Task 241318

Name boinc2docker_9892_1564889284.254119_1
Workunit 107412
Created 4 Aug 2019, 3:28:09 UTC
Sent 4 Aug 2019, 3:57:00 UTC
Report deadline 11 Aug 2019, 3:57:00 UTC
Received 4 Aug 2019, 13:48:49 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 837
Run time 10 min 37 sec
CPU time 8 min 31 sec
Validate state Valid
Credit 24.71
Device peak FLOPS 15.56 GFLOPS
Application version boinc2docker v1.07 (vbox64_mt)
x86_64-pc-linux-gnu
Peak working set size 108.72 MB
Peak swap size 114.62 MB
Peak disk usage 238.02 MB

Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
2019-08-04 09:20:25 (11332): vboxwrapper (7.9.26200): starting
2019-08-04 09:20:25 (11332): Feature: Checkpoint interval offset (78 seconds)
2019-08-04 09:20:25 (11332): Detected: VirtualBox COM Interface (Version: 5.2.8)
2019-08-04 09:20:25 (11332): Detected: Minimum checkpoint interval (600.000000 seconds)
2019-08-04 09:20:25 (11332): Create VM. (boinc_ad9fa6d1d5dad320, slot#8)
2019-08-04 09:20:25 (11332): Updating drive controller type and model for desired configuration.
2019-08-04 09:20:26 (11332): Setting Memory Size for VM. (3288MB)
2019-08-04 09:20:26 (11332): Setting CPU Count for VM. (4)
2019-08-04 09:20:26 (11332): Setting Chipset Options for VM.
2019-08-04 09:20:26 (11332): Setting Boot Options for VM.
2019-08-04 09:20:26 (11332): Enabling VM Network Access.
2019-08-04 09:20:26 (11332): Setting Network Configuration for NAT.
2019-08-04 09:20:26 (11332): Disabling USB Support for VM.
2019-08-04 09:20:26 (11332): Disabling COM Port Support for VM.
2019-08-04 09:20:26 (11332): Disabling LPT Port Support for VM.
2019-08-04 09:20:26 (11332): Disabling Audio Support for VM.
2019-08-04 09:20:26 (11332): Disabling Clipboard Support for VM.
2019-08-04 09:20:26 (11332): Disabling Drag and Drop Support for VM.
2019-08-04 09:20:26 (11332): Adding storage controller(s) to VM.
2019-08-04 09:20:26 (11332): Adding virtual ISO 9660 disk drive to VM. (vm_isocontext.iso)
2019-08-04 09:20:26 (11332): Adding VirtualBox Guest Additions to VM.
2019-08-04 09:20:26 (11332): Adding network bandwidth throttle group to VM. (Defaulting to 1024GB)
2019-08-04 09:20:26 (11332): Enabling shared directory for VM.
2019-08-04 09:20:27 (11332): Starting VM. (boinc_ad9fa6d1d5dad320, slot#8)
2019-08-04 09:20:39 (11332): Guest Log: BIOS: VirtualBox 5.2.8

2019-08-04 09:20:39 (11332): Guest Log: CPUID EDX: 0x178bfbff

2019-08-04 09:20:39 (11332): Guest Log: BIOS: Boot : bseqnr=1, bootseq=0032

2019-08-04 09:20:39 (11332): Guest Log: int13_harddisk: function 02, unmapped device for ELDL=80

2019-08-04 09:20:39 (11332): Guest Log: BIOS: Boot from Hard Disk 0 failed

2019-08-04 09:20:39 (11332): Guest Log: BIOS: Boot : bseqnr=2, bootseq=0003

2019-08-04 09:20:39 (11332): Guest Log: BIOS: Booting from CD-ROM...

2019-08-04 09:20:39 (11332): Guest Log: BIOS: KBD: unsupported int 16h function 03

2019-08-04 09:20:39 (11332): Guest Log: BIOS: AX=0305 BX=0000 CX=0000 DX=0000 

2019-08-04 09:20:39 (11332): Successfully started VM. (PID = '12624')
2019-08-04 09:20:39 (11332): Reporting VM Process ID to BOINC.
2019-08-04 09:20:44 (11332): VM state change detected. (old = 'poweroff', new = 'running')
2019-08-04 09:20:55 (11332): Preference change detected
2019-08-04 09:20:55 (11332): Setting CPU throttle for VM. (100%)
2019-08-04 09:20:55 (11332): Setting checkpoint interval to 600 seconds. (Higher value of (Preference: 60 seconds) or (Vbox_job.xml: 600 seconds))
2019-08-04 09:21:10 (11332): Guest Log: net.ipv4.ip_forward = 1

2019-08-04 09:21:10 (11332): Guest Log: sysctl: cannot stat /proc/sys/net/ipv6/conf/all/forwarding: No such file or directory

2019-08-04 09:21:10 (11332): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-08-04 09:21:10 (11332): Guest Log: sysctl: "cannot stat %s" is an unknown key

2019-08-04 09:21:10 (11332): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-08-04 09:21:10 (11332): Guest Log: Segmentation fault

2019-08-04 09:21:10 (11332): Guest Log: automount ...

2019-08-04 09:21:10 (11332): Guest Log: vgdrvHeartbeatInit: Setting up heartbeat to trigger every 2000 milliseconds

2019-08-04 09:21:10 (11332): Guest Log: vboxguest: misc device minor 56, IRQ 20, I/O port d020, MMIO at 00000000f0400000 (size 0x400000)

2019-08-04 09:21:10 (11332): Guest Log: Is the disk unpartitioned?, test for the 'boot2docker format-me' string

2019-08-04 09:21:10 (11332): Guest Log: automount over.

2019-08-04 09:21:10 (11332): Guest Log: Setting hostname to boot2docker Done.

2019-08-04 09:21:10 (11332): Guest Log: Sun Aug  4 09:21:07 UTC 2019 dhcp -------------------------------

2019-08-04 09:21:15 (11332): Guest Log: udevadm settle - timeout of 5 seconds reached, the event queue contains:

2019-08-04 09:21:15 (11332): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1370)

2019-08-04 09:21:20 (11332): Guest Log: Sun Aug  4 09:21:13 UTC 2019 dhcp -------------------------------

2019-08-04 09:21:20 (11332): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000147 main     Log opened 2019-08-04T09:21:13.555083000Z

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000315 main     OS Product: Linux

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000365 main     OS Release: 4.1.19-boot2docker

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000414 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000463 main     Executable: /sbin/VBoxService

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000464 main     Process ID: 898

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000466 main     Package type: LINUX_64BITS_GENERIC

2019-08-04 09:21:20 (11332): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.00:00:00.001884 main     5.0.16 r105871 started. Verbose level = 0a

2019-08-04 09:21:20 (11332): Guest Log: d64 (Mar  4 2016 17:38:55) release log

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000147 main     Log opened 2019-08-04T09:21:13.555083000Z

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000315 main     OS Product: Linux

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000365 main     OS Release: 4.1.19-boot2docker

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000414 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.015253 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

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.015351 vminfo   Error: Unable to connect to system D-Bus (1/3): D-Bus not installed

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000463 main     Executable: /sbin/VBoxService

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000464 main     Process ID: 898

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.000466 main     Package type: LINUX_64BITS_GENERIC

2019-08-04 09:21:20 (11332): Guest Log: 00:00:00.001884 main     5.0.16 r105871 started. Verbose level = 0

2019-08-04 09:21:20 (11332): Guest Log: Mounting BOINC shared/...

2019-08-04 09:21:20 (11332): Guest Log: -------------------

2019-08-04 09:21:20 (11332): Guest Log: Sun Aug  4 13:21:16 UTC 2019

2019-08-04 09:21:25 (11332): Guest Log: 00:00:05.018505 vminfo   Error: Unable to connect to system D-Bus (2/3): D-Bus not installed

2019-08-04 09:21:25 (11332): Guest Log: Sun Aug  4 13:21:21 UTC 2019

2019-08-04 09:21:25 (11332): Guest Log: 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default 

2019-08-04 09:21:25 (11332): Guest Log:     link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00

2019-08-04 09:21:25 (11332): Guest Log:     inet 127.0.0.1/8 scope host lo

2019-08-04 09:21:25 (11332): Guest Log:        valid_lft forever preferred_lft forever

2019-08-04 09:21:25 (11332): Guest Log:     inet6 ::1/128 scope host 

2019-08-04 09:21:25 (11332): Guest Log:        valid_lft forever preferred_lft forever

2019-08-04 09:21:25 (11332): Guest Log: 2: dummy0: <BROADCAST,NOARP> mtu 1500 qdisc noop state DOWN group default 

2019-08-04 09:21:25 (11332): Guest Log:     link/ether 4a:84:d7:02:8e:d5 brd ff:ff:ff:ff:ff:ff

2019-08-04 09:21:25 (11332): Guest Log: 3: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc pfifo_fast state UP group default qlen 1000

2019-08-04 09:21:25 (11332): Guest Log:     link/ether 08:00:27:41:fb:e1 brd ff:ff:ff:ff:ff:ff

2019-08-04 09:21:25 (11332): Guest Log:     inet 10.0.2.15/24 brd 10.0.2.255 scope global eth0

2019-08-04 09:21:25 (11332): Guest Log:        valid_lft forever preferred_lft forever

2019-08-04 09:21:25 (11332): Guest Log:     inet6 fe80::a00:27ff:fe41:fbe1/64 scope link 

2019-08-04 09:21:25 (11332): Guest Log:        valid_lft forever preferred_lft forever

2019-08-04 09:21:25 (11332): Guest Log: -------------------

2019-08-04 09:21:25 (11332): Guest Log: Linking /etc/docker to /var/lib/boot2docker for persistence

2019-08-04 09:21:25 (11332): Guest Log: Waiting for Docker daemon to start...

2019-08-04 09:21:25 (11332): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE

2019-08-04 09:21:25 (11332): Guest Log: Running boinc_app...

2019-08-04 09:21:25 (11332): Guest Log: Importing Docker image from BOINC...

2019-08-04 09:21:30 (11332): Guest Log: 00:00:10.019298 vminfo   Error: Unable to connect to system D-Bus (3/3): D-Bus not installed

2019-08-04 09:22:25 (11332): Guest Log: Prerun diagnostics...

2019-08-04 09:22:25 (11332): Guest Log: REPOSITORY                TAG                 IMAGE ID            CREATED             SIZE

2019-08-04 09:22:25 (11332): Guest Log: carlosred/autodock-vina   latest              f9dc0bf006e4        13 months ago       697 MB

2019-08-04 09:22:25 (11332): Guest Log: CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES

2019-08-04 09:22:25 (11332): Guest Log: 705.2M	/var/lib/docker

2019-08-04 09:22:25 (11332): Guest Log:               total        used        free      shared  buff/cache   available

2019-08-04 09:22:25 (11332): Guest Log: Mem:           3219          55        2245         869         917        2249

2019-08-04 09:22:25 (11332): Guest Log: Swap:           752           0         752

2019-08-04 09:22:25 (11332): Guest Log: Prerun commands...

2019-08-04 09:22:25 (11332): Guest Log: Running... 

2019-08-04 09:22:25 (11332): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 09:22:25 (11332): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 09:22:25 (11332): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 09:22:25 (11332): Guest Log:  22  211k   22 47643    0     0   139k      0  0:00:01 --:--:--  0:00:01  238k

2019-08-04 09:22:25 (11332): Guest Log: 100  211k  100  211k    0     0   451k      0 --:--:-- --:--:-- --:--:--  639k

2019-08-04 09:22:25 (11332): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 09:22:25 (11332): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 09:22:25 (11332): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 09:22:25 (11332): Guest Log: 102  3878  102  3878    0     0  17110      0 --:--:-- --:--:-- --:--:-- 51026

2019-08-04 09:22:25 (11332): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 09:22:25 (11332): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 09:22:25 (11332): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 09:22:25 (11332): Guest Log: 102  3983  102  3983    0     0  17915      0 --:--:-- --:--:-- --:--:-- 57724

2019-08-04 09:22:25 (11332): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 09:22:25 (11332): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 09:22:25 (11332): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 09:22:25 (11332): Guest Log:  76  171k   76  131k    0     0   345k      0 --:--:-- --:--:-- --:--:--  527k

2019-08-04 09:22:25 (11332): Guest Log: 100  171k  100  171k    0     0   398k      0 --:--:-- --:--:-- --:--:--  571k

2019-08-04 09:22:25 (11332): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 09:22:25 (11332): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 09:22:25 (11332): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 09:22:25 (11332): Guest Log: 102  3781  102  3781    0     0  24777      0 --:--:-- --:--:-- --:--:-- 54797

2019-08-04 09:22:25 (11332): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 09:22:25 (11332): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 09:22:25 (11332): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 09:22:25 (11332): Guest Log: 102  3781  102  3781    0     0  18598      0 --:--:-- --:--:-- --:--:-- 50413

2019-08-04 09:22:25 (11332): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 09:22:25 (11332): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 09:22:25 (11332): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 09:22:25 (11332): Guest Log: 157   157  157   157    0     0    722      0 --:--:-- --:--:-- --:--:--  2180

2019-08-04 09:22:25 (11332): Guest Log: #################################################################

2019-08-04 09:22:25 (11332): Guest Log: # If you used AutoDock Vina in your work, please cite:          #

2019-08-04 09:22:25 (11332): Guest Log: #                                                               #

2019-08-04 09:22:25 (11332): Guest Log: # O. Trott, A. J. Olson,                                        #

2019-08-04 09:22:25 (11332): Guest Log: # AutoDock Vina: improving the speed and accuracy of docking    #

2019-08-04 09:22:25 (11332): Guest Log: # with a new scoring function, efficient optimization and       #

2019-08-04 09:22:25 (11332): Guest Log: # multithreading, Journal of Computational Chemistry 31 (2010)  #

2019-08-04 09:22:25 (11332): Guest Log: # 455-461                                                       #

2019-08-04 09:22:25 (11332): Guest Log: #                                                               #

2019-08-04 09:22:25 (11332): Guest Log: # DOI 10.1002/jcc.21334                                         #

2019-08-04 09:22:25 (11332): Guest Log: #                                                               #

2019-08-04 09:22:25 (11332): Guest Log: # Please see http://vina.scripps.edu for more information.      #

2019-08-04 09:22:25 (11332): Guest Log: #################################################################

2019-08-04 09:22:25 (11332): Guest Log: Reading input ... done.

2019-08-04 09:22:25 (11332): Guest Log: Setting up the scoring function ... done.

2019-08-04 09:22:30 (11332): Guest Log: Analyzing the binding site ... done.

2019-08-04 09:22:30 (11332): Guest Log: Using random seed: -1861816851

2019-08-04 09:22:30 (11332): Guest Log: Performing search ... 

2019-08-04 09:22:30 (11332): Guest Log: 0%   10   20   30   40   50   60   70   80   90   100%

2019-08-04 09:22:30 (11332): Guest Log: |----|----|----|----|----|----|----|----|----|----|

2019-08-04 09:30:47 (11332): Guest Log: ***************************************************

2019-08-04 09:30:47 (11332): Guest Log: done.

2019-08-04 09:30:47 (11332): Guest Log: Refining results ... done.

2019-08-04 09:30:47 (11332): Guest Log: mode |   affinity | dist from best mode

2019-08-04 09:30:48 (11332): Guest Log:      | (kcal/mol) | rmsd l.b.| rmsd u.b.

2019-08-04 09:30:48 (11332): Guest Log: -----+------------+----------+----------

2019-08-04 09:30:48 (11332): Guest Log:    1        -10.9      0.000      0.000

2019-08-04 09:30:48 (11332): Guest Log:    2        -10.7      2.081      3.383

2019-08-04 09:30:48 (11332): Guest Log:    3        -10.6      2.638      3.780

2019-08-04 09:30:48 (11332): Guest Log:    4        -10.5      2.799      4.645

2019-08-04 09:30:48 (11332): Guest Log:    5        -10.3      2.642      3.983

2019-08-04 09:30:48 (11332): Guest Log:    6        -10.2      0.976      2.121

2019-08-04 09:30:48 (11332): Guest Log:    7         -9.7      3.028      4.001

2019-08-04 09:30:48 (11332): Guest Log:    8         -9.2      3.891      8.144

2019-08-04 09:30:48 (11332): Guest Log:    9         -8.7      3.700     12.273

2019-08-04 09:30:48 (11332): Guest Log: Writing output ... done.

2019-08-04 09:30:48 (11332): Guest Log: Postrun commands...

2019-08-04 09:30:48 (11332): Guest Log: boinc_app exited (0)

2019-08-04 09:30:48 (11332): Guest Log: Saving results...

2019-08-04 09:30:48 (11332): Guest Log: 1OPK.pdbqt

2019-08-04 09:30:48 (11332): Guest Log: ZINC00000567.pdbqt

2019-08-04 09:30:48 (11332): Guest Log: all.pdbqt

2019-08-04 09:30:48 (11332): Guest Log: ligand.pdbqt

2019-08-04 09:30:48 (11332): Guest Log: ligand_experiment.pdbqt

2019-08-04 09:30:48 (11332): Guest Log: protein.pdbqt

2019-08-04 09:30:48 (11332): VM Completion File Detected.
2019-08-04 09:30:48 (11332): Powering off VM.
2019-08-04 09:30:49 (11332): Successfully stopped VM.
2019-08-04 09:30:54 (11332): Deregistering VM. (boinc_ad9fa6d1d5dad320, slot#8)
2019-08-04 09:30:54 (11332): Removing virtual disk drive(s) from VM.
2019-08-04 09:30:54 (11332): Removing network bandwidth throttle group from VM.
2019-08-04 09:30:54 (11332): Removing storage controller(s) from VM.
2019-08-04 09:30:54 (11332): Removing VM from VirtualBox.
09:30:59 (11332): called boinc_finish(0)

</stderr_txt>
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