ntdll!ZwDelayExecution+0x0 
299cf660 028ad11b 00000064 028ad0f0 028ad0f0 00000000 KERNELBASE!Sleep+0x0 
299cf88c 77280419 00000000 77280400 299cf8f8 773b662d rosetta_4.07_windows_intelx86!xmlMutexLock+0x0 
299cf89c 773b662d 00000000 8e92afb1 00000000 00000000 KERNEL32!BaseThreadInitThunk+0x0 
299cf8f8 773b65fd ffffffff 773d51bc 00000000 00000000 ntdll!RtlGetAppContainerNamedObjectPath+0x0 
299cf908 00000000 028ad0f0 00000000 00000000 00000000 ntdll!RtlGetAppContainerNamedObjectPath+0x0 

*** Dump of thread ID 4584 (state: Waiting): ***

- Information -
Status: Wait Reason: ExecutionDelay, , Kernel Time: 0.000000, User Time: 0.000000, Wait Time: 55205524.000000

- Registers -
eax=00000000 ebx=1679f95c ecx=00000000 edx=00000000 esi=00000000 edi=1679f95c
eip=773c07ec esp=1679f91c ebp=1679f980
cs=0023  ss=002b  ds=002b  es=002b  fs=0053  gs=002b             efl=00000202

- Callstack -
ChildEBP RetAddr  Args to Child
1679f980 766edb6f 000007d0 00000000 1679fa78 02128d91 ntdll!ZwDelayExecution+0x0 
1679f990 02128d91 000007d0 c217a620 0b329578 02128f70 KERNELBASE!Sleep+0x0 
1679fa78 02128f77 00000000 0289a2f5 00000000 c217a6e4 rosetta_4.07_windows_intelx86!xmlMutexLock+0x0 
1679fabc 77280419 0b329578 77280400 1679fb28 773b662d rosetta_4.07_windows_intelx86!xmlMutexLock+0x0 
1679facc 773b662d 0b329578 b177ac61 00000000 00000000 KERNEL32!BaseThreadInitThunk+0x0 
1679fb28 773b65fd ffffffff 773d51bc 00000000 00000000 ntdll!RtlGetAppContainerNamedObjectPath+0x0 
1679fb38 00000000 0289a29e 0b329578 00000000 00000000 ntdll!RtlGetAppContainerNamedObjectPath+0x0 


*** Debug Message Dump ****


*** Foreground Window Data ***
    Window Name      : 
    Window Class     : 
    Window Process ID: 0
    Window Thread ID : 0

Exiting...

</stderr_txt>
]]>

.
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Jim1348

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Message 90716 - Posted: 24 Apr 2019, 12:38:01 UTC

I think a lot of the error messages are just due to insufficient memory.
Mine all have at least 16 GB (on 12 cores), so at least 1.33 GB/core, and usually 32 GB (on 8 to 12 cores).
https://boinc.bakerlab.org/rosetta/results.php?userid=52455

I don't know if the OS matters or not; I have just been running Ubuntu lately, but on both AMD Ryzen and Intel chips.
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Message 90720 - Posted: 24 Apr 2019, 17:12:30 UTC - in response to Message 90716.  

I think a lot of the error messages are just due to insufficient memory.

At least in my case, I don't think so. I have two cores, 6GB RAM + 6GB page file, usually not even half of it is in use. I run just one Rosetta task at a time, the other core is for SETI, which is using 30MB or so. Tasks which error out usually are using around 500MB (peak). Everything else is running stable here, only not Rosetta, even Rosetta Mini runs OK, except for one single WU so far. If there was not enough RAM, not only Rosseta should have issues and Windows would throw error messages at me.
.
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Jim1348

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Message 90722 - Posted: 25 Apr 2019, 6:50:44 UTC - in response to Message 90720.  
Last modified: 25 Apr 2019, 6:57:19 UTC

I would suspect the anti-virus in that case, and maybe try a different one. The exclusions don't always work for real-time monitoring.
But Microsoft's own Windows Defender should be OK, though I have not used it much on Win10, but mainly on Win7 which uses a different version of WD.

Otherwise, I have no idea, but I see that the work units that errored on your machine completed successfully on other machines, so the work units do not appear to be bad for everyone at least.
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Message 90723 - Posted: 25 Apr 2019, 8:49:13 UTC - in response to Message 90722.  

But Microsoft's own Windows Defender should be OK

That's what I'm using, with BOINC data dir excluded from scanning. Works for all other projects.

I see that the work units that errored on your machine completed successfully on other machines, so the work units do not appear to be bad for everyone at least.

Well, the two right now, but not always the case. I also don't think there's much wrong with the WUs, it's the application, that's not running stable. Rosetta Mini is waaay better, unfortunately we can't choose which application we want to run like on other projects.
.
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Jim1348

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Message 90725 - Posted: 25 Apr 2019, 16:48:40 UTC - in response to Message 90723.  

I also don't think there's much wrong with the WUs, it's the application, that's not running stable. Rosetta Mini is waaay better, unfortunately we can't choose which application we want to run like on other projects.

I just had a 4.08 hang for a while at over 24 hours and less than 8% complete. I thought it was a goner. But I suspended it and then resumed it a few minute later, and it apparently completed shortly thereafter without a problem. The progress must have been in error.
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Message 90770 - Posted: 15 May 2019, 19:00:37 UTC

10v4nme2_4535_result_0558_0001_SAVE_ALL_OUT_830741_283_1

Peak working set size: 229.64 MB
Peak swap size: 215.95 MB

Stderr output:
<core_client_version>7.12.1</core_client_version>
<![CDATA[
<message>
(unknown error) - exit code -1073740940 (0xc0000374)</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.07_windows_intelx86.exe @10v4nme2_4535_result_0558_0001.flags -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 1404927
Starting watchdog...
Watchdog active.

</stderr_txt>
]]>

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Message boards : Number crunching : Rosetta 4.0+



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