Task 217052

Name boinc2docker_12224_1556847420.476743_0
Workunit 99445
Created 3 May 2019, 1:37:04 UTC
Sent 3 May 2019, 23:53:37 UTC
Report deadline 10 May 2019, 23:53:37 UTC
Received 5 May 2019, 20:46:26 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 967
Run time 3 min 29 sec
CPU time 1 min 52 sec
Validate state Valid
Credit 7.75
Device peak FLOPS 5.91 GFLOPS
Application version boinc2docker v1.07 (vbox64_mt)
x86_64-apple-darwin
Peak working set size 2,722.38 MB
Peak swap size 11,116.87 MB
Peak disk usage 340.72 MB

Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
2019-05-05 21:45:12 (50803): vboxwrapper (7.7.26199): starting
2019-05-05 21:45:13 (50803): Feature: Checkpoint interval offset (238 seconds)
2019-05-05 21:45:13 (50803): Detected: VirtualBox VboxManage Interface (Version: 5.2.16)
2019-05-05 21:45:13 (50803): Detected: Sandbox Configuration Enabled
2019-05-05 21:45:13 (50803): Detected: Minimum checkpoint interval (600.000000 seconds)
2019-05-05 21:45:13 (50803): Create VM. (boinc_3c0530aa48b9829b, slot#0)
2019-05-05 21:45:13 (50803): Updating drive controller type and model for desired configuration.
2019-05-05 21:45:13 (50803): Setting Memory Size for VM. (3534MB)
2019-05-05 21:45:13 (50803): Setting CPU Count for VM. (2)
2019-05-05 21:45:13 (50803): Setting Chipset Options for VM.
2019-05-05 21:45:13 (50803): Setting Boot Options for VM.
2019-05-05 21:45:13 (50803): Setting Network Configuration for NAT.
2019-05-05 21:45:13 (50803): Enabling VM Network Access.
2019-05-05 21:45:13 (50803): Disabling USB Support for VM.
2019-05-05 21:45:13 (50803): Disabling COM Port Support for VM.
2019-05-05 21:45:14 (50803): Disabling Audio Support for VM.
2019-05-05 21:45:14 (50803): Disabling Clipboard Support for VM.
2019-05-05 21:45:14 (50803): Disabling Drag and Drop Support for VM.
2019-05-05 21:45:14 (50803): Adding storage controller(s) to VM.
2019-05-05 21:45:14 (50803): Adding virtual ISO 9660 disk drive to VM. (vm_isocontext.iso)
2019-05-05 21:45:14 (50803): Adding VirtualBox Guest Additions to VM.
2019-05-05 21:45:14 (50803): Adding network bandwidth throttle group to VM. (Defaulting to 1024GB)
2019-05-05 21:45:14 (50803): Enabling shared directory for VM.
2019-05-05 21:45:14 (50803): Starting VM. (boinc_3c0530aa48b9829b, slot#0)
2019-05-05 21:45:16 (50803): Successfully started VM. (PID = '50856')
2019-05-05 21:45:16 (50803): Reporting VM Process ID to BOINC.
2019-05-05 21:45:16 (50803): Guest Log: BIOS: VirtualBox 5.2.16
2019-05-05 21:45:16 (50803): Guest Log: CPUID EDX: 0x178bfbff
2019-05-05 21:45:16 (50803): VM state change detected. (old = 'poweroff', new = 'running')
2019-05-05 21:45:16 (50803): Preference change detected
2019-05-05 21:45:16 (50803): Setting CPU throttle for VM. (60%)
2019-05-05 21:45:16 (50803): Setting checkpoint interval to 600 seconds. (Higher value of (Preference: 60 seconds) or (Vbox_job.xml: 600 seconds))
2019-05-05 21:45:18 (50803): Guest Log: BIOS: Boot : bseqnr=1, bootseq=0032
2019-05-05 21:45:18 (50803): Guest Log: int13_harddisk: function 02, unmapped device for ELDL=80
2019-05-05 21:45:18 (50803): Guest Log: BIOS: Boot from Hard Disk 0 failed
2019-05-05 21:45:18 (50803): Guest Log: BIOS: Boot : bseqnr=2, bootseq=0003
2019-05-05 21:45:18 (50803): Guest Log: BIOS: Booting from CD-ROM...
2019-05-05 21:45:21 (50803): Guest Log: BIOS: KBD: unsupported int 16h function 03
2019-05-05 21:45:21 (50803): Guest Log: BIOS: AX=0305 BX=0000 CX=0000 DX=0000 
2019-05-05 21:45:52 (50803): Guest Log: vgdrvHeartbeatInit: Setting up heartbeat to trigger every 2000 milliseconds
2019-05-05 21:45:52 (50803): Guest Log: vboxguest: misc device minor 56, IRQ 20, I/O port d020, MMIO at 00000000f0400000 (size 0x400000)
2019-05-05 21:45:53 (50803): Guest Log: net.ipv4.ip_forward = 1
2019-05-05 21:45:53 (50803): Guest Log: sysctl: cannot stat /proc/sys/net/ipv6/conf/all/forwarding: No such file or directory
2019-05-05 21:45:53 (50803): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory
2019-05-05 21:45:53 (50803): Guest Log: sysctl: "cannot stat %s" is an unknown key
2019-05-05 21:45:53 (50803): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory
2019-05-05 21:45:53 (50803): Guest Log: Segmentation fault
2019-05-05 21:45:55 (50803): Guest Log: automount ...
2019-05-05 21:45:56 (50803): Guest Log: Is the disk unpartitioned?, test for the 'boot2docker format-me' string
2019-05-05 21:45:57 (50803): Guest Log: automount over.
2019-05-05 21:45:59 (50803): Guest Log: Setting hostname to boot2docker Done.
2019-05-05 21:45:59 (50803): Guest Log: Sun May  5 21:45:56 UTC 2019 dhcp -------------------------------
2019-05-05 21:46:08 (50803): Guest Log: udevadm settle - timeout of 5 seconds reached, the event queue contains:
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/ACPI0003:00/power_supply/AC (1335)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/device:01 (1337)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/input/input6 (1338)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/input/input6/event5 (1339)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:00 (1342)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/APP0001:00 (1350)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0000:00 (1351)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0100:00 (1352)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0103:00 (1353)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0200:00 (1354)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0303:00 (1355)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1356)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0B00:00 (1357)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0F03:00 (1358)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:00 (1360)
2019-05-05 21:46:08 (50803): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:03 (1363)
2019-05-05 21:46:10 (50803): Guest Log: Sun May  5 21:46:03 UTC 2019 dhcp -------------------------------
2019-05-05 21:46:12 (50803): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.000653 main     Log opened 2019-05-05T21:46:04.844164000Z
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.000892 main     OS Product: Linux
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.000990 main     OS Release: 4.1.19-boot2docker
2019-05-05 21:46:12 (50803): Guest Log: VBo00:00:00.001106 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016
2019-05-05 21:46:12 (50803): Guest Log: Se00:00:00.001201 main     Executable: /sbin/VBoxService
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.001203 main     Process ID: 821
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.001204 main     Package type: LINUX_64BITS_GENERIC
2019-05-05 21:46:12 (50803): Guest Log: ice 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:300:00:00.003747 main     5.0.16 r105871 started. Verbose level = 0
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.000653 main     Log opened 2019-05-05T21:46:04.844164000Z
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.000892 main     OS Product: Linux
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.000990 main     OS Release: 4.1.19-boot2docker
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.001106 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.001201 main     Executable: /sbin/VBoxService
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.001203 main     Process ID: 821
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.001204 main     Package type: LINUX_64BITS_GENERIC
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.003747 main     5.0.16 r105871 started. Verbose level = 0
2019-05-05 21:46:12 (50803): Guest Log: 00:00:00.193812 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
2019-05-05 21:46:13 (50803): Guest Log: Mounting BOINC shared/...
2019-05-05 21:46:13 (50803): Guest Log: -------------------
2019-05-05 21:46:13 (50803): Guest Log: Sun May  5 19:46:12 UTC 2019
2019-05-05 21:46:21 (50803): Guest Log: 00:00:05.207636 vminfo   Error: Unable to connect to system D-Bus (2/3): D-Bus not installed
2019-05-05 21:46:24 (50803): Guest Log: Sun May  5 19:46:18 UTC 2019
2019-05-05 21:46:24 (50803): Guest Log: 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default 
2019-05-05 21:46:24 (50803): Guest Log:     link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
2019-05-05 21:46:24 (50803): Guest Log:     inet 127.0.0.1/8 scope host lo
2019-05-05 21:46:24 (50803): Guest Log:        valid_lft forever preferred_lft forever
2019-05-05 21:46:24 (50803): Guest Log:     inet6 ::1/128 scope host 
2019-05-05 21:46:24 (50803): Guest Log:        valid_lft forever preferred_lft forever
2019-05-05 21:46:24 (50803): Guest Log: 2: dummy0: <BROADCAST,NOARP> mtu 1500 qdisc noop state DOWN group default 
2019-05-05 21:46:24 (50803): Guest Log:     link/ether 86:f2:b2:8e:48:c4 brd ff:ff:ff:ff:ff:ff
2019-05-05 21:46:24 (50803): Guest Log: 3: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc pfifo_fast state UP group default qlen 1000
2019-05-05 21:46:24 (50803): Guest Log:     link/ether 08:00:27:31:83:8c brd ff:ff:ff:ff:ff:ff
2019-05-05 21:46:24 (50803): Guest Log:     inet 10.0.2.15/24 brd 10.0.2.255 scope global eth0
2019-05-05 21:46:24 (50803): Guest Log:        valid_lft forever preferred_lft forever
2019-05-05 21:46:24 (50803): Guest Log:     inet6 fe80::a00:27ff:fe31:838c/64 scope link 
2019-05-05 21:46:24 (50803): Guest Log:        valid_lft forever preferred_lft forever
2019-05-05 21:46:24 (50803): Guest Log: -------------------
2019-05-05 21:46:24 (50803): Guest Log: Linking /etc/docker to /var/lib/boot2docker for persistence
2019-05-05 21:46:24 (50803): Guest Log: Waiting for Docker daemon to start...
2019-05-05 21:46:28 (50803): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
2019-05-05 21:46:28 (50803): Guest Log: Running boinc_app...
2019-05-05 21:46:28 (50803): Guest Log: Importing Docker image from BOINC...
2019-05-05 21:46:28 (50803): Guest Log: 00:00:10.210845 vminfo   Error: Unable to connect to system D-Bus (3/3): D-Bus not installed
2019-05-05 21:47:50 (50803): Guest Log: Prerun diagnostics...
2019-05-05 21:47:50 (50803): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
2019-05-05 21:47:50 (50803): Guest Log: carlosred/bowtie    built               4beacb78841d        10 months ago       758.7 MB
2019-05-05 21:47:50 (50803): Guest Log: CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES
2019-05-05 21:47:51 (50803): Guest Log: 753.8M	/var/lib/docker
2019-05-05 21:47:51 (50803): Guest Log:               total        used        free      shared  buff/cache   available
2019-05-05 21:47:51 (50803): Guest Log: Mem:           3461          55        2448         917         957        2448
2019-05-05 21:47:51 (50803): Guest Log: Swap:           815           0         815
2019-05-05 21:47:51 (50803): Guest Log: Prerun commands...
2019-05-05 21:47:51 (50803): Guest Log: Running... 
2019-05-05 21:47:52 (50803): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
2019-05-05 21:47:52 (50803): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed
2019-05-05 21:48:31 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
2019-05-05 21:48:31 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
2019-05-05 21:48:31 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
2019-05-05 21:48:31 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
2019-05-05 21:48:31 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
2019-05-05 21:48:31 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:04 --:--:--     0
2019-05-05 21:48:31 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:05 --:--:--     0
2019-05-05 21:48:31 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:06 --:--:--     0
2019-05-05 21:48:31 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:07 --:--:--     0
2019-05-05 21:48:31 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:08 --:--:--     0
2019-05-05 21:48:31 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:10 --:--:--     0
2019-05-05 21:48:32 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:11 --:--:--     0
2019-05-05 21:48:32 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:12 --:--:--     0
2019-05-05 21:48:32 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:13 --:--:--     0
2019-05-05 21:48:32 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:14 --:--:--     0
2019-05-05 21:48:32 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:15 --:--:--     0
2019-05-05 21:48:32 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:16 --:--:--     0
2019-05-05 21:48:32 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:17 --:--:--     0
2019-05-05 21:48:32 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:18 --:--:--     0
2019-05-05 21:48:32 (50803): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:19 --:--:--     0curl: (6) Could not resolve host: boinc.tacc.utexas.edu
2019-05-05 21:48:32 (50803): Guest Log: unzip:  cannot find or open s_cerevisiae.ebwt.zip, s_cerevisiae.ebwt.zip.zip or s_cerevisiae.ebwt.zip.ZIP.
2019-05-05 21:48:32 (50803): Guest Log: Could not locate a Bowtie index corresponding to basename "s_cerevisiae"
2019-05-05 21:48:32 (50803): Guest Log: Command: /usr/local/bin/bowtie-align-s --wrapper basic-0 -c s_cerevisiae ATTGTAGTTCGAGTAAGTAATGTGGGTTTG 
2019-05-05 21:48:33 (50803): Guest Log: Postrun commands...
2019-05-05 21:48:33 (50803): Guest Log: boinc_app exited (0)
2019-05-05 21:48:33 (50803): Guest Log: Saving results...
2019-05-05 21:48:33 (50803): Guest Log: res_bowtie.txt
2019-05-05 21:48:33 (50803): VM Completion File Detected.
2019-05-05 21:48:33 (50803): Powering off VM.
2019-05-05 21:48:34 (50803): Successfully stopped VM.
2019-05-05 21:48:34 (50803): Deregistering VM. (boinc_3c0530aa48b9829b, slot#0)
2019-05-05 21:48:34 (50803): Removing network bandwidth throttle group from VM.
2019-05-05 21:48:34 (50803): Removing storage controller(s) from VM.
2019-05-05 21:48:34 (50803): Removing VM from VirtualBox.
2019-05-05 21:48:34 (50803): Removing virtual ISO 9660 disk from VirtualBox.
21:48:39 (50803): called boinc_finish(0)

</stderr_txt>
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