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fahclient crashes / linux

https://foldingforum.org/viewtopic.php?t=35267

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fahclient crashes / linux

Posted: Fri May 15, 2020 9:37 pm
by jhaering
Hi,

i use fahclient under linux. in the beginning the applications were executed. currently the applications and the fahclient crash.

Code: Select all

*********************** Log Started 2020-05-15T21:16:04Z ***********************
21:16:04:************************* Folding@home Client *************************
21:16:04:    Website: http://folding.stanford.edu/
21:16:04:  Copyright: (c) 2009-2014 Stanford University
21:16:04:     Author: Joseph Coffland <[email protected]>
21:16:04:       Args: --child --lifeline 633 /etc/fahclient/config.xml --run-as fahclient
21:16:04:             --pid-file=/var/run/fahclient.pid --daemon
21:16:04:     Config: /etc/fahclient/config.xml
21:16:04:******************************** Build ********************************
21:16:04:    Version: 7.4.4
21:16:04:       Date: Mar 4 2014
21:16:04:       Time: 12:02:38
21:16:04:    SVN Rev: 4130
21:16:04:     Branch: fah/trunk/client
21:16:04:   Compiler: GNU 4.4.7
21:16:04:    Options: -std=gnu++98 -O3 -funroll-loops -mfpmath=sse -ffast-math
21:16:04:             -fno-unsafe-math-optimizations -msse2
21:16:04:   Platform: linux2 3.2.0-1-amd64
21:16:04:       Bits: 64
21:16:04:       Mode: Release
21:16:04:******************************* System ********************************
21:16:04:        CPU: AMD Ryzen 5 3600 6-Core Processor
21:16:04:     CPU ID: AuthenticAMD Family 23 Model 113 Stepping 0
21:16:04:       CPUs: 12
21:16:04:     Memory: 31.41GiB
21:16:04:Free Memory: 23.44GiB
21:16:04:    Threads: POSIX_THREADS
21:16:04: OS Version: 4.19
21:16:04:Has Battery: false
21:16:04: On Battery: false
21:16:04: UTC Offset: 2
21:16:04:        PID: 1102
21:16:04:        CWD: /var/lib/fahclient
21:16:04:         OS: Linux 4.19.0-9-amd64 x86_64
21:16:04:    OS Arch: AMD64
21:16:04:       GPUs: 0
21:16:04:       CUDA: Not detected
21:16:04:***********************************************************************
21:16:04:<config>
21:16:04:  <!-- Client Control -->
21:16:04:  <fold-anon v='true'/>
21:16:04:
21:16:04:  <!-- Folding Slot Configuration -->
21:16:04:  <cpus v='10'/>
21:16:04:  <gpu v='false'/>
21:16:04:
21:16:04:  <!-- User Information -->
21:16:04:  <team v='43829'/>
21:16:04:  <user v='jhaering'/>
21:16:04:
21:16:04:  <!-- Folding Slots -->
21:16:04:  <slot id='0' type='CPU'/>
21:16:04:</config>
21:16:04:Switching to user fahclient
21:16:04:Trying to access database...
21:16:04:Successfully acquired database lock
21:16:04:Enabled folding slot 00: READY cpu:10
21:16:05:WU00:FS00:Starting
21:16:05:WU00:FS00:Removing old file './work/00/logfile_01-20200514-204340.txt'
21:16:05:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 00 -suffix 01 -version 704 -lifeline 1102 -checkpoint 15 -np 10
21:16:05:WU00:FS00:Started FahCore on PID 1111
21:16:05:WU00:FS00:Core PID:1115
21:16:05:WU00:FS00:FahCore 0xa7 started
21:16:05:WU00:FS00:0xa7:*********************** Log Started 2020-05-15T21:16:05Z ***********************
21:16:05:WU00:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
21:16:05:WU00:FS00:0xa7:       Type: 0xa7
21:16:05:WU00:FS00:0xa7:       Core: Gromacs
21:16:05:WU00:FS00:0xa7:       Args: -dir 00 -suffix 01 -version 704 -lifeline 1111 -checkpoint 15 -np
21:16:05:WU00:FS00:0xa7:             10
21:16:05:WU00:FS00:0xa7:************************************ CBang *************************************
21:16:05:WU00:FS00:0xa7:       Date: Nov 5 2019
21:16:05:WU00:FS00:0xa7:       Time: 06:06:57
21:16:05:WU00:FS00:0xa7:   Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
21:16:05:WU00:FS00:0xa7:     Branch: master
21:16:05:WU00:FS00:0xa7:   Compiler: GNU 8.3.0
21:16:05:WU00:FS00:0xa7:    Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
21:16:05:WU00:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
21:16:05:WU00:FS00:0xa7:       Bits: 64
21:16:05:WU00:FS00:0xa7:       Mode: Release
21:16:05:WU00:FS00:0xa7:************************************ System ************************************
21:16:05:WU00:FS00:0xa7:        CPU: AMD Ryzen 5 3600 6-Core Processor
21:16:05:WU00:FS00:0xa7:     CPU ID: AuthenticAMD Family 23 Model 113 Stepping 0
21:16:05:WU00:FS00:0xa7:       CPUs: 12
21:16:05:WU00:FS00:0xa7:     Memory: 31.41GiB
21:16:05:WU00:FS00:0xa7:Free Memory: 23.44GiB
21:16:05:WU00:FS00:0xa7:    Threads: POSIX_THREADS
21:16:05:WU00:FS00:0xa7: OS Version: 4.19
21:16:05:WU00:FS00:0xa7:Has Battery: false
21:16:05:WU00:FS00:0xa7: On Battery: false
21:16:05:WU00:FS00:0xa7: UTC Offset: 2
21:16:05:WU00:FS00:0xa7:        PID: 1115
21:16:05:WU00:FS00:0xa7:        CWD: /var/lib/fahclient/work
21:16:05:WU00:FS00:0xa7:******************************** Build - libFAH ********************************
21:16:05:WU00:FS00:0xa7:    Version: 0.0.18
21:16:05:WU00:FS00:0xa7:     Author: Joseph Coffland <[email protected]>
21:16:05:WU00:FS00:0xa7:  Copyright: 2019 foldingathome.org
21:16:05:WU00:FS00:0xa7:   Homepage: https://foldingathome.org/
21:16:05:WU00:FS00:0xa7:       Date: Nov 5 2019
21:16:05:WU00:FS00:0xa7:       Time: 06:13:26
21:16:05:WU00:FS00:0xa7:   Revision: 490c9aa2957b725af319379424d5c5cb36efb656
21:16:05:WU00:FS00:0xa7:     Branch: master
21:16:05:WU00:FS00:0xa7:   Compiler: GNU 8.3.0
21:16:05:WU00:FS00:0xa7:    Options: -std=c++11 -O3 -funroll-loops -fno-pie
21:16:05:WU00:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
21:16:05:WU00:FS00:0xa7:       Bits: 64
21:16:05:WU00:FS00:0xa7:       Mode: Release
21:16:05:WU00:FS00:0xa7:************************************ Build *************************************
21:16:05:WU00:FS00:0xa7:       SIMD: avx_256
21:16:05:WU00:FS00:0xa7:********************************************************************************
21:16:05:WU00:FS00:0xa7:Project: 14521 (Run 0, Clone 760, Gen 36)
21:16:05:WU00:FS00:0xa7:Unit: 0x0000003780fccb0a5e42d9a582576a6a
21:16:05:WU00:FS00:0xa7:Reading tar file core.xml
21:16:05:WU00:FS00:0xa7:Reading tar file frame36.tpr
21:16:05:WU00:FS00:0xa7:Digital signatures verified
21:16:05:WU00:FS00:0xa7:Calling: mdrun -s frame36.tpr -o frame36.trr -x frame36.xtc -cpt 15 -nt 10
21:16:06:WU00:FS00:0xa7:Steps: first=9000000 total=250000
21:16:06:WU00:FS00:0xa7:ERROR:
21:16:06:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
21:16:06:WU00:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
21:16:06:WU00: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
21:16:06:WU00:FS00:0xa7:ERROR:
21:16:06:WU00:FS00:0xa7:ERROR:Fatal error:
21:16:06:WU00:FS00:0xa7:ERROR:There is no domain decomposition for 10 ranks that is compatible with the given box and a minimum cell size of 1.46925 nm
21:16:06:WU00:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
21:16:06:WU00:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
21:16:06:WU00:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
21:16:06:WU00:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
21:16:06:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
21:16:11:WU00:FS00:0xa7:WARNING:Unexpected exit() call
21:16:11:WU00:FS00:0xa7:WARNING:Unexpected exit from science code
21:16:11:WU00:FS00:0xa7:Saving result file ../logfile_01.txt
21:16:11:WU00:FS00:0xa7:Saving result file md.log
21:16:11:WU00:FS00:0xa7:Saving result file science.log
21:16:11:WU00:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
21:16:11:WU00:FS00:Starting
21:16:11:WU00:FS00:Removing old file './work/00/logfile_01-20200514-204350.txt'
21:16:11:WU00:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/cores.foldingathome.org/v7/lin/64bit/avx/Core_a7.fah/FahCore_a7 -dir 00 -suffix 01 -version 704 -lifeline 1102 -checkpoint 15 -np 10
21:16:11:WU00:FS00:Started FahCore on PID 1128
21:16:11:WU00:FS00:Core PID:1132
21:16:11:WU00:FS00:FahCore 0xa7 started
21:16:12:WU00:FS00:0xa7:*********************** Log Started 2020-05-15T21:16:11Z ***********************
21:16:12:WU00:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
21:16:12:WU00:FS00:0xa7:       Type: 0xa7
21:16:12:WU00:FS00:0xa7:       Core: Gromacs
21:16:12:WU00:FS00:0xa7:       Args: -dir 00 -suffix 01 -version 704 -lifeline 1128 -checkpoint 15 -np
21:16:12:WU00:FS00:0xa7:             10
21:16:12:WU00:FS00:0xa7:************************************ CBang *************************************
21:16:12:WU00:FS00:0xa7:       Date: Nov 5 2019
21:16:12:WU00:FS00:0xa7:       Time: 06:06:57
21:16:12:WU00:FS00:0xa7:   Revision: 46c96f1aa8419571d83f3e63f9c99a0d602f6da9
21:16:12:WU00:FS00:0xa7:     Branch: master
21:16:12:WU00:FS00:0xa7:   Compiler: GNU 8.3.0
21:16:12:WU00:FS00:0xa7:    Options: -std=c++11 -O3 -funroll-loops -fno-pie -fPIC
21:16:12:WU00:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
21:16:12:WU00:FS00:0xa7:       Bits: 64
21:16:12:WU00:FS00:0xa7:       Mode: Release
21:16:12:WU00:FS00:0xa7:************************************ System ************************************
21:16:12:WU00:FS00:0xa7:        CPU: AMD Ryzen 5 3600 6-Core Processor
21:16:12:WU00:FS00:0xa7:     CPU ID: AuthenticAMD Family 23 Model 113 Stepping 0
21:16:12:WU00:FS00:0xa7:       CPUs: 12
21:16:12:WU00:FS00:0xa7:     Memory: 31.41GiB
21:16:12:WU00:FS00:0xa7:Free Memory: 23.44GiB
21:16:12:WU00:FS00:0xa7:    Threads: POSIX_THREADS
21:16:12:WU00:FS00:0xa7: OS Version: 4.19
21:16:12:WU00:FS00:0xa7:Has Battery: false
21:16:12:WU00:FS00:0xa7: On Battery: false
21:16:12:WU00:FS00:0xa7: UTC Offset: 2
21:16:12:WU00:FS00:0xa7:        PID: 1132
21:16:12:WU00:FS00:0xa7:        CWD: /var/lib/fahclient/work
21:16:12:WU00:FS00:0xa7:******************************** Build - libFAH ********************************
21:16:12:WU00:FS00:0xa7:    Version: 0.0.18
21:16:12:WU00:FS00:0xa7:     Author: Joseph Coffland <[email protected]>
21:16:12:WU00:FS00:0xa7:  Copyright: 2019 foldingathome.org
21:16:12:WU00:FS00:0xa7:   Homepage: https://foldingathome.org/
21:16:12:WU00:FS00:0xa7:       Date: Nov 5 2019
21:16:12:WU00:FS00:0xa7:       Time: 06:13:26
21:16:12:WU00:FS00:0xa7:   Revision: 490c9aa2957b725af319379424d5c5cb36efb656
21:16:12:WU00:FS00:0xa7:     Branch: master
21:16:12:WU00:FS00:0xa7:   Compiler: GNU 8.3.0
21:16:12:WU00:FS00:0xa7:    Options: -std=c++11 -O3 -funroll-loops -fno-pie
21:16:12:WU00:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
21:16:12:WU00:FS00:0xa7:       Bits: 64
21:16:12:WU00:FS00:0xa7:       Mode: Release
21:16:12:WU00:FS00:0xa7:************************************ Build *************************************
21:16:12:WU00:FS00:0xa7:       SIMD: avx_256
21:16:12:WU00:FS00:0xa7:********************************************************************************
21:16:12:WU00:FS00:0xa7:Project: 14521 (Run 0, Clone 760, Gen 36)
21:16:12:WU00:FS00:0xa7:Unit: 0x0000003780fccb0a5e42d9a582576a6a
21:16:12:WU00:FS00:0xa7:Reading tar file core.xml
21:16:12:WU00:FS00:0xa7:Reading tar file frame36.tpr
21:16:12:WU00:FS00:0xa7:Digital signatures verified
21:16:12:WU00:FS00:0xa7:Calling: mdrun -s frame36.tpr -o frame36.trr -x frame36.xtc -cpt 15 -nt 10
21:16:12:WU00:FS00:0xa7:Steps: first=9000000 total=250000
21:16:12:WU00:FS00:0xa7:ERROR:
21:16:12:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
21:16:12:WU00:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
21:16:12:WU00: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
21:16:12:WU00:FS00:0xa7:ERROR:
21:16:12:WU00:FS00:0xa7:ERROR:Fatal error:
21:16:12:WU00:FS00:0xa7:ERROR:There is no domain decomposition for 10 ranks that is compatible with the given box and a minimum cell size of 1.46925 nm
21:16:12:WU00:FS00:0xa7:ERROR:Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
21:16:12:WU00:FS00:0xa7:ERROR:Look in the log file for details on the domain decomposition
21:16:12:WU00:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
21:16:12:WU00:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
21:16:12:WU00:FS00:0xa7:ERROR:-------------------------------------------------------
21:16:17:WU00:FS00:0xa7:WARNING:Unexpected exit() call
21:16:17:WARNING:Unexpected exit from science code
21:16:17:Saving result file ../logfile_01.txt
21:16:17:Saving result file md.log
21:16:17:Saving result file science.log
21:16:17:Caught signal SIGSEGV(11) on PID 1132
21:16:17:Caught signal SIGSEGV(11) on PID 1132
21:16:17:Caught signal SIGSEGV(11
What's wrong? Solution?

Greetings

Jürgen Häring

Re: fahclient crashes / linux

Posted: Fri May 15, 2020 9:53 pm
by PantherX
Welcome to the F@H Forum jhaering,

Please note that the issue is Project: 14521 can't fold on 10 CPUs you can reduce the value to 8 and it will hopefully work.

You can do that by using Advanced Control (AKA FAHControl) -> Configure -> Slots tab -> CPU Slot -> Edit -> Change value from -1 to 8 -> OK -> Save

Alternatively, you can stop the client, edit the config.xml file and then restart the client.

Code: Select all

  <slot id='0' type='CPU'>
    <cpus v='8'/>
  </slot>
I will notify the researcher about this to avoid the issue from happening again :)

Re: fahclient crashes / linux

Posted: Fri May 15, 2020 10:01 pm
by PantherX
I also noticed two things:

1) You're running an older version of the client. There's a newer version and you can read about it here: viewtopic.php?f=24&t=34466
2) You're not using a passkey which is recommended to use for security reasons and bonus points. You can review the article here and make an informed decision: https://foldingathome.org/support/faq/points/passkey/

Re: fahclient crashes / linux

Posted: Sat May 16, 2020 7:59 am
by jhaering
Hi PantherX,

thanks for the tips. I have installed the new version. Now also the fahclient runs stable.

Greetings

Jürgen Häring
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