14700 (689, 1, 0)

[DeHackEd]

Code: Select all

01:58:28:WU00:FS00:Connecting to 65.254.110.245:80
01:58:28:WU00:FS00:Assigned to work server 155.247.166.219
01:58:28:WU00:FS00:Requesting new work unit for slot 00: READY cpu:16 from 155.247.166.219
01:58:28:WU00:FS00:Connecting to 155.247.166.219:8080
01:58:28:WU00:FS00:Downloading 3.01MiB
01:58:33:WU00:FS00:Download complete
01:58:33:WU00:FS00:Received Unit: id:00 state:DOWNLOAD error:NO_ERROR project:14700 run:689 clone:1 gen:0 core:0xa7 unit:0x000000010002894b5ea9fccab51a8e6a
01:58:33:WU00:FS00:Starting
01:58:33:WU00:FS00:Running FahCore: /opt/foldingathome/FAHCoreWrapper /opt/foldingathome/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 00 -suffix 01 -version 706 -lifeline 4644 -checkpoint 15 -np 16
01:58:33:WU00:FS00:Started FahCore on PID 10645
01:58:34:WU00:FS00:Core PID:10650
01:58:34:WU00:FS00:FahCore 0xa7 started
01:58:34:WU00:FS00:0xa7:*********************** Log Started 2020-05-06T01:58:34Z ***********************
01:58:34:WU00:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
01:58:34:WU00:FS00:0xa7:       Type: 0xa7
01:58:34:WU00:FS00:0xa7:       Core: Gromacs
01:58:34:WU00:FS00:0xa7:       Args: -dir 00 -suffix 01 -version 706 -lifeline 10645 -checkpoint 15 -np
01:58:34:WU00:FS00:0xa7:             16
01:58:34:WU00:FS00:0xa7:************************************ CBang *************************************
01:58:34:WU00:FS00:0xa7:       Date: Nov 5 2019
01:58:34:WU00:FS00:0xa7:       Time: 06:06:57
01:58:34:WU00:FS00:0xa7:   Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
01:58:34:WU00:FS00:0xa7:     Branch: master
01:58:34:WU00:FS00:0xa7:   Compiler: GNU 8.3.0
01:58:34:WU00:FS00:0xa7:    Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
01:58:34:WU00:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
01:58:34:WU00:FS00:0xa7:       Bits: 64
01:58:34:WU00:FS00:0xa7:       Mode: Release
01:58:34:WU00:FS00:0xa7:************************************ System ************************************
01:58:34:WU00:FS00:0xa7:        CPU: AMD Ryzen 9 3900X 12-Core Processor
01:58:34:WU00:FS00:0xa7:     CPU ID: AuthenticAMD Family 23 Model 113 Stepping 0
01:58:34:WU00:FS00:0xa7:       CPUs: 24
01:58:34:WU00:FS00:0xa7:     Memory: 31.22GiB
01:58:34:WU00:FS00:0xa7:Free Memory: 5.56GiB
01:58:34:WU00:FS00:0xa7:    Threads: POSIX_THREADS
01:58:34:WU00:FS00:0xa7: OS Version: 4.9
01:58:34:WU00:FS00:0xa7:Has Battery: false
01:58:34:WU00:FS00:0xa7: On Battery: false
01:58:34:WU00:FS00:0xa7: UTC Offset: 0
01:58:34:WU00:FS00:0xa7:        PID: 10650
01:58:34:WU00:FS00:0xa7:        CWD: /opt/foldingathome/work
01:58:34:WU00:FS00:0xa7:******************************** Build - libFAH ********************************
01:58:34:WU00:FS00:0xa7:    Version: 0.0.18
01:58:34:WU00:FS00:0xa7:     Author: Joseph Coffland <[email protected]>
01:58:34:WU00:FS00:0xa7:  Copyright: 2019 foldingathome.org
01:58:34:WU00:FS00:0xa7:   Homepage: https://foldingathome.org/
01:58:34:WU00:FS00:0xa7:       Date: Nov 5 2019
01:58:34:WU00:FS00:0xa7:       Time: 06:13:26
01:58:34:WU00:FS00:0xa7:   Revision: 490c9aa2957b725af319379424d5c5cb36efb656
01:58:34:WU00:FS00:0xa7:     Branch: master
01:58:34:WU00:FS00:0xa7:   Compiler: GNU 8.3.0
01:58:34:WU00:FS00:0xa7:    Options: -std=c++11 -O3 -funroll-loops -fno-pie
01:58:34:WU00:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
01:58:34:WU00:FS00:0xa7:       Bits: 64
01:58:34:WU00:FS00:0xa7:       Mode: Release
01:58:34:WU00:FS00:0xa7:************************************ Build *************************************
01:58:34:WU00:FS00:0xa7:       SIMD: avx_256
01:58:34:WU00:FS00:0xa7:********************************************************************************
01:58:34:WU00:FS00:0xa7:Project: 14700 (Run 689, Clone 1, Gen 0)
01:58:34:WU00:FS00:0xa7:Unit: 0x000000010002894b5ea9fccab51a8e6a
01:58:34:WU00:FS00:0xa7:Reading tar file core.xml
01:58:34:WU00:FS00:0xa7:Reading tar file frame0.tpr
01:58:34:WU00:FS00:0xa7:Digital signatures verified
01:58:34:WU00:FS00:0xa7:Calling: mdrun -s frame0.tpr -o frame0.trr -cpt 15 -nt 16
01:58:34:WU00:FS00:0xa7:Steps: first=0 total=250000
01:58:36:WU00:FS00:0xa7:Completed 1 out of 250000 steps (0%)
01:58:36:WU00:FS00:0xa7:ERROR:
01:58:36:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
01:58:36:WU00:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
01:58:36:WU00:FS00:0xa7:ERROR:Source code file: /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/mdlib/pme.c, line: 754
01:58:36:WU00:FS00:0xa7:ERROR:
01:58:36:WU00:FS00:0xa7:ERROR:Fatal error:
01:58:36:WU00:FS00:0xa7:ERROR:4 particles communicated to PME rank 10 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
01:58:36:WU00:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
01:58:36:WU00:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
01:58:36:WU00:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
01:58:36:WU00:FS00:0xa7:ERROR:-------------------------------------------------------

Code: Select all

[3065017.183142] FahCore_a7[10710]: segfault at 10 ip 0000000001200897 sp 00007ffda3261d60 error 4 in FahCore_a7[406000+10cc000]

Running client-type=advanced

Core is stuck in a crash loop, restarting and crashing again. Interestingly the number of failed particles varies between 1 and 4, but the rest of the error message is consistent.

One other user reported it faulty, so I'm dumping it.

[PantherX]

Welcome to the F@H Forum DeHackEd,

Thanks for reporting this. I have informed the researcher about this. I think that 16 CPUs might be too much for this project but let's wait and see what happens.

[Neil-B]

Ran a number of these whilst in Beta ... 24/56 core and 32/56 core slots ran project with no issues so not sure it is a too many CPUs issue.

[PantherX]

Humm... In that case, maybe _r2w_ben can explain what this means has they have been awesome at documenting the results (viewtopic.php?f=72&t=34350):
4 particles communicated to PME rank 10 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x

[Neil-B]

The only thing I saw that was slightly odd was that for a few of this family of projects 14700, 14717 and 14800 I saw a stats anomaly for my 24/56 core slot where WUs returned low PPDs (14700 15%, 14717 5% and 14800 10% below minimum expected range), whereas the 32/56 core WUs for these Projects are is middle of range - All completed fine, but I mentioned it at the time as an anomaly (but probably not relevant).

I have a vague recollection there was a project a while back that had issues with mid range CPU counts?

[vvoelz]

Hi PantherX --

Thanks for letting us know about this. Sorry you stuck in a crash loop!

16 CPUs shouldn't be too much for this project. If anything I think you have a "bad WU". Each RUN (there are 3000 in this project alone) is a different ligand we are screening as part of the COVID moonshot. Very rarely, we have noticed that a simulation appears to be poorly equilibrated and "blows up". I will stop this clone for now, and will keep an eye out. Interestingly, you are the first person to simulation this particular RUN. (https://apps.foldingathome.org/wu#proje ... ne=1&gen=0) So maybe the clone is bad or the whole RUN is. Other RUNs in the project seem fine.

UPDATE: p14700, r689, c1 has been STOPPED.

[DeHackEd]

To clarify I opened the thread and I think I'm the second person to run it. There's one attempt listed on the WU status page (that's not me) with a code of "Faulty 2", and my client instead got stuck and I deleted it so I assume I just won't be reported at all.

[_r2w_ben]

Humm... In that case, maybe _r2w_ben can explain what this means has they have been awesome at documenting the results (viewtopic.php?f=72&t=34350):
4 particles communicated to PME rank 10 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x

When the failure mentions equilibrated, I think it's a bad work unit.

An incompatibility between the work unit and the number of cores assigned to a work unit looks like this:
There is no domain decomposition for ## ranks that is compatible with the given box and a minimum cell size of ## nm

Code: Select all

08:33:22:WU03:FS00:0xa7:ERROR:-------------------------------------------------------
08:33:22:WU03:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
08:33:22:WU03:FS00:0xa7:ERROR:Source code file: /host/debian-stable-64bit-core-a7-avx-release/gromacs-core/build/gromacs/src/gromacs/mdlib/domdec.c, line: 6902
08:33:22:WU03:FS00:0xa7:ERROR:
08:33:22:WU03:FS00:0xa7:ERROR:Fatal error:
08:33:22:WU03:FS00:0xa7:ERROR:There is no domain decomposition for 60 ranks that is compatible with the given box and a minimum cell size of 1.37225 nm
08:33:22:WU03:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
08:33:22:WU03:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
08:33:22:WU03:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
08:33:22:WU03:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
08:33:22:WU03:FS00:0xa7:ERROR:-------------------------------------------------------

[PantherX]

Ah, thanks for the clarification, vvoelz & _r2w_ben