Task 241276

Name boinc2docker_7717_1564889269.869428_1
Workunit 107391
Created 4 Aug 2019, 3:27:53 UTC
Sent 4 Aug 2019, 3:57:00 UTC
Report deadline 11 Aug 2019, 3:57:00 UTC
Received 4 Aug 2019, 15:57:13 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 837
Run time 8 min 25 sec
CPU time 7 min 43 sec
Validate state Valid
Credit 21.56
Device peak FLOPS 15.56 GFLOPS
Application version boinc2docker v1.07 (vbox64_mt)
x86_64-pc-linux-gnu
Peak working set size 109.62 MB
Peak swap size 115.02 MB
Peak disk usage 238.02 MB

Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
2019-08-04 11:05:08 (16864): vboxwrapper (7.9.26200): starting
2019-08-04 11:05:08 (16864): Feature: Checkpoint interval offset (409 seconds)
2019-08-04 11:05:08 (16864): Detected: VirtualBox COM Interface (Version: 5.2.8)
2019-08-04 11:05:08 (16864): Detected: Minimum checkpoint interval (600.000000 seconds)
2019-08-04 11:05:08 (16864): Create VM. (boinc_c82a17b17502ee3b, slot#10)
2019-08-04 11:05:08 (16864): Updating drive controller type and model for desired configuration.
2019-08-04 11:05:16 (16864): Setting Memory Size for VM. (3288MB)
2019-08-04 11:05:16 (16864): Setting CPU Count for VM. (4)
2019-08-04 11:05:16 (16864): Setting Chipset Options for VM.
2019-08-04 11:05:16 (16864): Setting Boot Options for VM.
2019-08-04 11:05:16 (16864): Enabling VM Network Access.
2019-08-04 11:05:16 (16864): Setting Network Configuration for NAT.
2019-08-04 11:05:16 (16864): Disabling USB Support for VM.
2019-08-04 11:05:16 (16864): Disabling COM Port Support for VM.
2019-08-04 11:05:16 (16864): Disabling LPT Port Support for VM.
2019-08-04 11:05:16 (16864): Disabling Audio Support for VM.
2019-08-04 11:05:16 (16864): Disabling Clipboard Support for VM.
2019-08-04 11:05:16 (16864): Disabling Drag and Drop Support for VM.
2019-08-04 11:05:16 (16864): Adding storage controller(s) to VM.
2019-08-04 11:05:16 (16864): Adding virtual ISO 9660 disk drive to VM. (vm_isocontext.iso)
2019-08-04 11:05:16 (16864): Adding VirtualBox Guest Additions to VM.
2019-08-04 11:05:16 (16864): Adding network bandwidth throttle group to VM. (Defaulting to 1024GB)
2019-08-04 11:05:16 (16864): Enabling shared directory for VM.
2019-08-04 11:05:17 (16864): Starting VM. (boinc_c82a17b17502ee3b, slot#10)
2019-08-04 11:05:28 (16864): Guest Log: BIOS: VirtualBox 5.2.8

2019-08-04 11:05:28 (16864): Guest Log: CPUID EDX: 0x178bfbff

2019-08-04 11:05:28 (16864): Guest Log: BIOS: Boot : bseqnr=1, bootseq=0032

2019-08-04 11:05:28 (16864): Guest Log: int13_harddisk: function 02, unmapped device for ELDL=80

2019-08-04 11:05:28 (16864): Guest Log: BIOS: Boot from Hard Disk 0 failed

2019-08-04 11:05:28 (16864): Guest Log: BIOS: Boot : bseqnr=2, bootseq=0003

2019-08-04 11:05:28 (16864): Guest Log: BIOS: Booting from CD-ROM...

2019-08-04 11:05:28 (16864): Successfully started VM. (PID = '16720')
2019-08-04 11:05:28 (16864): Reporting VM Process ID to BOINC.
2019-08-04 11:05:33 (16864): VM state change detected. (old = 'poweroff', new = 'running')
2019-08-04 11:06:03 (16864): Guest Log: BIOS: KBD: unsupported int 16h function 03

2019-08-04 11:06:03 (16864): Guest Log: BIOS: AX=0305 BX=0000 CX=0000 DX=0000 

2019-08-04 11:06:03 (16864): Preference change detected
2019-08-04 11:06:03 (16864): Setting CPU throttle for VM. (100%)
2019-08-04 11:06:05 (16864): Setting checkpoint interval to 600 seconds. (Higher value of (Preference: 60 seconds) or (Vbox_job.xml: 600 seconds))
2019-08-04 11:06:22 (16864): Guest Log: vgdrvHeartbeatInit: Setting up heartbeat to trigger every 2000 milliseconds

2019-08-04 11:06:22 (16864): Guest Log: vboxguest: misc device minor 56, IRQ 20, I/O port d020, MMIO at 00000000f0400000 (size 0x400000)

2019-08-04 11:06:22 (16864): Guest Log: net.ipv4.ip_forward = 1

2019-08-04 11:06:22 (16864): Guest Log: sysctl: cannot stat /proc/sys/net/ipv6/conf/all/forwarding: No such file or directory

2019-08-04 11:06:22 (16864): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-08-04 11:06:22 (16864): Guest Log: sysctl: "cannot stat %s" is an unknown key

2019-08-04 11:06:22 (16864): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-08-04 11:06:22 (16864): Guest Log: Segmentation fault

2019-08-04 11:06:22 (16864): Guest Log: automount ...

2019-08-04 11:06:27 (16864): Guest Log: Is the disk unpartitioned?, test for the 'boot2docker format-me' string

2019-08-04 11:06:32 (16864): Guest Log: automount over.

2019-08-04 11:06:32 (16864): Guest Log: Setting hostname to boot2docker Done.

2019-08-04 11:06:32 (16864): Guest Log: Sun Aug  4 11:06:29 UTC 2019 dhcp -------------------------------

2019-08-04 11:06:37 (16864): Guest Log: udevadm settle - timeout of 5 seconds reached, the event queue contains:

2019-08-04 11:06:37 (16864): Guest Log:   /sys/devices/pci0000:00/0000:00:0d.0/ata1/host0/target0:0:0/0:0:0:0/block/sr0 (1635)

2019-08-04 11:06:37 (16864): Guest Log:   /sys/devices/pci0000:00/0000:00:0d.0/ata3/host2/target2:0:0/2:0:0:0/block/sr1 (1636)

2019-08-04 11:06:42 (16864): Guest Log: Sun Aug  4 11:06:35 UTC 2019 dhcp -------------------------------

2019-08-04 11:06:42 (16864): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000099 main     Log opened 2019-08-04T11:06:35.852064000Z

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000215 main     OS Product: Linux

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000273 main     OS Release: 4.1.19-boot2docker

2019-08-04 11:06:42 (16864): Guest Log: VB00:00:00.000309 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-08-04 11:06:42 (16864): Guest Log: xS00:00:00.000343 main     Executable: /sbin/VBoxService

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000345 main     Process ID: 912

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000346 main     Package type: LINUX_64BITS_GENERIC

2019-08-04 11:06:42 (16864): Guest Log: ice 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:00:00:00.001653 main     5.0.16 r105871 started. Verbose level = 0

2019-08-04 11:06:42 (16864): Guest Log: 8:55) release log

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000099 main     Log opened 2019-08-04T11:06:35.852064000Z

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000215 main     OS Product: Linux

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000273 main     OS Release: 4.1.19-boot2docker

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000:00:00.011894 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 11:06:42 (16864): Guest Log: 309 00:00:00.011959 vminfo   Error: Unable to connect to system D-Bus (1/3): D-Bus not installed

2019-08-04 11:06:42 (16864): Guest Log: ain     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000343 main     Executable: /sbin/VBoxService

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000345 main     Process ID: 912

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.000346 main     Package type: LINUX_64BITS_GENERIC

2019-08-04 11:06:42 (16864): Guest Log: 00:00:00.001653 main     5.0.16 r105871 started. Verbose level = 0

2019-08-04 11:06:42 (16864): Guest Log: Mounting BOINC shared/...

2019-08-04 11:06:42 (16864): Guest Log: -------------------

2019-08-04 11:06:42 (16864): Guest Log: Sun Aug  4 15:06:37 UTC 2019

2019-08-04 11:06:47 (16864): Guest Log: 00:00:05.019028 vminfo   Error: Unable to connect to system D-Bus (2/3): D-Bus not installed

2019-08-04 11:06:47 (16864): Guest Log: Sun Aug  4 15:06:43 UTC 2019

2019-08-04 11:06:47 (16864): Guest Log: 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default 

2019-08-04 11:06:47 (16864): Guest Log:     link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00

2019-08-04 11:06:47 (16864): Guest Log:     inet 127.0.0.1/8 scope host lo

2019-08-04 11:06:47 (16864): Guest Log:        valid_lft forever preferred_lft forever

2019-08-04 11:06:47 (16864): Guest Log:     inet6 ::1/128 scope host 

2019-08-04 11:06:47 (16864): Guest Log:        valid_lft forever preferred_lft forever

2019-08-04 11:06:47 (16864): Guest Log: 2: dummy0: <BROADCAST,NOARP> mtu 1500 qdisc noop state DOWN group default 

2019-08-04 11:06:47 (16864): Guest Log:     link/ether 4e:d2:fc:0e:a3:cf brd ff:ff:ff:ff:ff:ff

2019-08-04 11:06:47 (16864): Guest Log: 3: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc pfifo_fast state UP group default qlen 1000

2019-08-04 11:06:47 (16864): Guest Log:     link/ether 08:00:27:70:49:1f brd ff:ff:ff:ff:ff:ff

2019-08-04 11:06:47 (16864): Guest Log:     inet 10.0.2.15/24 brd 10.0.2.255 scope global eth0

2019-08-04 11:06:47 (16864): Guest Log:        valid_lft forever preferred_lft forever

2019-08-04 11:06:47 (16864): Guest Log:     inet6 fe80::a00:27ff:fe70:491f/64 scope link 

2019-08-04 11:06:47 (16864): Guest Log:        valid_lft forever preferred_lft forever

2019-08-04 11:06:47 (16864): Guest Log: -------------------

2019-08-04 11:06:47 (16864): Guest Log: Linking /etc/docker to /var/lib/boot2docker for persistence

2019-08-04 11:06:47 (16864): Guest Log: Waiting for Docker daemon to start...

2019-08-04 11:06:47 (16864): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE

2019-08-04 11:06:47 (16864): Guest Log: Running boinc_app...

2019-08-04 11:06:47 (16864): Guest Log: Importing Docker image from BOINC...

2019-08-04 11:06:52 (16864): Guest Log: 00:00:10.019559 vminfo   Error: Unable to connect to system D-Bus (3/3): D-Bus not installed

2019-08-04 11:07:47 (16864): Guest Log: Prerun diagnostics...

2019-08-04 11:07:47 (16864): Guest Log: REPOSITORY                TAG                 IMAGE ID            CREATED             SIZE

2019-08-04 11:07:47 (16864): Guest Log: carlosred/autodock-vina   latest              f9dc0bf006e4        13 months ago       697 MB

2019-08-04 11:07:47 (16864): Guest Log: CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES

2019-08-04 11:07:47 (16864): Guest Log: 705.2M	/var/lib/docker

2019-08-04 11:07:47 (16864): Guest Log:               total        used        free      shared  buff/cache   available

2019-08-04 11:07:47 (16864): Guest Log: Mem:           3219          55        2245         869         917        2248

2019-08-04 11:07:47 (16864): Guest Log: Swap:           754           0         754

2019-08-04 11:07:47 (16864): Guest Log: Prerun commands...

2019-08-04 11:07:47 (16864): Guest Log: Running... 

2019-08-04 11:07:47 (16864): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 11:07:47 (16864): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 11:07:47 (16864): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 11:07:47 (16864): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 11:07:47 (16864): Guest Log: 100  211k  100  211k    0     0   475k      0 --:--:-- --:--:-- --:--:--  699k

2019-08-04 11:07:47 (16864): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 11:07:47 (16864): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 11:07:47 (16864): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 11:07:47 (16864): Guest Log: 102  3878  102  3878    0     0  17548      0 --:--:-- --:--:-- --:--:-- 52405

2019-08-04 11:07:47 (16864): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 11:07:47 (16864): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 11:07:47 (16864): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 11:07:47 (16864): Guest Log: 102  3983  102  3983    0     0  20498      0 --:--:-- --:--:-- --:--:-- 56900

2019-08-04 11:07:47 (16864): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 11:07:47 (16864): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 11:07:47 (16864): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 11:07:47 (16864): Guest Log:  54  171k   54 95427    0     0   259k      0 --:--:-- --:--:-- --:--:--  403k

2019-08-04 11:07:47 (16864): Guest Log: 100  171k  100  171k    0     0   413k      0 --:--:-- --:--:-- --:--:--  597k

2019-08-04 11:07:47 (16864): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 11:07:47 (16864): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 11:07:47 (16864): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 11:07:47 (16864): Guest Log: 102  3781  102  3781    0     0  16466      0 --:--:-- --:--:-- --:--:-- 53253

2019-08-04 11:07:47 (16864): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 11:07:47 (16864): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 11:07:47 (16864): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 11:07:47 (16864): Guest Log: 102  3781  102  3781    0     0  18752      0 --:--:-- --:--:-- --:--:-- 50413

2019-08-04 11:07:47 (16864): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-08-04 11:07:47 (16864): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-08-04 11:07:47 (16864): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-08-04 11:07:47 (16864): Guest Log: 157   157  157   157    0     0   1005      0 --:--:-- --:--:-- --:--:--  2121

2019-08-04 11:07:47 (16864): Guest Log: #################################################################

2019-08-04 11:07:47 (16864): Guest Log: # If you used AutoDock Vina in your work, please cite:          #

2019-08-04 11:07:47 (16864): Guest Log: #                                                               #

2019-08-04 11:07:47 (16864): Guest Log: # O. Trott, A. J. Olson,                                        #

2019-08-04 11:07:47 (16864): Guest Log: # AutoDock Vina: improving the speed and accuracy of docking    #

2019-08-04 11:07:47 (16864): Guest Log: # with a new scoring function, efficient optimization and       #

2019-08-04 11:07:47 (16864): Guest Log: # multithreading, Journal of Computational Chemistry 31 (2010)  #

2019-08-04 11:07:47 (16864): Guest Log: # 455-461                                                       #

2019-08-04 11:07:47 (16864): Guest Log: #                                                               #

2019-08-04 11:07:47 (16864): Guest Log: # DOI 10.1002/jcc.21334                                         #

2019-08-04 11:07:47 (16864): Guest Log: #                                                               #

2019-08-04 11:07:47 (16864): Guest Log: # Please see http://vina.scripps.edu for more information.      #

2019-08-04 11:07:47 (16864): Guest Log: #################################################################

2019-08-04 11:07:47 (16864): Guest Log: Reading input ... done.

2019-08-04 11:07:47 (16864): Guest Log: Setting up the scoring function ... done.

2019-08-04 11:07:47 (16864): Guest Log: Analyzing the binding site ... done.

2019-08-04 11:07:47 (16864): Guest Log: Using random seed: 868401956

2019-08-04 11:07:47 (16864): Guest Log: Performing search ... 

2019-08-04 11:07:47 (16864): Guest Log: 0%   10   20   30   40   50   60   70   80   90   100%

2019-08-04 11:07:47 (16864): Guest Log: |----|----|----|----|----|----|----|----|----|----|

2019-08-04 11:13:54 (16864): Guest Log: ***************************************************

2019-08-04 11:13:54 (16864): Guest Log: done.

2019-08-04 11:13:54 (16864): Guest Log: Refining results ... done.

2019-08-04 11:13:54 (16864): Guest Log: mode |   affinity | dist from best mode

2019-08-04 11:13:54 (16864): Guest Log:      | (kcal/mol) | rmsd l.b.| rmsd u.b.

2019-08-04 11:13:54 (16864): Guest Log: -----+------------+----------+----------

2019-08-04 11:13:54 (16864): Guest Log:    1        -12.4      0.000      0.000

2019-08-04 11:13:54 (16864): Guest Log:    2        -10.8      3.374     12.347

2019-08-04 11:13:54 (16864): Guest Log:    3        -10.6      2.498     12.537

2019-08-04 11:13:54 (16864): Guest Log:    4        -10.2      1.805     13.706

2019-08-04 11:13:54 (16864): Guest Log:    5        -10.1      3.402     12.251

2019-08-04 11:13:54 (16864): Guest Log:    6        -10.0      2.204     12.708

2019-08-04 11:13:54 (16864): Guest Log:    7         -9.4      2.422     14.060

2019-08-04 11:13:54 (16864): Guest Log: Writing output ... done.

2019-08-04 11:13:59 (16864): Guest Log: Postrun commands...

2019-08-04 11:13:59 (16864): Guest Log: boinc_app exited (0)

2019-08-04 11:13:59 (16864): Guest Log: Saving results...

2019-08-04 11:13:59 (16864): Guest Log: 1OPK.pdbqt

2019-08-04 11:13:59 (16864): Guest Log: ZINC00000567.pdbqt

2019-08-04 11:13:59 (16864): Guest Log: all.pdbqt

2019-08-04 11:13:59 (16864): Guest Log: ligand.pdbqt

2019-08-04 11:13:59 (16864): Guest Log: ligand_experiment.pdbqt

2019-08-04 11:13:59 (16864): Guest Log: protein.pdbqt

2019-08-04 11:13:59 (16864): VM Completion File Detected.
2019-08-04 11:13:59 (16864): Powering off VM.
2019-08-04 11:14:00 (16864): Successfully stopped VM.
2019-08-04 11:14:05 (16864): Deregistering VM. (boinc_c82a17b17502ee3b, slot#10)
2019-08-04 11:14:05 (16864): Removing virtual disk drive(s) from VM.
2019-08-04 11:14:05 (16864): Removing network bandwidth throttle group from VM.
2019-08-04 11:14:05 (16864): Removing storage controller(s) from VM.
2019-08-04 11:14:06 (16864): Removing VM from VirtualBox.
11:14:11 (16864): called boinc_finish(0)

</stderr_txt>
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