Task 225871

Name boinc2docker_9493_1556847387.532406_3
Workunit 99369
Created 10 May 2019, 23:40:32 UTC
Sent 10 May 2019, 23:52:43 UTC
Report deadline 17 May 2019, 23:52:43 UTC
Received 11 May 2019, 0:35:05 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 286
Run time 2 min 6 sec
CPU time 1 min 20 sec
Validate state Valid
Credit 12.25
Device peak FLOPS 14.75 GFLOPS
Application version boinc2docker v1.07 (vbox64_mt)
x86_64-apple-darwin
Peak working set size 124.39 MB
Peak swap size 4,703.83 MB
Peak disk usage 340.70 MB

Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
2019-05-10 19:03:41 (16099): vboxwrapper (7.7.26197): starting
2019-05-10 19:03:43 (16099): Feature: Checkpoint interval offset (21 seconds)
2019-05-10 19:03:43 (16099): Detected: VirtualBox VboxManage Interface (Version: 6.0.6)
2019-05-10 19:03:43 (16099): Detected: Minimum checkpoint interval (600.000000 seconds)
2019-05-10 19:03:43 (16099): Create VM. (boinc_c6321bd55a110ac7, slot#18)
2019-05-10 19:03:43 (16099): Updating drive controller type and model for desired configuration.
2019-05-10 19:03:43 (16099): Setting Memory Size for VM. (3534MB)
2019-05-10 19:03:43 (16099): Setting CPU Count for VM. (4)
2019-05-10 19:03:44 (16099): Setting Chipset Options for VM.
2019-05-10 19:03:44 (16099): Setting Boot Options for VM.
2019-05-10 19:03:44 (16099): Setting Network Configuration for NAT.
2019-05-10 19:03:44 (16099): Enabling VM Network Access.
2019-05-10 19:03:44 (16099): Disabling USB Support for VM.
2019-05-10 19:03:44 (16099): Disabling COM Port Support for VM.
2019-05-10 19:03:44 (16099): Disabling LPT Port Support for VM.
2019-05-10 19:03:44 (16099): Disabling Audio Support for VM.
2019-05-10 19:03:44 (16099): Disabling Clipboard Support for VM.
2019-05-10 19:03:44 (16099): Disabling Drag and Drop Support for VM.
2019-05-10 19:03:45 (16099): Adding storage controller(s) to VM.
2019-05-10 19:03:45 (16099): Adding virtual ISO 9660 disk drive to VM. (vm_isocontext.iso)
2019-05-10 19:03:45 (16099): Adding VirtualBox Guest Additions to VM.
2019-05-10 19:03:45 (16099): Adding network bandwidth throttle group to VM. (Defaulting to 1024GB)
2019-05-10 19:03:45 (16099): Enabling shared directory for VM.
2019-05-10 19:03:45 (16099): Starting VM. (boinc_c6321bd55a110ac7, slot#18)
2019-05-10 19:03:47 (16099): Successfully started VM. (PID = '16512')
2019-05-10 19:03:47 (16099): Reporting VM Process ID to BOINC.
2019-05-10 19:03:47 (16099): Guest Log: BIOS: VirtualBox 6.0.6
2019-05-10 19:03:47 (16099): Guest Log: CPUID EDX: 0x178bfbff
2019-05-10 19:03:47 (16099): VM state change detected. (old = 'poweroff', new = 'running')
2019-05-10 19:03:47 (16099): Preference change detected
2019-05-10 19:03:47 (16099): Setting CPU throttle for VM. (100%)
2019-05-10 19:03:47 (16099): Setting checkpoint interval to 1800 seconds. (Higher value of (Preference: 1800 seconds) or (Vbox_job.xml: 600 seconds))
2019-05-10 19:03:52 (16099): Guest Log: BIOS: Boot : bseqnr=1, bootseq=0032
2019-05-10 19:03:52 (16099): Guest Log: int13_harddisk: function 02, unmapped device for ELDL=80
2019-05-10 19:03:52 (16099): Guest Log: BIOS: Boot from Hard Disk 0 failed
2019-05-10 19:03:52 (16099): Guest Log: BIOS: Boot : bseqnr=2, bootseq=0003
2019-05-10 19:03:52 (16099): Guest Log: BIOS: Booting from CD-ROM...
2019-05-10 19:03:58 (16099): Guest Log: BIOS: KBD: unsupported int 16h function 03
2019-05-10 19:03:58 (16099): Guest Log: BIOS: AX=0305 BX=0000 CX=0000 DX=0000 
2019-05-10 19:04:12 (16099): Guest Log: vgdrvHeartbeatInit: Setting up heartbeat to trigger every 2000 milliseconds
2019-05-10 19:04:12 (16099): Guest Log: vboxguest: misc device minor 56, IRQ 20, I/O port d020, MMIO at 00000000f0400000 (size 0x400000)
2019-05-10 19:04:13 (16099): Guest Log: net.ipv4.ip_forward = 1
2019-05-10 19:04:13 (16099): Guest Log: sysctl: cannot stat /proc/sys/net/ipv6/conf/all/forwarding: No such file or directory
2019-05-10 19:04:13 (16099): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory
2019-05-10 19:04:13 (16099): Guest Log: sysctl: "cannot stat %s" is an unknown key
2019-05-10 19:04:13 (16099): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory
2019-05-10 19:04:13 (16099): Guest Log: Segmentation fault
2019-05-10 19:04:13 (16099): Guest Log: automount ...
2019-05-10 19:04:15 (16099): Guest Log: Is the disk unpartitioned?, test for the 'boot2docker format-me' string
2019-05-10 19:04:16 (16099): Guest Log: automount over.
2019-05-10 19:04:16 (16099): Guest Log: Setting hostname to boot2docker Done.
2019-05-10 19:04:16 (16099): Guest Log: Fri May 10 19:04:13 UTC 2019 dhcp -------------------------------
2019-05-10 19:04:21 (16099): Guest Log: udevadm settle - timeout of 5 seconds reached, the event queue contains:
2019-05-10 19:04:21 (16099): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1386)
2019-05-10 19:04:22 (16099): Guest Log: Fri May 10 19:04:19 UTC 2019 dhcp -------------------------------
2019-05-10 19:04:22 (16099): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.000124 main     Log opened 2019-05-10T19:04:20.140762000Z
2019-05-10 19:04:22 (16099): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.000124 main     Log opened 2019-05-10T19:04:20.140762000Z
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.003579 main     OS Product: Linux
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.003579 main     OS Product: Linux
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.004691 main     OS Release: 4.1.19-boot2docker
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.004691 main     OS Release: 4.1.19-boot2docker
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.005996 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.005996 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.007499 main     Executable: /sbin/VBoxService
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.007501 main     Process ID: 825
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.007503 main     Package type: LINUX_64BITS_GENERIC
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.007499 main     Executable: /sbin/VBoxService
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.007501 main     Process ID: 825
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.007503 main     Package type: LINUX_64BITS_GENERIC
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.012160 main     5.0.16 r105871 started. Verbose level = 0
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.012160 main     5.0.16 r105871 started. Verbose level = 0
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.051441 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
2019-05-10 19:04:22 (16099): Guest Log: 00:00:00.051556 vminfo   Error: Unable to connect to system D-Bus (1/3): D-Bus not installed
2019-05-10 19:04:22 (16099): Guest Log: Mounting BOINC shared/...
2019-05-10 19:04:23 (16099): Guest Log: -------------------
2019-05-10 19:04:23 (16099): Guest Log: Sat May 11 00:04:22 UTC 2019
2019-05-10 19:04:28 (16099): Guest Log: 00:00:05.053058 vminfo   Error: Unable to connect to system D-Bus (2/3): D-Bus not installed
2019-05-10 19:04:28 (16099): Guest Log: Sat May 11 00:04:27 UTC 2019
2019-05-10 19:04:28 (16099): Guest Log: 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default 
2019-05-10 19:04:28 (16099): Guest Log:     link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
2019-05-10 19:04:28 (16099): Guest Log:     inet 127.0.0.1/8 scope host lo
2019-05-10 19:04:28 (16099): Guest Log:        valid_lft forever preferred_lft forever
2019-05-10 19:04:28 (16099): Guest Log: 2: dummy0: <BROADCAST,NOARP> mtu 1500 qdisc noop state DOWN group default 
2019-05-10 19:04:28 (16099): Guest Log:     link/ether 66:f6:79:c5:cc:40 brd ff:ff:ff:ff:ff:ff
2019-05-10 19:04:28 (16099): Guest Log: 3: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc pfifo_fast state UP group default qlen 1000
2019-05-10 19:04:28 (16099): Guest Log:     link/ether 08:00:27:bb:83:b0 brd ff:ff:ff:ff:ff:ff
2019-05-10 19:04:28 (16099): Guest Log:     inet 10.0.2.15/24 brd 10.0.2.255 scope global eth0
2019-05-10 19:04:28 (16099): Guest Log:        valid_lft forever preferred_lft forever
2019-05-10 19:04:28 (16099): Guest Log: -------------------
2019-05-10 19:04:28 (16099): Guest Log: Linking /etc/docker to /var/lib/boot2docker for persistence
2019-05-10 19:04:28 (16099): Guest Log: Waiting for Docker daemon to start...
2019-05-10 19:04:31 (16099): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
2019-05-10 19:04:31 (16099): Guest Log: Running boinc_app...
2019-05-10 19:04:31 (16099): Guest Log: Importing Docker image from BOINC...
2019-05-10 19:04:34 (16099): Guest Log: 00:00:10.054762 vminfo   Error: Unable to connect to system D-Bus (3/3): D-Bus not installed
2019-05-10 19:05:19 (16099): Guest Log: Prerun diagnostics...
2019-05-10 19:05:19 (16099): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
2019-05-10 19:05:19 (16099): Guest Log: carlosred/bowtie    built               4beacb78841d        11 months ago       758.7 MB
2019-05-10 19:05:19 (16099): Guest Log: CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES
2019-05-10 19:05:19 (16099): Guest Log: 753.8M	/var/lib/docker
2019-05-10 19:05:19 (16099): Guest Log:               total        used        free      shared  buff/cache   available
2019-05-10 19:05:19 (16099): Guest Log: Mem:           3461          58        2443         917         958        2444
2019-05-10 19:05:19 (16099): Guest Log: Swap:           813           0         813
2019-05-10 19:05:19 (16099): Guest Log: Prerun commands...
2019-05-10 19:05:19 (16099): Guest Log: Running... 
2019-05-10 19:05:20 (16099): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
2019-05-10 19:05:20 (16099): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed
2019-05-10 19:05:39 (16099): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
2019-05-10 19:05:39 (16099): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
2019-05-10 19:05:39 (16099): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
2019-05-10 19:05:39 (16099): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
2019-05-10 19:05:39 (16099): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
2019-05-10 19:05:39 (16099): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:04 --:--:--     0
2019-05-10 19:05:39 (16099): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:05 --:--:--     0
2019-05-10 19:05:39 (16099): Guest Log:   0 14.4M    0 43297    0     0   6848      0  0:36:50  0:00:06  0:36:44  9204
2019-05-10 19:05:39 (16099): Guest Log:   5 14.4M    5  739k    0     0   101k      0  0:02:26  0:00:07  0:02:19  159k
2019-05-10 19:05:39 (16099): Guest Log:  11 14.4M   11 1695k    0     0   204k      0  0:01:12  0:00:08  0:01:04  366k
2019-05-10 19:05:39 (16099): Guest Log:  18 14.4M   18 2736k    0     0   294k      0  0:00:50  0:00:09  0:00:41  590k
2019-05-10 19:05:39 (16099): Guest Log:  26 14.4M   26 3983k    0     0   386k      0  0:00:38  0:00:10  0:00:28  864k
2019-05-10 19:05:39 (16099): Guest Log:  35 14.4M   35 5233k    0     0   463k      0  0:00:31  0:00:11  0:00:20 1042k
2019-05-10 19:05:39 (16099): Guest Log:  43 14.4M   43 6483k    0     0   526k      0  0:00:28  0:00:12  0:00:16 1149k
2019-05-10 19:05:39 (16099): Guest Log:  52 14.4M   52 7731k    0     0   581k      0  0:00:25  0:00:13  0:00:12 1207k
2019-05-10 19:05:39 (16099): Guest Log:  60 14.4M   60 8980k    0     0   627k      0  0:00:23  0:00:14  0:00:09 1249k
2019-05-10 19:05:39 (16099): Guest Log:  69 14.4M   69  9.9M    0     0   668k      0  0:00:22  0:00:15  0:00:07 1249k
2019-05-10 19:05:39 (16099): Guest Log:  77 14.4M   77 11.2M    0     0   704k      0  0:00:20  0:00:16  0:00:04 1249k
2019-05-10 19:05:39 (16099): Guest Log:  86 14.4M   86 12.4M    0     0   735k      0  0:00:20  0:00:17  0:00:03 1249k
2019-05-10 19:05:39 (16099): Guest Log:  94 14.4M   94 13.6M    0     0   764k      0  0:00:19  0:00:18  0:00:01 1250k
2019-05-10 19:05:39 (16099): Guest Log: 100 14.4M  100 14.4M    0     0   780k      0  0:00:18  0:00:18 --:--:-- 1249k
2019-05-10 19:05:39 (16099): Guest Log: Archive:  s_cerevisiae.ebwt.zip
2019-05-10 19:05:39 (16099): Guest Log:   inflating: s_cerevisiae.1.ebwt     
2019-05-10 19:05:39 (16099): Guest Log:   inflating: s_cerevisiae.2.ebwt     
2019-05-10 19:05:39 (16099): Guest Log:   inflating: s_cerevisiae.3.ebwt     
2019-05-10 19:05:39 (16099): Guest Log:   inflating: s_cerevisiae.4.ebwt     
2019-05-10 19:05:39 (16099): Guest Log:   inflating: s_cerevisiae.rev.1.ebwt  
2019-05-10 19:05:39 (16099): Guest Log:   inflating: s_cerevisiae.rev.2.ebwt  
2019-05-10 19:05:39 (16099): Guest Log:   inflating: make_s_cerevisiae.sh    
2019-05-10 19:05:39 (16099): Guest Log: # reads processed: 1
2019-05-10 19:05:39 (16099): Guest Log: # reads with at least one reported alignment: 1 (100.00%)
2019-05-10 19:05:39 (16099): Guest Log: # reads that failed to align: 0 (0.00%)
2019-05-10 19:05:39 (16099): Guest Log: Reported 1 alignments
2019-05-10 19:05:40 (16099): Guest Log: Postrun commands...
2019-05-10 19:05:40 (16099): Guest Log: boinc_app exited (0)
2019-05-10 19:05:40 (16099): Guest Log: Saving results...
2019-05-10 19:05:40 (16099): Guest Log: make_s_cerevisiae.sh
2019-05-10 19:05:40 (16099): Guest Log: res_bowtie.txt
2019-05-10 19:05:40 (16099): VM Completion File Detected.
2019-05-10 19:05:40 (16099): Powering off VM.
2019-05-10 19:05:40 (16099): Successfully stopped VM.
2019-05-10 19:05:40 (16099): Deregistering VM. (boinc_c6321bd55a110ac7, slot#18)
2019-05-10 19:05:40 (16099): Removing network bandwidth throttle group from VM.
2019-05-10 19:05:41 (16099): Removing storage controller(s) from VM.
2019-05-10 19:05:41 (16099): Removing VM from VirtualBox.
2019-05-10 19:05:41 (16099): Removing virtual ISO 9660 disk from VirtualBox.
19:05:46 (16099): called boinc_finish(0)

</stderr_txt>
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