Task 236558

Name boinc2docker_23289_1560466937.531251_4
Workunit 102131
Created 21 Jun 2019, 1:50:30 UTC
Sent 21 Jun 2019, 1:54:27 UTC
Report deadline 28 Jun 2019, 1:54:27 UTC
Received 21 Jun 2019, 2:03:35 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 692
Run time 1 min 16 sec
CPU time
Validate state Valid
Credit 3.66
Device peak FLOPS 19.43 GFLOPS
Application version boinc2docker v1.07 (vbox64_mt)
x86_64-pc-linux-gnu
Peak working set size 99.02 MB
Peak swap size 109.79 MB
Peak disk usage 340.70 MB

Stderr output

<core_client_version>7.6.33</core_client_version>
<![CDATA[
<stderr_txt>
2019-06-21 04:02:07 (18204): vboxwrapper (7.9.26200): starting
2019-06-21 04:02:07 (18204): Feature: Checkpoint interval offset (489 seconds)
2019-06-21 04:02:07 (18204): Detected: VirtualBox COM Interface (Version: 5.2.18)
2019-06-21 04:02:07 (18204): Detected: Minimum checkpoint interval (600.000000 seconds)
2019-06-21 04:02:07 (18204): Create VM. (boinc_bf37dc5625868fa1, slot#5)
2019-06-21 04:02:07 (18204): Updating drive controller type and model for desired configuration.
2019-06-21 04:02:07 (18204): Setting Memory Size for VM. (3534MB)
2019-06-21 04:02:07 (18204): Setting CPU Count for VM. (4)
2019-06-21 04:02:07 (18204): Setting Chipset Options for VM.
2019-06-21 04:02:07 (18204): Setting Boot Options for VM.
2019-06-21 04:02:07 (18204): Enabling VM Network Access.
2019-06-21 04:02:07 (18204): Setting Network Configuration for NAT.
2019-06-21 04:02:07 (18204): Disabling USB Support for VM.
2019-06-21 04:02:07 (18204): Disabling COM Port Support for VM.
2019-06-21 04:02:07 (18204): Disabling LPT Port Support for VM.
2019-06-21 04:02:07 (18204): Disabling Audio Support for VM.
2019-06-21 04:02:07 (18204): Disabling Clipboard Support for VM.
2019-06-21 04:02:07 (18204): Disabling Drag and Drop Support for VM.
2019-06-21 04:02:07 (18204): Adding storage controller(s) to VM.
2019-06-21 04:02:07 (18204): Adding virtual ISO 9660 disk drive to VM. (vm_isocontext.iso)
2019-06-21 04:02:07 (18204): Adding VirtualBox Guest Additions to VM.
2019-06-21 04:02:07 (18204): Adding network bandwidth throttle group to VM. (Defaulting to 1024GB)
2019-06-21 04:02:07 (18204): Enabling shared directory for VM.
2019-06-21 04:02:07 (18204): Starting VM. (boinc_bf37dc5625868fa1, slot#5)
2019-06-21 04:02:15 (18204): Guest Log: BIOS: VirtualBox 5.2.18

2019-06-21 04:02:15 (18204): Guest Log: CPUID EDX: 0x178bfbff

2019-06-21 04:02:15 (18204): Guest Log: BIOS: Boot : bseqnr=1, bootseq=0032

2019-06-21 04:02:15 (18204): Guest Log: int13_harddisk: function 02, unmapped device for ELDL=80

2019-06-21 04:02:15 (18204): Guest Log: BIOS: Boot from Hard Disk 0 failed

2019-06-21 04:02:15 (18204): Guest Log: BIOS: Boot : bseqnr=2, bootseq=0003

2019-06-21 04:02:15 (18204): Guest Log: BIOS: Booting from CD-ROM...

2019-06-21 04:02:15 (18204): Guest Log: BIOS: KBD: unsupported int 16h function 03

2019-06-21 04:02:15 (18204): Guest Log: BIOS: AX=0305 BX=0000 CX=0000 DX=0000 

2019-06-21 04:02:15 (18204): Successfully started VM. (PID = '20060')
2019-06-21 04:02:15 (18204): Reporting VM Process ID to BOINC.
2019-06-21 04:02:20 (18204): VM state change detected. (old = 'poweroff', new = 'running')
2019-06-21 04:02:25 (18204): Guest Log: vgdrvHeartbeatInit: Setting up heartbeat to trigger every 2000 milliseconds

2019-06-21 04:02:25 (18204): Guest Log: vboxguest: misc device minor 56, IRQ 20, I/O port d020, MMIO at 00000000f0400000 (size 0x400000)

2019-06-21 04:02:25 (18204): Guest Log: net.ipv4.ip_forward = 1

2019-06-21 04:02:25 (18204): Guest Log: sysctl: cannot stat /proc/sys/net/ipv6/conf/all/forwarding: No such file or directory

2019-06-21 04:02:25 (18204): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-06-21 04:02:25 (18204): Guest Log: sysctl: "cannot stat %s" is an unknown key

2019-06-21 04:02:25 (18204): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-06-21 04:02:25 (18204): Guest Log: Segmentation fault

2019-06-21 04:02:25 (18204): Guest Log: automount ...

2019-06-21 04:02:25 (18204): Guest Log: Is the disk unpartitioned?, test for the 'boot2docker format-me' string

2019-06-21 04:02:25 (18204): Guest Log: automount over.

2019-06-21 04:02:25 (18204): Guest Log: Setting hostname to boot2docker Done.

2019-06-21 04:02:25 (18204): Guest Log: Fri Jun 21 04:02:21 UTC 2019 dhcp -------------------------------

2019-06-21 04:02:30 (18204): Guest Log: udevadm settle - timeout of 5 seconds reached, the event queue contains:

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1110)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00 (1347)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:00 (1348)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:01 (1349)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:02 (1350)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:03 (1351)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00 (1352)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00/input/input0 (1353)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00/input/input0/event0 (1354)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00 (1355)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00/input/input1 (1356)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00/input/input1/event1 (1357)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00 (1358)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00 (1359)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/ACPI0003:00 (1360)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/ACPI0003:00/power_supply/AC (1361)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00 (1362)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/device:01 (1363)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/input/input7 (1364)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/input/input7/event6 (1365)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0400:00 (1366)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0400:01 (1367)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:00 (1368)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:01 (1369)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:02 (1370)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:03 (1371)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0C02:00 (1372)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0C0A:00 (1373)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP8390:00 (1374)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00 (1375)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/APP0001:00 (1376)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0000:00 (1377)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0100:00 (1378)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0103:00 (1379)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0200:00 (1380)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0303:00 (1381)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1382)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0B00:00 (1383)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0F03:00 (1384)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:02 (1385)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:00 (1386)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:01 (1387)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:02 (1388)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:03 (1389)

2019-06-21 04:02:30 (18204): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:01 (1390)

2019-06-21 04:02:30 (18204): Guest Log: Fri Jun 21 04:02:27 UTC 2019 dhcp -------------------------------

2019-06-21 04:02:30 (18204): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.000094 main     Log opened 2019-06-21T04:02:27.475093000Z

2019-06-21 04:02:30 (18204): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.0000:00:00.002835 main     OS Product: Linux

2019-06-21 04:02:30 (18204): Guest Log: 094 m00:00:00.002906 main     OS Release: 4.1.19-boot2docker

2019-06-21 04:02:30 (18204): Guest Log: in 00:00:00.002942 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-06-21 04:02:30 (18204): Guest Log:    00:00:00.002976 main     Executable: /sbin/VBoxService

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.002978 main     Process ID: 934

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.002979 main     Package type: LINUX_64BITS_GENERICo

2019-06-21 04:02:30 (18204): Guest Log: g opened 2019-06-21T04:02:27.475093000Z

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.004004 main     5.0.16 r105871 started. Verbose level = 0

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.002835 main     OS Product: Linux

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.002906 main     OS Release: 4.1.19-boot2docker

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.002942 main     OS Version: #1 SMP Sun Apr 17 00:00:00.008049 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

2019-06-21 04:02:30 (18204): Guest Log: :40:00:00:00.008119 vminfo   Error: Unable to connect to system D-Bus (1/3): D-Bus not installed5

2019-06-21 04:02:30 (18204): Guest Log:  UTC 2016

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.002976 main     Executable: /sbin/VBoxService

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.002978 main     Process ID: 934

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.002979 main     Package type: LINUX_64BITS_GENERIC

2019-06-21 04:02:30 (18204): Guest Log: 00:00:00.004004 main     5.0.16 r105871 started. Verbose level = 0

2019-06-21 04:02:30 (18204): Guest Log: Mounting BOINC shared/...

2019-06-21 04:02:30 (18204): Guest Log: -------------------

2019-06-21 04:02:30 (18204): Guest Log: Fri Jun 21 02:02:29 UTC 2019

2019-06-21 04:02:30 (18204): Preference change detected
2019-06-21 04:02:30 (18204): Setting CPU throttle for VM. (100%)
2019-06-21 04:02:30 (18204): Setting checkpoint interval to 600 seconds. (Higher value of (Preference: 180 seconds) or (Vbox_job.xml: 600 seconds))
2019-06-21 04:02:35 (18204): Guest Log: 00:00:05.009474 vminfo   Error: Unable to connect to system D-Bus (2/3): D-Bus not installed

2019-06-21 04:02:35 (18204): Guest Log: Fri Jun 21 02:02:36 UTC 2019

2019-06-21 04:02:35 (18204): Guest Log: 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default 

2019-06-21 04:02:35 (18204): Guest Log:     link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00

2019-06-21 04:02:35 (18204): Guest Log:     inet 127.0.0.1/8 scope host lo

2019-06-21 04:02:35 (18204): Guest Log:        valid_lft forever preferred_lft forever

2019-06-21 04:02:35 (18204): Guest Log: 2: dummy0: <BROADCAST,NOARP> mtu 1500 qdisc noop state DOWN group default 

2019-06-21 04:02:35 (18204): Guest Log:     link/ether 3e:cd:b6:8e:68:f1 brd ff:ff:ff:ff:ff:ff

2019-06-21 04:02:35 (18204): Guest Log: 3: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc pfifo_fast state UP group default qlen 1000

2019-06-21 04:02:35 (18204): Guest Log:     link/ether 08:00:27:15:a7:40 brd ff:ff:ff:ff:ff:ff

2019-06-21 04:02:35 (18204): Guest Log:     inet 10.0.2.15/24 brd 10.0.2.255 scope global eth0

2019-06-21 04:02:35 (18204): Guest Log:        valid_lft forever preferred_lft forever

2019-06-21 04:02:35 (18204): Guest Log: -------------------

2019-06-21 04:02:35 (18204): Guest Log: Linking /etc/docker to /var/lib/boot2docker for persistence

2019-06-21 04:02:35 (18204): Guest Log: Waiting for Docker daemon to start...

2019-06-21 04:02:40 (18204): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE

2019-06-21 04:02:40 (18204): Guest Log: Running boinc_app...

2019-06-21 04:02:40 (18204): Guest Log: Importing Docker image from BOINC...

2019-06-21 04:02:40 (18204): Guest Log: 00:00:10.010475 vminfo   Error: Unable to connect to system D-Bus (3/3): D-Bus not installed

2019-06-21 04:03:05 (18204): Guest Log: Prerun diagnostics...

2019-06-21 04:03:05 (18204): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE

2019-06-21 04:03:05 (18204): Guest Log: carlosred/bowtie    built               4beacb78841d        12 months ago       758.7 MB

2019-06-21 04:03:05 (18204): Guest Log: CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES

2019-06-21 04:03:05 (18204): Guest Log: 753.8M	/var/lib/docker

2019-06-21 04:03:05 (18204): Guest Log:               total        used        free      shared  buff/cache   available

2019-06-21 04:03:05 (18204): Guest Log: Mem:           3461          53        2447         917         960        2447

2019-06-21 04:03:05 (18204): Guest Log: Swap:           813           0         813

2019-06-21 04:03:05 (18204): Guest Log: Prerun commands...

2019-06-21 04:03:05 (18204): Guest Log: Running... 

2019-06-21 04:03:05 (18204): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-06-21 04:03:05 (18204): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-06-21 04:03:05 (18204): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (7) Failed to connect to boinc.tacc.utexas.edu port 5060: Connection refused

2019-06-21 04:03:05 (18204): Guest Log: unzip:  cannot find or open s_cerevisiae.ebwt.zip, s_cerevisiae.ebwt.zip.zip or s_cerevisiae.ebwt.zip.ZIP.

2019-06-21 04:03:05 (18204): Guest Log: Could not locate a Bowtie index corresponding to basename "s_cerevisiae"

2019-06-21 04:03:05 (18204): Guest Log: Command: /usr/local/bin/bowtie-align-s --wrapper basic-0 -c s_cerevisiae ATTGTAGTTCGAGTAAGTAATGTGGGTTTG 

2019-06-21 04:03:10 (18204): Guest Log: Postrun commands...

2019-06-21 04:03:10 (18204): Guest Log: boinc_app exited (0)

2019-06-21 04:03:10 (18204): Guest Log: Saving results...

2019-06-21 04:03:10 (18204): Guest Log: res_bowtie.txt

2019-06-21 04:03:10 (18204): VM Completion File Detected.
2019-06-21 04:03:10 (18204): Powering off VM.
2019-06-21 04:03:11 (18204): Successfully stopped VM.
2019-06-21 04:03:16 (18204): Deregistering VM. (boinc_bf37dc5625868fa1, slot#5)
2019-06-21 04:03:16 (18204): Removing virtual disk drive(s) from VM.
2019-06-21 04:03:16 (18204): Removing network bandwidth throttle group from VM.
2019-06-21 04:03:16 (18204): Removing storage controller(s) from VM.
2019-06-21 04:03:16 (18204): Removing VM from VirtualBox.
04:03:21 (18204): called boinc_finish(0)

</stderr_txt>
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