Project: 14816 (Run 2472, Clone 1, Gen 0) Gromacs error

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Project: 14816 (Run 2472, Clone 1, Gen 0) Gromacs error

Postby DeeGee » Sun Jul 26, 2020 8:48 pm

The client doesn't seem to error out the WU properly, and tries to restart it endlessly.

Code: Select all
19:41:58:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
19:42:46:WU01:FS00:Starting
19:42:46:WU01:FS00:Removing old file 'work/01/logfile_01-20200726-191046.txt'
19:42:46:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/deegee/FAH/cores/cores.foldingathome.org/lin/64bit-avx-256/a7-0.0.19/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 706 -lifeline 3544 -checkpoint 15 -np 21
19:42:46:WU01:FS00:Started FahCore on PID 4164951
19:42:46:WU01:FS00:Core PID:4164955
19:42:46:WU01:FS00:FahCore 0xa7 started
19:42:47:WU01:FS00:0xa7:*********************** Log Started 2020-07-26T19:42:46Z ***********************
19:42:47:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
19:42:47:WU01:FS00:0xa7:       Type: 0xa7
19:42:47:WU01:FS00:0xa7:       Core: Gromacs
19:42:47:WU01:FS00:0xa7:       Args: -dir 01 -suffix 01 -version 706 -lifeline 4164951 -checkpoint 15
19:42:47:WU01:FS00:0xa7:             -np 21
19:42:47:WU01:FS00:0xa7:************************************ CBang *************************************
19:42:47:WU01:FS00:0xa7:       Date: Nov 27 2019
19:42:47:WU01:FS00:0xa7:       Time: 11:26:54
19:42:47:WU01:FS00:0xa7:   Revision: d25803215b59272441049dfa05a0a9bf7a6e3c48
19:42:47:WU01:FS00:0xa7:     Branch: master
19:42:47:WU01:FS00:0xa7:   Compiler: GNU 8.3.0
19:42:47:WU01:FS00:0xa7:    Options: -std=c++11 -ffunction-sections -fdata-sections -O3 -funroll-loops
19:42:47:WU01:FS00:0xa7:             -fno-pie -fPIC
19:42:47:WU01:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
19:42:47:WU01:FS00:0xa7:       Bits: 64
19:42:47:WU01:FS00:0xa7:       Mode: Release
19:42:47:WU01:FS00:0xa7:************************************ System ************************************
19:42:47:WU01:FS00:0xa7:        CPU: AMD Ryzen 9 3900X 12-Core Processor
19:42:47:WU01:FS00:0xa7:     CPU ID: AuthenticAMD Family 23 Model 113 Stepping 0
19:42:47:WU01:FS00:0xa7:       CPUs: 24
19:42:47:WU01:FS00:0xa7:     Memory: 31.33GiB
19:42:47:WU01:FS00:0xa7:Free Memory: 1.94GiB
19:42:47:WU01:FS00:0xa7:    Threads: POSIX_THREADS
19:42:47:WU01:FS00:0xa7: OS Version: 5.4
19:42:47:WU01:FS00:0xa7:Has Battery: false
19:42:47:WU01:FS00:0xa7: On Battery: false
19:42:47:WU01:FS00:0xa7: UTC Offset: 3
19:42:47:WU01:FS00:0xa7:        PID: 4164955
19:42:47:WU01:FS00:0xa7:        CWD: /home/deegee/FAH/work
19:42:47:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
19:42:47:WU01:FS00:0xa7:    Version: 0.0.19
19:42:47:WU01:FS00:0xa7:     Author: Joseph Coffland <joseph@cauldrondevelopment.com>
19:42:47:WU01:FS00:0xa7:  Copyright: 2019 foldingathome.org
19:42:47:WU01:FS00:0xa7:   Homepage: https://foldingathome.org/
19:42:47:WU01:FS00:0xa7:       Date: Nov 26 2019
19:42:47:WU01:FS00:0xa7:       Time: 00:41:42
19:42:47:WU01:FS00:0xa7:   Revision: d5b5c747532224f986b7cd02c968ed9a20c16d6e
19:42:47:WU01:FS00:0xa7:     Branch: master
19:42:47:WU01:FS00:0xa7:   Compiler: GNU 8.3.0
19:42:47:WU01:FS00:0xa7:    Options: -std=c++11 -ffunction-sections -fdata-sections -O3 -funroll-loops
19:42:47:WU01:FS00:0xa7:             -fno-pie
19:42:47:WU01:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
19:42:47:WU01:FS00:0xa7:       Bits: 64
19:42:47:WU01:FS00:0xa7:       Mode: Release
19:42:47:WU01:FS00:0xa7:************************************ Build *************************************
19:42:47:WU01:FS00:0xa7:       SIMD: avx_256
19:42:47:WU01:FS00:0xa7:********************************************************************************
19:42:47:WU01:FS00:0xa7:Project: 14816 (Run 2472, Clone 1, Gen 0)
19:42:47:WU01:FS00:0xa7:Unit: 0x00000007455e42065ec7cdc9fbb08dec
19:42:47:WU01:FS00:0xa7:Digital signatures verified
19:42:47:WU01:FS00:0xa7:Calling: mdrun -s frame0.tpr -o frame0.trr -cpt 15 -nt 21
19:42:47:WU01:FS00:0xa7:Steps: first=0 total=250000
19:42:47:WU01:FS00:0xa7:Completed 1 out of 250000 steps (0%)
19:42:48:WU01:FS00:0xa7:ERROR:
19:42:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:42:48:WU01:FS00:0xa7:ERROR:
19:42:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:42:48:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:42:48:WU01: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
19:42:48:WU01:FS00:0xa7:ERROR:
19:42:48:WU01:FS00:0xa7:ERROR:Fatal error:
19:42:48:WU01:FS00:0xa7:ERROR:2 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:42:48:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:42:48:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:42:48:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:42:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:42:48:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:42:48:WU01: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
19:42:48:WU01:FS00:0xa7:ERROR:
19:42:48:WU01:FS00:0xa7:ERROR:Fatal error:
19:42:48:WU01:FS00:0xa7:ERROR:2 particles communicated to PME rank 7 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:42:48:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:42:48:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:42:48:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:42:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:42:53:WU01:FS00:0xa7:ERROR:
19:42:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:42:53:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:42:53:WU01:FS00:0xa7:ERROR:
19:42:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:42:53:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:42:53:WU01: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
19:42:53:WU01:FS00:0xa7:ERROR:
19:42:53:WU01:FS00:0xa7:ERROR:Fatal error:
19:42:53:WU01:FS00:0xa7:ERROR:5 particles communicated to PME rank 7 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:42:53:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:42:53:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:42:53:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:42:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:42:53:WU01:FS00:0xa7:ERROR:
19:42:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:42:53:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:42:53:WU01: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
19:42:53:WU01:FS00:0xa7:ERROR:
19:42:53:WU01:FS00:0xa7:ERROR:Fatal error:
19:42:53:WU01:FS00:0xa7:ERROR:13 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:42:53:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:42:53:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:42:53:WU01: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
19:42:53:WU01:FS00:0xa7:ERROR:
19:42:53:WU01:FS00:0xa7:ERROR:Fatal error:
19:42:53:WU01:FS00:0xa7:ERROR:2 particles communicated to PME rank 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:42:53:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:42:53:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:42:53:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:42:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:42:53:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:42:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:42:58:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
19:43:46:WU01:FS00:Starting
19:43:46:WU01:FS00:Removing old file 'work/01/logfile_01-20200726-191146.txt'
19:43:46:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/deegee/FAH/cores/cores.foldingathome.org/lin/64bit-avx-256/a7-0.0.19/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 706 -lifeline 3544 -checkpoint 15 -np 21
19:43:46:WU01:FS00:Started FahCore on PID 4166103
19:43:46:WU01:FS00:Core PID:4166107
19:43:46:WU01:FS00:FahCore 0xa7 started
19:43:47:WU01:FS00:0xa7:*********************** Log Started 2020-07-26T19:43:46Z ***********************
19:43:47:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
19:43:47:WU01:FS00:0xa7:       Type: 0xa7
19:43:47:WU01:FS00:0xa7:       Core: Gromacs
19:43:47:WU01:FS00:0xa7:       Args: -dir 01 -suffix 01 -version 706 -lifeline 4166103 -checkpoint 15
19:43:47:WU01:FS00:0xa7:             -np 21
19:43:47:WU01:FS00:0xa7:************************************ CBang *************************************
19:43:47:WU01:FS00:0xa7:       Date: Nov 27 2019
19:43:47:WU01:FS00:0xa7:       Time: 11:26:54
19:43:47:WU01:FS00:0xa7:   Revision: d25803215b59272441049dfa05a0a9bf7a6e3c48
19:43:47:WU01:FS00:0xa7:     Branch: master
19:43:47:WU01:FS00:0xa7:   Compiler: GNU 8.3.0
19:43:47:WU01:FS00:0xa7:    Options: -std=c++11 -ffunction-sections -fdata-sections -O3 -funroll-loops
19:43:47:WU01:FS00:0xa7:             -fno-pie -fPIC
19:43:47:WU01:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
19:43:47:WU01:FS00:0xa7:       Bits: 64
19:43:47:WU01:FS00:0xa7:       Mode: Release
19:43:47:WU01:FS00:0xa7:************************************ System ************************************
19:43:47:WU01:FS00:0xa7:        CPU: AMD Ryzen 9 3900X 12-Core Processor
19:43:47:WU01:FS00:0xa7:     CPU ID: AuthenticAMD Family 23 Model 113 Stepping 0
19:43:47:WU01:FS00:0xa7:       CPUs: 24
19:43:47:WU01:FS00:0xa7:     Memory: 31.33GiB
19:43:47:WU01:FS00:0xa7:Free Memory: 1.92GiB
19:43:47:WU01:FS00:0xa7:    Threads: POSIX_THREADS
19:43:47:WU01:FS00:0xa7: OS Version: 5.4
19:43:47:WU01:FS00:0xa7:Has Battery: false
19:43:47:WU01:FS00:0xa7: On Battery: false
19:43:47:WU01:FS00:0xa7: UTC Offset: 3
19:43:47:WU01:FS00:0xa7:        PID: 4166107
19:43:47:WU01:FS00:0xa7:        CWD: /home/deegee/FAH/work
19:43:47:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
19:43:47:WU01:FS00:0xa7:    Version: 0.0.19
19:43:47:WU01:FS00:0xa7:     Author: Joseph Coffland <joseph@cauldrondevelopment.com>
19:43:47:WU01:FS00:0xa7:  Copyright: 2019 foldingathome.org
19:43:47:WU01:FS00:0xa7:   Homepage: https://foldingathome.org/
19:43:47:WU01:FS00:0xa7:       Date: Nov 26 2019
19:43:47:WU01:FS00:0xa7:       Time: 00:41:42
19:43:47:WU01:FS00:0xa7:   Revision: d5b5c747532224f986b7cd02c968ed9a20c16d6e
19:43:47:WU01:FS00:0xa7:     Branch: master
19:43:47:WU01:FS00:0xa7:   Compiler: GNU 8.3.0
19:43:47:WU01:FS00:0xa7:    Options: -std=c++11 -ffunction-sections -fdata-sections -O3 -funroll-loops
19:43:47:WU01:FS00:0xa7:             -fno-pie
19:43:47:WU01:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
19:43:47:WU01:FS00:0xa7:       Bits: 64
19:43:47:WU01:FS00:0xa7:       Mode: Release
19:43:47:WU01:FS00:0xa7:************************************ Build *************************************
19:43:47:WU01:FS00:0xa7:       SIMD: avx_256
19:43:47:WU01:FS00:0xa7:********************************************************************************
19:43:47:WU01:FS00:0xa7:Project: 14816 (Run 2472, Clone 1, Gen 0)
19:43:47:WU01:FS00:0xa7:Unit: 0x00000007455e42065ec7cdc9fbb08dec
19:43:47:WU01:FS00:0xa7:Digital signatures verified
19:43:47:WU01:FS00:0xa7:Calling: mdrun -s frame0.tpr -o frame0.trr -cpt 15 -nt 21
19:43:47:WU01:FS00:0xa7:Steps: first=0 total=250000
19:43:48:WU01:FS00:0xa7:Completed 1 out of 250000 steps (0%)
19:43:48:WU01:FS00:0xa7:ERROR:
19:43:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:43:48:WU01:FS00:0xa7:ERROR:
19:43:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:43:48:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:43:48:WU01: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
19:43:48:WU01:FS00:0xa7:ERROR:
19:43:48:WU01:FS00:0xa7:ERROR:Fatal error:
19:43:48:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:43:48:WU01: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
19:43:48:WU01:FS00:0xa7:ERROR:
19:43:48:WU01:FS00:0xa7:ERROR:Fatal error:
19:43:48:WU01:FS00:0xa7:ERROR:2 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:43:48:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:43:48:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:43:48:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:43:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:43:48:WU01:FS00:0xa7:ERROR:2 particles communicated to PME rank 7 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:43:48:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:43:48:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:43:48:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:43:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:43:53:WU01:FS00:0xa7:ERROR:
19:43:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:43:53:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:43:53:WU01:FS00:0xa7:ERROR:
19:43:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:43:53:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:43:53:WU01: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
19:43:53:WU01:FS00:0xa7:ERROR:
19:43:53:WU01:FS00:0xa7:ERROR:Fatal error:
19:43:53:WU01:FS00:0xa7:ERROR:12 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:43:53:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:43:53:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:43:53:WU01: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
19:43:53:WU01:FS00:0xa7:ERROR:
19:43:53:WU01:FS00:0xa7:ERROR:Fatal error:
19:43:53:WU01:FS00:0xa7:ERROR:2 particles communicated to PME rank 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:43:53:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:43:53:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:43:53:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:43:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:43:53:WU01:FS00:0xa7:ERROR:
19:43:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:43:53:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:43:53:WU01: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
19:43:53:WU01:FS00:0xa7:ERROR:
19:43:53:WU01:FS00:0xa7:ERROR:Fatal error:
19:43:53:WU01:FS00:0xa7:ERROR:6 particles communicated to PME rank 7 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:43:53:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:43:53:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:43:53:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:43:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:43:53:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:43:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:43:58:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
19:44:46:WU01:FS00:Starting
19:44:46:WU01:FS00:Removing old file 'work/01/logfile_01-20200726-191246.txt'
19:44:46:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /home/deegee/FAH/cores/cores.foldingathome.org/lin/64bit-avx-256/a7-0.0.19/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 706 -lifeline 3544 -checkpoint 15 -np 21
19:44:46:WU01:FS00:Started FahCore on PID 4167195
19:44:46:WU01:FS00:Core PID:4167199
19:44:46:WU01:FS00:FahCore 0xa7 started
19:44:47:WU01:FS00:0xa7:*********************** Log Started 2020-07-26T19:44:46Z ***********************
19:44:47:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
19:44:47:WU01:FS00:0xa7:       Type: 0xa7
19:44:47:WU01:FS00:0xa7:       Core: Gromacs
19:44:47:WU01:FS00:0xa7:       Args: -dir 01 -suffix 01 -version 706 -lifeline 4167195 -checkpoint 15
19:44:47:WU01:FS00:0xa7:             -np 21
19:44:47:WU01:FS00:0xa7:************************************ CBang *************************************
19:44:47:WU01:FS00:0xa7:       Date: Nov 27 2019
19:44:47:WU01:FS00:0xa7:       Time: 11:26:54
19:44:47:WU01:FS00:0xa7:   Revision: d25803215b59272441049dfa05a0a9bf7a6e3c48
19:44:47:WU01:FS00:0xa7:     Branch: master
19:44:47:WU01:FS00:0xa7:   Compiler: GNU 8.3.0
19:44:47:WU01:FS00:0xa7:    Options: -std=c++11 -ffunction-sections -fdata-sections -O3 -funroll-loops
19:44:47:WU01:FS00:0xa7:             -fno-pie -fPIC
19:44:47:WU01:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
19:44:47:WU01:FS00:0xa7:       Bits: 64
19:44:47:WU01:FS00:0xa7:       Mode: Release
19:44:47:WU01:FS00:0xa7:************************************ System ************************************
19:44:47:WU01:FS00:0xa7:        CPU: AMD Ryzen 9 3900X 12-Core Processor
19:44:47:WU01:FS00:0xa7:     CPU ID: AuthenticAMD Family 23 Model 113 Stepping 0
19:44:47:WU01:FS00:0xa7:       CPUs: 24
19:44:47:WU01:FS00:0xa7:     Memory: 31.33GiB
19:44:47:WU01:FS00:0xa7:Free Memory: 1.91GiB
19:44:47:WU01:FS00:0xa7:    Threads: POSIX_THREADS
19:44:47:WU01:FS00:0xa7: OS Version: 5.4
19:44:47:WU01:FS00:0xa7:Has Battery: false
19:44:47:WU01:FS00:0xa7: On Battery: false
19:44:47:WU01:FS00:0xa7: UTC Offset: 3
19:44:47:WU01:FS00:0xa7:        PID: 4167199
19:44:47:WU01:FS00:0xa7:        CWD: /home/deegee/FAH/work
19:44:47:WU01:FS00:0xa7:******************************** Build - libFAH ********************************
19:44:47:WU01:FS00:0xa7:    Version: 0.0.19
19:44:47:WU01:FS00:0xa7:     Author: Joseph Coffland <joseph@cauldrondevelopment.com>
19:44:47:WU01:FS00:0xa7:  Copyright: 2019 foldingathome.org
19:44:47:WU01:FS00:0xa7:   Homepage: https://foldingathome.org/
19:44:47:WU01:FS00:0xa7:       Date: Nov 26 2019
19:44:47:WU01:FS00:0xa7:       Time: 00:41:42
19:44:47:WU01:FS00:0xa7:   Revision: d5b5c747532224f986b7cd02c968ed9a20c16d6e
19:44:47:WU01:FS00:0xa7:     Branch: master
19:44:47:WU01:FS00:0xa7:   Compiler: GNU 8.3.0
19:44:47:WU01:FS00:0xa7:    Options: -std=c++11 -ffunction-sections -fdata-sections -O3 -funroll-loops
19:44:47:WU01:FS00:0xa7:             -fno-pie
19:44:47:WU01:FS00:0xa7:   Platform: linux2 4.19.0-5-amd64
19:44:47:WU01:FS00:0xa7:       Bits: 64
19:44:47:WU01:FS00:0xa7:       Mode: Release
19:44:47:WU01:FS00:0xa7:************************************ Build *************************************
19:44:47:WU01:FS00:0xa7:       SIMD: avx_256
19:44:47:WU01:FS00:0xa7:********************************************************************************
19:44:47:WU01:FS00:0xa7:Project: 14816 (Run 2472, Clone 1, Gen 0)
19:44:47:WU01:FS00:0xa7:Unit: 0x00000007455e42065ec7cdc9fbb08dec
19:44:47:WU01:FS00:0xa7:Digital signatures verified
19:44:47:WU01:FS00:0xa7:Calling: mdrun -s frame0.tpr -o frame0.trr -cpt 15 -nt 21
19:44:47:WU01:FS00:0xa7:Steps: first=0 total=250000
19:44:48:WU01:FS00:0xa7:Completed 1 out of 250000 steps (0%)
19:44:48:WU01:FS00:0xa7:ERROR:
19:44:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:44:48:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:44:48:WU01: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
19:44:48:WU01:FS00:0xa7:ERROR:
19:44:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:44:48:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:44:48:WU01: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
19:44:48:WU01:FS00:0xa7:ERROR:
19:44:48:WU01:FS00:0xa7:ERROR:Fatal error:
19:44:48:WU01:FS00:0xa7:ERROR:2 particles communicated to PME rank 7 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:44:48:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:44:48:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:44:48:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:44:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:44:48:WU01:FS00:0xa7:ERROR:
19:44:48:WU01:FS00:0xa7:ERROR:Fatal error:
19:44:48:WU01:FS00:0xa7:ERROR:2 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:44:48:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:44:48:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:44:48:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:44:48:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:44:53:WU01:FS00:0xa7:ERROR:
19:44:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:44:53:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:44:53:WU01: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
19:44:53:WU01:FS00:0xa7:ERROR:
19:44:53:WU01:FS00:0xa7:ERROR:Fatal error:
19:44:53:WU01:FS00:0xa7:ERROR:12 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:44:53:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:44:53:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:44:53:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:44:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:44:53:WU01:FS00:0xa7:ERROR:
19:44:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:44:53:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:44:53:WU01: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
19:44:53:WU01:FS00:0xa7:ERROR:
19:44:53:WU01:FS00:0xa7:ERROR:Fatal error:
19:44:53:WU01:FS00:0xa7:ERROR:2 particles communicated to PME rank 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:44:53:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:44:53:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:44:53:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:44:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:44:53:WU01:FS00:0xa7:ERROR:
19:44:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
19:44:53:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20191026-456f0d636-unknown
19:44:53:WU01: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
19:44:53:WU01:FS00:0xa7:ERROR:
19:44:53:WU01:FS00:0xa7:ERROR:Fatal error:
19:44:53:WU01:FS00:0xa7:ERROR:6 particles communicated to PME rank 7 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
19:44:53:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
19:44:53:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
19:44:53:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
19:44:53:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
User avatar
DeeGee
 
Posts: 57
Joined: Thu Oct 02, 2008 2:15 pm
Location: Finland

Re: Project: 14816 (Run 2472, Clone 1, Gen 0) Gromacs error

Postby bruce » Mon Jul 27, 2020 3:33 am

Perhaps it's not as "endless" as you think it is. You've posted three "interrrupted" errors 0x66 but each one reports multiple problems with PME rank 0, 1, and 7. FAHClient is only counting the 0x66 errors and it SHOULD abort eventually.

The PME errors are a chanllenging issue for GROMACS. I suspect there will be some changes when the next version of a GROMACS FAHCore is released. (There's one in development.)
bruce
 
Posts: 19970
Joined: Thu Nov 29, 2007 11:13 pm
Location: So. Cal.


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