13141 (Run 723, Clone 0, Gen 70) // GROMACS Fatal Error

Moderators: Site Moderators, PandeGroup

13141 (Run 723, Clone 0, Gen 70) // GROMACS Fatal Error

Postby parkut » Fri Oct 27, 2017 1:13 pm

Code: Select all
23:19:41:WU01:FS00:Starting
23:19:41:WU01:FS00:Running FahCore: /usr/bin/FAHCoreWrapper /var/lib/fahclient/cores/fahwebx.stanford.edu/cores/Linux/AMD64/Core_a7.fah/FahCore_a7 -dir 01 -suffix 01 -version 704 -lifeline 1013 -checkpoint 15 -np 4
23:19:41:WU01:FS00:Started FahCore on PID 2219
23:19:41:WU01:FS00:Core PID:2223
23:19:41:WU01:FS00:FahCore 0xa7 started
23:19:42:WU01:FS00:0xa7:*********************** Log Started 2017-10-25T23:19:41Z ***********************
23:19:42:WU01:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
23:19:42:WU01:FS00:0xa7:       Type: 0xa7
23:19:42:WU01:FS00:0xa7:       Core: Gromacs
23:19:42:WU01:FS00:0xa7:    Website: http://folding.stanford.edu/
23:19:42:WU01:FS00:0xa7:  Copyright: (c) 2009-2016 Stanford University
23:19:42:WU01:FS00:0xa7:     Author: Joseph Coffland <joseph@cauldrondevelopment.com>
23:19:42:WU01:FS00:0xa7:       Args: -dir 01 -suffix 01 -version 704 -lifeline 2219 -checkpoint 15 -np 4
23:19:42:WU01:FS00:0xa7:     Config: <none>
23:19:42:WU01:FS00:0xa7:************************************ Build *************************************
23:19:42:WU01:FS00:0xa7:    Version: 0.0.11
23:19:42:WU01:FS00:0xa7:       Date: Sep 20 2016
23:19:42:WU01:FS00:0xa7:       Time: 06:40:11
23:19:42:WU01:FS00:0xa7: Repository: Git
23:19:42:WU01:FS00:0xa7:   Revision: 957bd90e68d95ddcf1594dc15ff6c64cc4555146
23:19:42:WU01:FS00:0xa7:     Branch: master
23:19:42:WU01:FS00:0xa7:   Compiler: GNU 4.8.5
23:19:42:WU01:FS00:0xa7:    Options: -std=gnu++98 -O3 -funroll-loops -ffast-math -mfpmath=sse
23:19:42:WU01:FS00:0xa7:             -fno-unsafe-math-optimizations -msse2
23:19:42:WU01:FS00:0xa7:   Platform: linux2 4.6.0-1-amd64
23:19:42:WU01:FS00:0xa7:       Bits: 64
23:19:42:WU01:FS00:0xa7:       Mode: Release
23:19:42:WU01:FS00:0xa7:       SIMD: sse2
23:19:42:WU01:FS00:0xa7:************************************ System ************************************
23:19:42:WU01:FS00:0xa7:        CPU: Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz
23:19:42:WU01:FS00:0xa7:     CPU ID: GenuineIntel Family 6 Model 15 Stepping 11
23:19:42:WU01:FS00:0xa7:       CPUs: 4
23:19:42:WU01:FS00:0xa7:     Memory: 2.77GiB
23:19:42:WU01:FS00:0xa7:Free Memory: 2.21GiB
23:19:42:WU01:FS00:0xa7:    Threads: POSIX_THREADS
23:19:42:WU01:FS00:0xa7: OS Version: 3.10
23:19:42:WU01:FS00:0xa7:Has Battery: false
23:19:42:WU01:FS00:0xa7: On Battery: false
23:19:42:WU01:FS00:0xa7: UTC Offset: -4
23:19:42:WU01:FS00:0xa7:        PID: 2223
23:19:42:WU01:FS00:0xa7:        CWD: /var/lib/fahclient/work
23:19:42:WU01:FS00:0xa7:         OS: Linux 3.10.0-693.5.2.el7.x86_64 x86_64
23:19:42:WU01:FS00:0xa7:    OS Arch: AMD64
23:19:42:WU01:FS00:0xa7:********************************************************************************
23:19:42:WU01:FS00:0xa7:Project: 13141 (Run 723, Clone 0, Gen 70)
23:19:42:WU01:FS00:0xa7:Unit: 0x0000004dab436c6559a5a4079f11be16
23:19:42:WU01:FS00:0xa7:Reading tar file core.xml
23:19:42:WU01:FS00:0xa7:Reading tar file frame70.tpr
23:19:42:WU01:FS00:0xa7:Digital signatures verified
23:19:42:WU01:FS00:0xa7:Calling: mdrun -s frame70.tpr -o frame70.trr -cpt 15 -nt 4
23:19:43:WU01:FS00:0xa7:Steps: first=14000000 total=200000
23:19:46:WU01:FS00:0xa7:Completed 1 out of 200000 steps (0%)
23:24:30:WU01:FS00:0xa7:Completed 2000 out of 200000 steps (1%)
23:29:10:WU01:FS00:0xa7:Completed 4000 out of 200000 steps (2%)
23:33:59:WU01:FS00:0xa7:Completed 6000 out of 200000 steps (3%)
23:38:50:WU01:FS00:0xa7:Completed 8000 out of 200000 steps (4%)
--snip--
03:58:55:WU01:FS00:0xa7:Completed 116000 out of 200000 steps (58%)
04:03:45:WU01:FS00:0xa7:Completed 118000 out of 200000 steps (59%)
04:08:28:WU01:FS00:0xa7:ERROR:
04:08:28:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
04:08:28:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20160919-669094a-unknown
04:08:28:WU01:FS00:0xa7:ERROR:Source code file: /host/debian-testing-64bit-core-a7-sse-release/gromacs-core/build/gromacs/src/gromacs/mdlib/pme.c, line: 754
04:08:28:WU01:FS00:0xa7:ERROR:
04:08:28:WU01:FS00:0xa7:ERROR:Fatal error:
04:08:28:WU01:FS00:0xa7:ERROR:1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
04:08:28:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
04:08:28:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
04:08:28:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
04:08:28:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
04:08:28:WU01:FS00:0xa7:ERROR:
04:08:28:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
04:08:28:WU01:FS00:0xa7:ERROR:Program GROMACS, VERSION 5.0.4-20160919-669094a-unknown
04:08:28:WU01:FS00:0xa7:ERROR:Source code file: /host/debian-testing-64bit-core-a7-sse-release/gromacs-core/build/gromacs/src/gromacs/mdlib/pme.c, line: 754
04:08:28:WU01:FS00:0xa7:ERROR:
04:08:28:WU01:FS00:0xa7:ERROR:Fatal error:
04:08:28:WU01:FS00:0xa7:ERROR:10 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.
04:08:28:WU01:FS00:0xa7:ERROR:This usually means that your system is not well equilibrated.
04:08:28:WU01:FS00:0xa7:ERROR:For more information and tips for troubleshooting, please check the GROMACS
04:08:28:WU01:FS00:0xa7:ERROR:website at http://www.gromacs.org/Documentation/Errors
04:08:28:WU01:FS00:0xa7:ERROR:-------------------------------------------------------
04:08:33:WU01:FS00:FahCore returned: INTERRUPTED (102 = 0x66)
User avatar
parkut
 
Posts: 416
Joined: Tue Feb 12, 2008 7:33 am
Location: SE Michigan, USA

Re: 13141 (Run 723, Clone 0, Gen 70) // GROMACS Fatal Error

Postby Joe_H » Fri Oct 27, 2017 3:35 pm

There is one return of this WU in the database, and that it successfully processed for someone else. This might be just a one time error.
Image

iMac 2.8 i7 12 GB smp8, Mac Pro 2.8 quad 12 GB smp6
MacBook Pro 2.9 i7 8 GB smp3
Joe_H
Site Admin
 
Posts: 4534
Joined: Tue Apr 21, 2009 4:41 pm
Location: W. MA


Return to Issues with a specific WU

Who is online

Users browsing this forum: No registered users and 2 guests

cron