Task 13582

Name mdsim2_30117_1550048903.546169_2
Workunit 2863
Created 20 Feb 2019, 9:11:34 UTC
Sent 20 Feb 2019, 9:11:45 UTC
Report deadline 27 Feb 2019, 9:11:45 UTC
Received 20 Feb 2019, 17:21:14 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 231
Run time 3 hours 49 min 51 sec
CPU time 1 days 4 hours 57 min 16 sec
Validate state Valid
Credit 1,742.31
Device peak FLOPS 29.04 GFLOPS
Application version MD sim v1.00 (vbox64_mt)
x86_64-pc-linux-gnu
Peak working set size 394.11 MB
Peak swap size 4,415.84 MB
Peak disk usage 208.25 MB

Stderr output

<core_client_version>7.9.3</core_client_version>
<![CDATA[
<stderr_txt>
)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:01 (1402)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:02 (1403)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:03 (1404)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0C02:00 (1405)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0C0A:00 (1406)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP8390:00 (1407)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00 (1408)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/APP0001:00 (1409)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0000:00 (1410)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0100:00 (1411)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0103:00 (1412)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0200:00 (1413)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0303:00 (1414)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1415)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0B00:00 (1416)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0F03:00 (1417)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:02 (1418)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:00 (1419)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:01 (1420)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:02 (1421)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:03 (1422)
2019-02-20 15:42:18 (23911): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:01 (1423)
2019-02-20 15:42:19 (23911): Guest Log: Wed Feb 20 15:42:17 UTC 2019 dhcp -------------------------------
2019-02-20 15:42:19 (23911): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000064 main     Log opened 2019-02-20T15:42:17.306572000Z
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000144 main     OS Product: Linux
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000167 main     OS Release: 4.1.19-boot2docker
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000182 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016
2019-02-20 15:42:19 (23911): Guest Log: VB00:00:00.000205 main     Executable: /sbin/VBoxService
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000206 main     Process ID: 827
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000206 main     Package type: LINUX_64BITS_GENERIC
2019-02-20 15:42:19 (23911): Guest Log: Service 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000953 main     5.0.16 r105871 started. Verbose level = 0
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000064 main     Log opened 2019-02-20T15:42:17.306572000Z
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000144 main     OS Product: Linux
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.003372 vminfo   rtldrNativeLoad: dlopen('libdbus-1.so.3', RTLD_NOW | RTLD_LOCAL) failed: libdbus-1.so.3: cannot open shared object file: No such file or directory
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.003422 vminfo   Error: Unable to connect to system D-Bus (1/3): D-Bus not installed
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000167 main     OS Release: 4.1.19-boot2docker
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000182 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000205 main     Executable: /sbin/VBoxService
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000206 main     Process ID: 827
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000206 main     Package type: LINUX_64BITS_GENERIC
2019-02-20 15:42:19 (23911): Guest Log: 00:00:00.000953 main     5.0.16 r105871 started. Verbose level = 0
2019-02-20 15:42:19 (23911): Guest Log: Mounting BOINC shared/...
2019-02-20 15:42:20 (23911): Guest Log: -------------------
2019-02-20 15:42:20 (23911): Guest Log: Wed Feb 20 15:42:17 UTC 2019
2019-02-20 15:42:25 (23911): Guest Log: 00:00:05.007011 vminfo   Error: Unable to connect to system D-Bus (2/3): D-Bus not installed
2019-02-20 15:42:25 (23911): Guest Log: Wed Feb 20 15:42:24 UTC 2019
2019-02-20 15:42:25 (23911): Guest Log: 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default 
2019-02-20 15:42:25 (23911): Guest Log:     link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
2019-02-20 15:42:25 (23911): Guest Log:     inet 127.0.0.1/8 scope host lo
2019-02-20 15:42:25 (23911): Guest Log:        valid_lft forever preferred_lft forever
2019-02-20 15:42:25 (23911): Guest Log:     inet6 ::1/128 scope host 
2019-02-20 15:42:25 (23911): Guest Log:        valid_lft forever preferred_lft forever
2019-02-20 15:42:25 (23911): Guest Log: 2: dummy0: <BROADCAST,NOARP> mtu 1500 qdisc noop state DOWN group default 
2019-02-20 15:42:25 (23911): Guest Log:     link/ether 5e:1f:91:ab:f1:be brd ff:ff:ff:ff:ff:ff
2019-02-20 15:42:25 (23911): Guest Log: 3: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc pfifo_fast state UP group default qlen 1000
2019-02-20 15:42:25 (23911): Guest Log:     link/ether 08:00:27:60:e8:92 brd ff:ff:ff:ff:ff:ff
2019-02-20 15:42:25 (23911): Guest Log:     inet 10.0.2.15/24 brd 10.0.2.255 scope global eth0
2019-02-20 15:42:25 (23911): Guest Log:        valid_lft forever preferred_lft forever
2019-02-20 15:42:25 (23911): Guest Log:     inet6 fe80::a00:27ff:fe60:e892/64 scope link 
2019-02-20 15:42:25 (23911): Guest Log:        valid_lft forever preferred_lft forever
2019-02-20 15:42:25 (23911): Guest Log: -------------------
2019-02-20 15:42:25 (23911): Guest Log: Linking /etc/docker to /var/lib/boot2docker for persistence
2019-02-20 15:42:25 (23911): Guest Log: Waiting for Docker daemon to start...
2019-02-20 15:42:26 (23911): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
2019-02-20 15:42:26 (23911): Guest Log: Running boinc_app...
2019-02-20 15:42:26 (23911): Guest Log: Importing Docker image from BOINC...
2019-02-20 15:42:30 (23911): Guest Log: 00:00:10.007626 vminfo   Error: Unable to connect to system D-Bus (3/3): D-Bus not installed
2019-02-20 15:42:39 (23911): Guest Log: Prerun diagnostics...
2019-02-20 15:42:39 (23911): Guest Log: REPOSITORY              TAG                 IMAGE ID            CREATED             SIZE
2019-02-20 15:42:39 (23911): Guest Log: claughton/gromacs2018   latest              af5cb836fee4        9 months ago        465.8 MB
2019-02-20 15:42:39 (23911): Guest Log: CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES
2019-02-20 15:42:39 (23911): Guest Log: 474.2M	/var/lib/docker
2019-02-20 15:42:39 (23911): Guest Log:               total        used        free      shared  buff/cache   available
2019-02-20 15:42:39 (23911): Guest Log: Mem:           2307          57        1568         638         681        1572
2019-02-20 15:42:39 (23911): Guest Log: Swap:           524           0         524
2019-02-20 15:42:39 (23911): Guest Log: Prerun commands...
2019-02-20 15:42:39 (23911): Guest Log: md_0_1.tpr
2019-02-20 15:42:39 (23911): Guest Log: Running... 
2019-02-20 15:42:40 (23911): Guest Log:                        :-) GROMACS - gmx mdrun, 2018 (-:
2019-02-20 15:42:40 (23911): Guest Log:                             GROMACS is written by:
2019-02-20 15:42:40 (23911): Guest Log:      Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   
2019-02-20 15:42:40 (23911): Guest Log:  Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof  
2019-02-20 15:42:40 (23911): Guest Log:  Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
2019-02-20 15:42:40 (23911): Guest Log:     Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
2019-02-20 15:42:40 (23911): Guest Log:   Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg   Pieter Meulenhoff 
2019-02-20 15:42:40 (23911): Guest Log:    Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk   
2019-02-20 15:42:40 (23911): Guest Log:    Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers  
2019-02-20 15:42:40 (23911): Guest Log:    Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf   
2019-02-20 15:42:40 (23911): Guest Log:                            and the project leaders:
2019-02-20 15:42:40 (23911): Guest Log:         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
2019-02-20 15:42:40 (23911): Guest Log: Copyright (c) 1991-2000, University of Groningen, The Netherlands.
2019-02-20 15:42:40 (23911): Guest Log: Copyright (c) 2001-2017, The GROMACS development team at
2019-02-20 15:42:40 (23911): Guest Log: Uppsala University, Stockholm University and
2019-02-20 15:42:40 (23911): Guest Log: the Royal Institute of Technology, Sweden.
2019-02-20 15:42:40 (23911): Guest Log: check out http://www.gromacs.org for more information.
2019-02-20 15:42:40 (23911): Guest Log: GROMACS is free software; you can redistribute it and/or modify it
2019-02-20 15:42:40 (23911): Guest Log: under the terms of the GNU Lesser General Public License
2019-02-20 15:42:40 (23911): Guest Log: as published by the Free Software Foundation; either version 2.1
2019-02-20 15:42:40 (23911): Guest Log: of the License, or (at your option) any later version.
2019-02-20 15:42:40 (23911): Guest Log: GROMACS:      gmx mdrun, version 2018
2019-02-20 15:42:40 (23911): Guest Log: Executable:   /opt/gromacs/sse2/bin/gmx
2019-02-20 15:42:40 (23911): Guest Log: Data prefix:  /opt/gromacs/sse2
2019-02-20 15:42:40 (23911): Guest Log: Working dir:  /
2019-02-20 15:42:40 (23911): Guest Log: Command line:
2019-02-20 15:42:40 (23911): Guest Log:   gmx mdrun -v -s /root/shared/md_0_1.tpr -g /root/shared/results/md_0_1.log -o /root/shared/results/md_0_1.trr -c /root/shared/results/md_0_1.gro -e /root/shared/results/md_0_1.edr -cpo /root/shared/results/md_0_1.cpt
2019-02-20 15:42:40 (23911): Guest Log: Back Off! I just backed up /root/shared/results/md_0_1.log to /root/shared/results/#md_0_1.log.4#
2019-02-20 15:42:40 (23911): Guest Log: Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log).
2019-02-20 15:42:40 (23911): Guest Log: The current CPU can measure timings more accurately than the code in
2019-02-20 15:42:40 (23911): Guest Log: gmx mdrun was configured to use. This might affect your simulation
2019-02-20 15:42:40 (23911): Guest Log: speed as accurate timings are needed for load-balancing.
2019-02-20 15:42:40 (23911): Guest Log: Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option.
2019-02-20 15:42:40 (23911): Guest Log: Reading file /root/shared/md_0_1.tpr, VERSION 2018 (single precision)
2019-02-20 15:42:40 (23911): Guest Log: Changing nstlist from 10 to 50, rlist from 1 to 1.116
2019-02-20 15:42:40 (23911): Guest Log: No option -multi
2019-02-20 15:42:40 (23911): Guest Log: Using 8 OpenMP threads 
2019-02-20 15:42:40 (23911): Guest Log: Back Off! I just backed up /root/shared/results/md_0_1.edr to /root/shared/results/#md_0_1.edr.4#
2019-02-20 15:42:40 (23911): Guest Log: starting mdrun 'LYSOZYME in water'
2019-02-20 15:42:40 (23911): Guest Log: 500000 steps,   1000.0 ps.
2019-02-20 17:17:53 (23911): Guest Log: step 122300, will finish Wed Feb 20 17:16:01 2019
2019-02-20 17:17:53 (23911): Guest Log: step 122400, will finish Wed Feb 20 17:16:01 2019
2019-02-20 17:17:53 (23911): Guest Log: step 122500, will finish Wed Feb 20 17:16:01 2019
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2019-02-20 17:17:53 (23911): Guest Log: step 122700, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 122800, will finish Wed Feb 20 17:16:01 2019
2019-02-20 17:17:53 (23911): Guest Log: step 122900, will finish Wed Feb 20 17:16:01 2019
2019-02-20 17:17:53 (23911): Guest Log: step 123000, will finish Wed Feb 20 17:16:01 2019
2019-02-20 17:17:53 (23911): Guest Log: step 123100, will finish Wed Feb 20 17:16:00 2019
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2019-02-20 17:17:53 (23911): Guest Log: step 124000, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 124100, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 124200, will finish Wed Feb 20 17:16:00 2019
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2019-02-20 17:17:53 (23911): Guest Log: step 125000, will finish Wed Feb 20 17:16:01 2019
2019-02-20 17:17:53 (23911): Guest Log: step 125100, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 125200, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 125300, will finish Wed Feb 20 17:16:00 2019
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2019-02-20 17:17:53 (23911): Guest Log: step 125500, will finish Wed Feb 20 17:16:00 2019
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2019-02-20 17:17:53 (23911): Guest Log: step 125700, will finish Wed Feb 20 17:16:00 2019
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2019-02-20 17:17:53 (23911): Guest Log: step 126000, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 126100, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 126200, will finish Wed Feb 20 17:16:00 2019
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2019-02-20 17:17:53 (23911): Guest Log: step 128000, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 128100, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 128200, will finish Wed Feb 20 17:16:00 2019
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2019-02-20 17:17:53 (23911): Guest Log: step 129000, will finish Wed Feb 20 17:16:00 2019
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2019-02-20 17:17:53 (23911): Guest Log: step 130200, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 130300, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 130400, will finish Wed Feb 20 17:16:00 2019
2019-02-20 17:17:53 (23911): Guest Log: step 130500, will finish Wed Feb 20 17:16:00 2019
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2019-02-20 17:17:55 (23911): Guest Log: step 499900, remaining wall clock time:     1 s          
2019-02-20 17:17:55 (23911): Guest Log: Writing final coordinates.
2019-02-20 17:17:55 (23911): Guest Log: step 500000, remaining wall clock time:     0 s          
2019-02-20 17:17:55 (23911): Guest Log:                Core t (s)   Wall t (s)        (%)
2019-02-20 17:17:55 (23911): Guest Log:        Time:    45707.720     5713.465      800.0
2019-02-20 17:17:55 (23911): Guest Log:                          1h35:13
2019-02-20 17:17:55 (23911): Guest Log:                  (ns/day)    (hour/ns)
2019-02-20 17:17:55 (23911): Guest Log: Performance:       15.122        1.587
2019-02-20 17:17:55 (23911): Guest Log: GROMACS reminds you: "That Was Really Cool" (Butthead)
2019-02-20 17:17:55 (23911): Guest Log: Postrun commands...
2019-02-20 17:17:55 (23911): Guest Log: boinc_app exited (0)
2019-02-20 17:17:55 (23911): Guest Log: Saving results...
2019-02-20 17:17:55 (23911): Guest Log: #md_0_1.edr.1#
2019-02-20 17:17:55 (23911): Guest Log: #md_0_1.edr.2#
2019-02-20 17:17:55 (23911): Guest Log: #md_0_1.edr.3#
2019-02-20 17:17:55 (23911): Guest Log: #md_0_1.edr.4#
2019-02-20 17:17:55 (23911): Guest Log: #md_0_1.log.1#
2019-02-20 17:17:55 (23911): Guest Log: #md_0_1.log.2#
2019-02-20 17:17:55 (23911): Guest Log: #md_0_1.log.3#
2019-02-20 17:17:55 (23911): Guest Log: #md_0_1.log.4#
2019-02-20 17:17:55 (23911): Guest Log: md_0_1.cpt
2019-02-20 17:17:55 (23911): Guest Log: md_0_1.edr
2019-02-20 17:17:55 (23911): Guest Log: md_0_1.gro
2019-02-20 17:17:55 (23911): Guest Log: md_0_1.log
2019-02-20 17:17:55 (23911): Guest Log: md_0_1_prev.cpt
2019-02-20 17:17:55 (23911): VM Completion File Detected.
2019-02-20 17:17:55 (23911): Powering off VM.
2019-02-20 17:17:56 (23911): Successfully stopped VM.
2019-02-20 17:17:56 (23911): Deregistering VM. (boinc_456001c7dfb451a3, slot#0)
2019-02-20 17:17:56 (23911): Removing network bandwidth throttle group from VM.
2019-02-20 17:17:56 (23911): Removing storage controller(s) from VM.
2019-02-20 17:17:56 (23911): Removing VM from VirtualBox.
2019-02-20 17:17:56 (23911): Removing virtual ISO 9660 disk from VirtualBox.
17:18:01 (23911): called boinc_finish(0)

</stderr_txt>
]]>


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