Task 126996

Name boinc2docker_13332_1555625345.954908_2
Workunit 53887
Created 25 Apr 2019, 22:13:57 UTC
Sent 25 Apr 2019, 22:15:21 UTC
Report deadline 2 May 2019, 22:15:21 UTC
Received 25 Apr 2019, 22:28:56 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 282
Run time 4 min 7 sec
CPU time 8 min 50 sec
Validate state Valid
Credit 8.79
Device peak FLOPS 13.41 GFLOPS
Application version boinc2docker v1.07 (vbox64_mt)
x86_64-pc-linux-gnu
Peak working set size 118.82 MB
Peak swap size 4,558.13 MB
Peak disk usage 237.93 MB

Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
2019-04-25 17:23:30 (19708): vboxwrapper (7.7.26197): starting
2019-04-25 17:23:30 (19708): Feature: Checkpoint interval offset (558 seconds)
2019-04-25 17:23:30 (19708): Detected: VirtualBox VboxManage Interface (Version: 6.0.4)
2019-04-25 17:23:30 (19708): Detected: Minimum checkpoint interval (600.000000 seconds)
2019-04-25 17:23:31 (19708): Create VM. (boinc_82babd2cc244e5c4, slot#14)
2019-04-25 17:23:31 (19708): Updating drive controller type and model for desired configuration.
2019-04-25 17:23:31 (19708): Setting Memory Size for VM. (3288MB)
2019-04-25 17:23:31 (19708): Setting CPU Count for VM. (4)
2019-04-25 17:23:31 (19708): Setting Chipset Options for VM.
2019-04-25 17:23:31 (19708): Setting Boot Options for VM.
2019-04-25 17:23:31 (19708): Setting Network Configuration for NAT.
2019-04-25 17:23:32 (19708): Enabling VM Network Access.
2019-04-25 17:23:32 (19708): Disabling USB Support for VM.
2019-04-25 17:23:32 (19708): Disabling COM Port Support for VM.
2019-04-25 17:23:32 (19708): Disabling LPT Port Support for VM.
2019-04-25 17:23:32 (19708): Disabling Audio Support for VM.
2019-04-25 17:23:32 (19708): Disabling Clipboard Support for VM.
2019-04-25 17:23:32 (19708): Disabling Drag and Drop Support for VM.
2019-04-25 17:23:32 (19708): Adding storage controller(s) to VM.
2019-04-25 17:23:33 (19708): Adding virtual ISO 9660 disk drive to VM. (vm_isocontext.iso)
2019-04-25 17:23:33 (19708): Adding VirtualBox Guest Additions to VM.
2019-04-25 17:23:33 (19708): Adding network bandwidth throttle group to VM. (Defaulting to 1024GB)
2019-04-25 17:23:33 (19708): Enabling shared directory for VM.
2019-04-25 17:23:34 (19708): Starting VM. (boinc_82babd2cc244e5c4, slot#14)
2019-04-25 17:23:35 (19708): Successfully started VM. (PID = '20119')
2019-04-25 17:23:35 (19708): Reporting VM Process ID to BOINC.
2019-04-25 17:23:36 (19708): Guest Log: BIOS: VirtualBox 6.0.4
2019-04-25 17:23:36 (19708): Guest Log: CPUID EDX: 0x178bfbff
2019-04-25 17:23:36 (19708): VM state change detected. (old = 'poweroff', new = 'running')
2019-04-25 17:23:36 (19708): Preference change detected
2019-04-25 17:23:36 (19708): Setting CPU throttle for VM. (100%)
2019-04-25 17:23:36 (19708): Setting checkpoint interval to 1800 seconds. (Higher value of (Preference: 1800 seconds) or (Vbox_job.xml: 600 seconds))
2019-04-25 17:23:39 (19708): Guest Log: BIOS: Boot : bseqnr=1, bootseq=0032
2019-04-25 17:23:39 (19708): Guest Log: int13_harddisk: function 02, unmapped device for ELDL=80
2019-04-25 17:23:39 (19708): Guest Log: BIOS: Boot from Hard Disk 0 failed
2019-04-25 17:23:39 (19708): Guest Log: BIOS: Boot : bseqnr=2, bootseq=0003
2019-04-25 17:23:39 (19708): Guest Log: BIOS: Booting from CD-ROM...
2019-04-25 17:23:46 (19708): Guest Log: BIOS: KBD: unsupported int 16h function 03
2019-04-25 17:23:46 (19708): Guest Log: BIOS: AX=0305 BX=0000 CX=0000 DX=0000 
2019-04-25 17:23:59 (19708): Guest Log: vgdrvHeartbeatInit: Setting up heartbeat to trigger every 2000 milliseconds
2019-04-25 17:23:59 (19708): Guest Log: vboxguest: misc device minor 56, IRQ 20, I/O port d020, MMIO at 00000000f0400000 (size 0x400000)
2019-04-25 17:24:00 (19708): Guest Log: net.ipv4.ip_forward = 1
2019-04-25 17:24:00 (19708): Guest Log: sysctl: cannot stat /proc/sys/net/ipv6/conf/all/forwarding: No such file or directory
2019-04-25 17:24:00 (19708): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory
2019-04-25 17:24:00 (19708): Guest Log: sysctl: "cannot stat %s" is an unknown key
2019-04-25 17:24:00 (19708): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory
2019-04-25 17:24:00 (19708): Guest Log: Segmentation fault
2019-04-25 17:24:01 (19708): Guest Log: automount ...
2019-04-25 17:24:01 (19708): Guest Log: Is the disk unpartitioned?, test for the 'boot2docker format-me' string
2019-04-25 17:24:01 (19708): Guest Log: automount over.
2019-04-25 17:24:01 (19708): Guest Log: Setting hostname to boot2docker Done.
2019-04-25 17:24:01 (19708): Guest Log: Thu Apr 25 17:23:59 UTC 2019 dhcp -------------------------------
2019-04-25 17:24:06 (19708): Guest Log: udevadm settle - timeout of 5 seconds reached, the event queue contains:
2019-04-25 17:24:06 (19708): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1388)
2019-04-25 17:24:08 (19708): Guest Log: Thu Apr 25 17:24:05 UTC 2019 dhcp -------------------------------
2019-04-25 17:24:08 (19708): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.000137 main     Log opened 2019-04-25T17:24:05.789717000Z
2019-04-25 17:24:08 (19708): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.000137 main     Log opened 2019-04-25T17:24:05.789717000Z
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.004265 main     OS Product: Linux
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.004265 main     OS Product: Linux
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.005508 main     OS Release: 4.1.19-boot2docker
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.005508 main     OS Release: 4.1.19-boot2docker
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.007099 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.007099 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.008763 main     Executable: /sbin/VBoxService
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.008765 main     Process ID: 934
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.008767 main     Package type: LINUX_64BITS_GENERIC
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.008763 main     Executable: /sbin/VBoxService
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.008765 main     Process ID: 934
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.008767 main     Package type: LINUX_64BITS_GENERIC
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.014919 main     5.0.16 r105871 started. Verbose level = 0
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.014919 main     5.0.16 r105871 started. Verbose level = 0
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.051787 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
2019-04-25 17:24:08 (19708): Guest Log: 00:00:00.051890 vminfo   Error: Unable to connect to system D-Bus (1/3): D-Bus not installed
2019-04-25 17:24:08 (19708): Guest Log: Mounting BOINC shared/...
2019-04-25 17:24:08 (19708): Guest Log: -------------------
2019-04-25 17:24:08 (19708): Guest Log: Thu Apr 25 22:24:08 UTC 2019
2019-04-25 17:24:14 (19708): Guest Log: 00:00:05.054555 vminfo   Error: Unable to connect to system D-Bus (2/3): D-Bus not installed
2019-04-25 17:24:14 (19708): Guest Log: Thu Apr 25 22:24:13 UTC 2019
2019-04-25 17:24:14 (19708): Guest Log: 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default 
2019-04-25 17:24:14 (19708): Guest Log:     link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
2019-04-25 17:24:14 (19708): Guest Log:     inet 127.0.0.1/8 scope host lo
2019-04-25 17:24:14 (19708): Guest Log:        valid_lft forever preferred_lft forever
2019-04-25 17:24:14 (19708): Guest Log: 2: dummy0: <BROADCAST,NOARP> mtu 1500 qdisc noop state DOWN group default 
2019-04-25 17:24:14 (19708): Guest Log:     link/ether d6:64:b2:af:65:16 brd ff:ff:ff:ff:ff:ff
2019-04-25 17:24:14 (19708): Guest Log: 3: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc pfifo_fast state UP group default qlen 1000
2019-04-25 17:24:14 (19708): Guest Log:     link/ether 08:00:27:1a:aa:c7 brd ff:ff:ff:ff:ff:ff
2019-04-25 17:24:14 (19708): Guest Log:     inet 10.0.2.15/24 brd 10.0.2.255 scope global eth0
2019-04-25 17:24:14 (19708): Guest Log:        valid_lft forever preferred_lft forever
2019-04-25 17:24:14 (19708): Guest Log: -------------------
2019-04-25 17:24:14 (19708): Guest Log: Linking /etc/docker to /var/lib/boot2docker for persistence
2019-04-25 17:24:14 (19708): Guest Log: Waiting for Docker daemon to start...
2019-04-25 17:24:17 (19708): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
2019-04-25 17:24:17 (19708): Guest Log: Running boinc_app...
2019-04-25 17:24:17 (19708): Guest Log: Importing Docker image from BOINC...
2019-04-25 17:24:19 (19708): Guest Log: 00:00:10.056098 vminfo   Error: Unable to connect to system D-Bus (3/3): D-Bus not installed
2019-04-25 17:24:58 (19708): Guest Log: Prerun diagnostics...
2019-04-25 17:24:58 (19708): Guest Log: REPOSITORY                TAG                 IMAGE ID            CREATED             SIZE
2019-04-25 17:24:58 (19708): Guest Log: carlosred/autodock-vina   latest              f9dc0bf006e4        10 months ago       697 MB
2019-04-25 17:24:58 (19708): Guest Log: CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES
2019-04-25 17:24:58 (19708): Guest Log: 705.2M	/var/lib/docker
2019-04-25 17:24:58 (19708): Guest Log:               total        used        free      shared  buff/cache   available
2019-04-25 17:24:58 (19708): Guest Log: Mem:           3219          54        2246         869         917        2249
2019-04-25 17:24:58 (19708): Guest Log: Swap:           755           0         755
2019-04-25 17:24:58 (19708): Guest Log: Prerun commands...
2019-04-25 17:24:58 (19708): Guest Log: Running... 
2019-04-25 17:25:04 (19708): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
2019-04-25 17:25:04 (19708): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed
2019-04-25 17:25:06 (19708): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:05 --:--:--     0
2019-04-25 17:25:06 (19708): Guest Log:  24  211k   24 51987    0     0   8040      0  0:00:26  0:00:06  0:00:20 52143
2019-04-25 17:25:06 (19708): Guest Log: 100  211k  100  211k    0     0  30675      0  0:00:07  0:00:07 --:--:--  133k
2019-04-25 17:25:09 (19708): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
2019-04-25 17:25:09 (19708): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed
2019-04-25 17:25:09 (19708): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
2019-04-25 17:25:09 (19708): Guest Log: 102  3878  102  3878    0     0   1225      0  0:00:03  0:00:03 --:--:-- 16091
2019-04-25 17:25:12 (19708): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
2019-04-25 17:25:12 (19708): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed
2019-04-25 17:25:12 (19708): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
2019-04-25 17:25:12 (19708): Guest Log: 102  3983  102  3983    0     0   1448      0  0:00:02  0:00:02 --:--:-- 15932
2019-04-25 17:25:14 (19708): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
2019-04-25 17:25:14 (19708): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed
2019-04-25 17:25:16 (19708): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
2019-04-25 17:25:16 (19708): Guest Log:  21  171k   21 37507    0     0  10930      0  0:00:16  0:00:03  0:00:13 42142
2019-04-25 17:25:16 (19708): Guest Log: 100  171k  100  171k    0     0  41117      0  0:00:04  0:00:04 --:--:--   98k
2019-04-25 17:25:19 (19708): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
2019-04-25 17:25:19 (19708): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed
2019-04-25 17:25:19 (19708): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
2019-04-25 17:25:19 (19708): Guest Log: 102  3781  102  3781    0     0   1248      0  0:00:03  0:00:03 --:--:-- 14161
2019-04-25 17:25:22 (19708): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
2019-04-25 17:25:22 (19708): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed
2019-04-25 17:25:22 (19708): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
2019-04-25 17:25:25 (19708): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
2019-04-25 17:25:25 (19708): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed
2019-04-25 17:25:25 (19708): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
2019-04-25 17:25:25 (19708): Guest Log: 148   148  148   148    0     0     48      0  0:00:03  0:00:03 --:--:--   552
2019-04-25 17:25:25 (19708): Guest Log: #################################################################
2019-04-25 17:25:25 (19708): Guest Log: # If you used AutoDock Vina in your work, please cite:          #
2019-04-25 17:25:25 (19708): Guest Log: #                                                               #
2019-04-25 17:25:25 (19708): Guest Log: # O. Trott, A. J. Olson,                                        #
2019-04-25 17:25:25 (19708): Guest Log: # AutoDock Vina: improving the speed and accuracy of docking    #
2019-04-25 17:25:25 (19708): Guest Log: # with a new scoring function, efficient optimization and       #
2019-04-25 17:25:25 (19708): Guest Log: # multithreading, Journal of Computational Chemistry 31 (2010)  #
2019-04-25 17:25:25 (19708): Guest Log: # 455-461                                                       #
2019-04-25 17:25:25 (19708): Guest Log: #                                                               #
2019-04-25 17:25:25 (19708): Guest Log: # DOI 10.1002/jcc.21334                                         #
2019-04-25 17:25:25 (19708): Guest Log: #                                                               #
2019-04-25 17:25:25 (19708): Guest Log: # Please see http://vina.scripps.edu for more information.      #
2019-04-25 17:25:25 (19708): Guest Log: #################################################################
2019-04-25 17:25:25 (19708): Guest Log: Detected 4 CPUs
2019-04-25 17:25:25 (19708): Guest Log: Reading input ... done.
2019-04-25 17:25:25 (19708): Guest Log: Setting up the scoring function ... done.
2019-04-25 17:25:33 (19708): Guest Log: Analyzing the binding site ... done.
2019-04-25 17:25:33 (19708): Guest Log: Using random seed: -2113937631
2019-04-25 17:25:33 (19708): Guest Log: Performing search ... 
2019-04-25 17:25:33 (19708): Guest Log: 0%   10   20   30   40   50   60   70   80   90   100%
2019-04-25 17:25:33 (19708): Guest Log: |----|----|----|----|----|----|----|----|----|----|
2019-04-25 17:27:27 (19708): Guest Log: ***************************************************
2019-04-25 17:27:27 (19708): Guest Log: done.
2019-04-25 17:27:28 (19708): Guest Log: Refining results ... done.
2019-04-25 17:27:28 (19708): Guest Log: mode |   affinity | dist from best mode
2019-04-25 17:27:28 (19708): Guest Log:      | (kcal/mol) | rmsd l.b.| rmsd u.b.
2019-04-25 17:27:28 (19708): Guest Log: -----+------------+----------+----------
2019-04-25 17:27:28 (19708): Guest Log:    1        -10.6      0.000      0.000
2019-04-25 17:27:28 (19708): Guest Log:    2        -10.3      2.212      3.403
2019-04-25 17:27:28 (19708): Guest Log:    3        -10.2      2.196      3.376
2019-04-25 17:27:28 (19708): Guest Log:    4        -10.0      1.560      2.382
2019-04-25 17:27:28 (19708): Guest Log:    5         -9.4      2.095      3.811
2019-04-25 17:27:28 (19708): Guest Log:    6         -9.0      2.017      2.654
2019-04-25 17:27:28 (19708): Guest Log:    7         -8.2      5.740     10.321
2019-04-25 17:27:28 (19708): Guest Log:    9         -7.7      5.839     10.048
2019-04-25 17:27:28 (19708): Guest Log: Writing output ... done.
2019-04-25 17:27:30 (19708): Guest Log: Postrun commands...
2019-04-25 17:27:30 (19708): Guest Log: boinc_app exited (0)
2019-04-25 17:27:30 (19708): Guest Log: Saving results...
2019-04-25 17:27:30 (19708): Guest Log: 1OPK.pdbqt
2019-04-25 17:27:30 (19708): Guest Log: ZINC00000567.pdbqt
2019-04-25 17:27:30 (19708): Guest Log: all.pdbqt
2019-04-25 17:27:30 (19708): Guest Log: ligand.pdbqt
2019-04-25 17:27:30 (19708): Guest Log: ligand_experiment.pdbqt
2019-04-25 17:27:30 (19708): Guest Log: protein.pdbqt
2019-04-25 17:27:30 (19708): VM Completion File Detected.
2019-04-25 17:27:30 (19708): Powering off VM.
2019-04-25 17:27:31 (19708): Successfully stopped VM.
2019-04-25 17:27:31 (19708): Deregistering VM. (boinc_82babd2cc244e5c4, slot#14)
2019-04-25 17:27:31 (19708): Removing network bandwidth throttle group from VM.
2019-04-25 17:27:31 (19708): Removing storage controller(s) from VM.
2019-04-25 17:27:31 (19708): Removing VM from VirtualBox.
2019-04-25 17:27:31 (19708): Removing virtual ISO 9660 disk from VirtualBox.
17:27:36 (19708): called boinc_finish(0)

</stderr_txt>
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