Task 182807

Name boinc2docker_8911_1556839443.356495_0
Workunit 82325
Created 2 May 2019, 23:24:07 UTC
Sent 3 May 2019, 10:40:43 UTC
Report deadline 10 May 2019, 10:40:43 UTC
Received 4 May 2019, 3:18:07 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 567
Run time 2 min 19 sec
CPU time 1 min 58 sec
Validate state Valid
Credit 4.67
Device peak FLOPS 12.54 GFLOPS
Application version boinc2docker v1.07 (vbox64_mt)
x86_64-pc-linux-gnu
Peak working set size 111.77 MB
Peak swap size 132.95 MB
Peak disk usage 524.69 MB

Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
2019-05-04 13:15:32 (6780): vboxwrapper (7.9.26200): starting
2019-05-04 13:15:32 (6780): Feature: Checkpoint interval offset (406 seconds)
2019-05-04 13:15:32 (6780): Detected: VirtualBox COM Interface (Version: 5.2.8)
2019-05-04 13:15:32 (6780): Detected: Minimum checkpoint interval (600.000000 seconds)
2019-05-04 13:15:32 (6780): Create VM. (boinc_344782e0542d1081, slot#51)
2019-05-04 13:15:32 (6780): Updating drive controller type and model for desired configuration.
2019-05-04 13:15:32 (6780): Setting Memory Size for VM. (5584MB)
2019-05-04 13:15:32 (6780): Setting CPU Count for VM. (4)
2019-05-04 13:15:32 (6780): Setting Chipset Options for VM.
2019-05-04 13:15:32 (6780): Setting Boot Options for VM.
2019-05-04 13:15:32 (6780): Enabling VM Network Access.
2019-05-04 13:15:32 (6780): Setting Network Configuration for NAT.
2019-05-04 13:15:32 (6780): Disabling USB Support for VM.
2019-05-04 13:15:32 (6780): Disabling COM Port Support for VM.
2019-05-04 13:15:32 (6780): Disabling LPT Port Support for VM.
2019-05-04 13:15:32 (6780): Disabling Audio Support for VM.
2019-05-04 13:15:32 (6780): Disabling Clipboard Support for VM.
2019-05-04 13:15:32 (6780): Disabling Drag and Drop Support for VM.
2019-05-04 13:15:32 (6780): Adding storage controller(s) to VM.
2019-05-04 13:15:32 (6780): Adding virtual ISO 9660 disk drive to VM. (vm_isocontext.iso)
2019-05-04 13:15:32 (6780): Adding VirtualBox Guest Additions to VM.
2019-05-04 13:15:32 (6780): Adding network bandwidth throttle group to VM. (Defaulting to 1024GB)
2019-05-04 13:15:32 (6780): Enabling shared directory for VM.
2019-05-04 13:15:32 (6780): Starting VM. (boinc_344782e0542d1081, slot#51)
2019-05-04 13:15:42 (6780): Guest Log: BIOS: VirtualBox 5.2.8

2019-05-04 13:15:42 (6780): Guest Log: CPUID EDX: 0x178bfbff

2019-05-04 13:15:42 (6780): Guest Log: BIOS: Boot : bseqnr=1, bootseq=0032

2019-05-04 13:15:42 (6780): Guest Log: int13_harddisk: function 02, unmapped device for ELDL=80

2019-05-04 13:15:42 (6780): Guest Log: BIOS: Boot from Hard Disk 0 failed

2019-05-04 13:15:42 (6780): Guest Log: BIOS: Boot : bseqnr=2, bootseq=0003

2019-05-04 13:15:42 (6780): Guest Log: BIOS: Booting from CD-ROM...

2019-05-04 13:15:42 (6780): Successfully started VM. (PID = '7052')
2019-05-04 13:15:42 (6780): Reporting VM Process ID to BOINC.
2019-05-04 13:15:47 (6780): Guest Log: BIOS: KBD: unsupported int 16h function 03

2019-05-04 13:15:47 (6780): Guest Log: BIOS: AX=0305 BX=0000 CX=0000 DX=0000 

2019-05-04 13:15:47 (6780): VM state change detected. (old = 'poweroff', new = 'running')
2019-05-04 13:15:57 (6780): Guest Log: vgdrvHeartbeatInit: Setting up heartbeat to trigger every 2000 milliseconds

2019-05-04 13:15:57 (6780): Guest Log: vboxguest: misc device minor 56, IRQ 20, I/O port d020, MMIO at 00000000f0400000 (size 0x400000)

2019-05-04 13:15:57 (6780): Guest Log: net.ipv4.ip_forward = 1

2019-05-04 13:15:57 (6780): Guest Log: sysctl: cannot stat /proc/sys/net/ipv6/conf/all/forwarding: No such file or directory

2019-05-04 13:15:57 (6780): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-05-04 13:15:57 (6780): Guest Log: sysctl: "cannot stat %s" is an unknown key

2019-05-04 13:15:57 (6780): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-05-04 13:15:57 (6780): Guest Log: Segmentation fault

2019-05-04 13:15:57 (6780): Guest Log: automount ...

2019-05-04 13:15:57 (6780): Guest Log: Is the disk unpartitioned?, test for the 'boot2docker format-me' string

2019-05-04 13:15:57 (6780): Guest Log: automount over.

2019-05-04 13:15:57 (6780): Guest Log: Setting hostname to boot2docker Done.

2019-05-04 13:15:57 (6780): Guest Log: Sat May  4 13:15:52 UTC 2019 dhcp -------------------------------

2019-05-04 13:15:57 (6780): Preference change detected
2019-05-04 13:15:57 (6780): Setting CPU throttle for VM. (90%)
2019-05-04 13:15:57 (6780): Setting checkpoint interval to 600 seconds. (Higher value of (Preference: 60 seconds) or (Vbox_job.xml: 600 seconds))
2019-05-04 13:16:02 (6780): Guest Log: udevadm settle - timeout of 5 seconds reached, the event queue contains:

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1108)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00 (1344)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:00 (1345)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:01 (1346)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:02 (1347)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:03 (1348)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00 (1349)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00/input/input0 (1350)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00/input/input0/event0 (1351)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00 (1352)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00/input/input1 (1353)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00/input/input1/event1 (1354)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00 (1355)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00 (1356)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/ACPI0003:00 (1357)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/ACPI0003:00/power_supply/AC (1358)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00 (1359)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/device:01 (1360)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/input/input7 (1361)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/input/input7/event6 (1362)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0400:00 (1363)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0400:01 (1364)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:00 (1365)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:01 (1366)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:02 (1367)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:03 (1368)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0C02:00 (1369)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0C0A:00 (1370)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP8390:00 (1371)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00 (1372)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/APP0001:00 (1373)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0000:00 (1374)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0100:00 (1375)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0103:00 (1376)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0200:00 (1377)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0303:00 (1378)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1379)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0B00:00 (1380)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0F03:00 (1381)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:02 (1382)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:00 (1383)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:01 (1384)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:02 (1385)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:03 (1386)

2019-05-04 13:16:02 (6780): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:01 (1387)

2019-05-04 13:16:02 (6780): Guest Log: Sat May  4 13:15:58 UTC 2019 dhcp -------------------------------

2019-05-04 13:16:02 (6780): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.000124 main     Log opened 2019-05-04T13:15:58.832012000Z

2019-05-04 13:16:02 (6780): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.000124 main     Log opened 2019-05-04T13:15:00:00:00.004071 main     OS Product: Linux5

2019-05-04 13:16:02 (6780): Guest Log: 8.800:00:00.004200 main     OS Release: 4.1.19-boot2docker

2019-05-04 13:16:02 (6780): Guest Log: 32000:00:00.004263 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-05-04 13:16:02 (6780): Guest Log: 1200:00:00.004324 main     Executable: /sbin/VBoxService

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.004326 main     Process ID: 898

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.004327 main     Package type: LINUX_64BITS_GENERIC

2019-05-04 13:16:02 (6780): Guest Log: 00Z

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.005466 main     5.0.16 r105871 started. Verbose level = 0

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.004071 main     OS Product: Linux

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.004200 main     OS Release: 4.1.19-boot2docker

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.009237 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

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.009312 vminfo   Error: Unable to connect to system D-Bus (1/3): D-Bus not installed

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.004263 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.004324 main     Executable: /sbin/VBoxService

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.004326 main     Process ID: 898

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.004327 main     Package type: LINUX_64BITS_GENERIC

2019-05-04 13:16:02 (6780): Guest Log: 00:00:00.005466 main     5.0.16 r105871 started. Verbose level = 0

2019-05-04 13:16:02 (6780): Guest Log: Mounting BOINC shared/...

2019-05-04 13:16:02 (6780): Guest Log: -------------------

2019-05-04 13:16:02 (6780): Guest Log: Sat May  4 03:16:02 UTC 2019

2019-05-04 13:16:07 (6780): Guest Log: 00:00:05.012804 vminfo   Error: Unable to connect to system D-Bus (2/3): D-Bus not installed

2019-05-04 13:16:07 (6780): Guest Log: Sat May  4 03:16:07 UTC 2019

2019-05-04 13:16:07 (6780): Guest Log: 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default 

2019-05-04 13:16:07 (6780): Guest Log:     link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00

2019-05-04 13:16:07 (6780): Guest Log:     inet 127.0.0.1/8 scope host lo

2019-05-04 13:16:07 (6780): Guest Log:        valid_lft forever preferred_lft forever

2019-05-04 13:16:07 (6780): Guest Log: 2: dummy0: <BROADCAST,NOARP> mtu 1500 qdisc noop state DOWN group default 

2019-05-04 13:16:07 (6780): Guest Log:     link/ether a2:d9:0e:ee:d0:2d brd ff:ff:ff:ff:ff:ff

2019-05-04 13:16:07 (6780): Guest Log: 3: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc pfifo_fast state UP group default qlen 1000

2019-05-04 13:16:07 (6780): Guest Log:     link/ether 08:00:27:50:34:73 brd ff:ff:ff:ff:ff:ff

2019-05-04 13:16:07 (6780): Guest Log:     inet 10.0.2.15/24 brd 10.0.2.255 scope global eth0

2019-05-04 13:16:07 (6780): Guest Log:        valid_lft forever preferred_lft forever

2019-05-04 13:16:07 (6780): Guest Log: -------------------

2019-05-04 13:16:07 (6780): Guest Log: Linking /etc/docker to /var/lib/boot2docker for persistence

2019-05-04 13:16:07 (6780): Guest Log: Waiting for Docker daemon to start...

2019-05-04 13:16:12 (6780): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE

2019-05-04 13:16:12 (6780): Guest Log: Running boinc_app...

2019-05-04 13:16:12 (6780): Guest Log: Importing Docker image from BOINC...

2019-05-04 13:16:12 (6780): Guest Log: 00:00:10.015261 vminfo   Error: Unable to connect to system D-Bus (3/3): D-Bus not installed

2019-05-04 13:17:32 (6780): Guest Log: Prerun diagnostics...

2019-05-04 13:17:32 (6780): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE

2019-05-04 13:17:32 (6780): Guest Log: carlosred/gromacs   latest              da5fd8ed5910        10 months ago       1.271 GB

2019-05-04 13:17:32 (6780): Guest Log: CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES

2019-05-04 13:17:32 (6780): Guest Log: 1.3G	/var/lib/docker

2019-05-04 13:17:32 (6780): Guest Log:               total        used        free      shared  buff/cache   available

2019-05-04 13:17:32 (6780): Guest Log: Mem:           5408          73        3771        1484        1563        3781

2019-05-04 13:17:32 (6780): Guest Log: Swap:          1299           0        1299

2019-05-04 13:17:32 (6780): Guest Log: Prerun commands...

2019-05-04 13:17:32 (6780): Guest Log: Running... 

2019-05-04 13:17:32 (6780): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-05-04 13:17:32 (6780): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-05-04 13:17:37 (6780): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:17:37 (6780): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:17:37 (6780): Guest Log:  34 80810   34 28100    0     0  20207      0  0:00:03  0:00:01  0:00:02 20201

2019-05-04 13:17:37 (6780): Guest Log: 100 80810  100 80810    0     0  39757      0  0:00:02  0:00:02 --:--:-- 39768

2019-05-04 13:17:37 (6780): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-05-04 13:17:37 (6780): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-05-04 13:17:37 (6780): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:17:37 (6780): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:17:37 (6780): Guest Log: 100  1206  100  1206    0     0   2164      0 --:--:-- --:--:-- --:--:--  2165

2019-05-04 13:17:37 (6780): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-05-04 13:17:37 (6780): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-05-04 13:17:37 (6780): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:17:37 (6780): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:17:37 (6780): Guest Log: 100  3467  100  3467    0     0   3612      0 --:--:-- --:--:-- --:--:--  3611

2019-05-04 13:17:37 (6780): Guest Log: /bin/bash: line 1:    16 Illegal instruction     gmx grompp -f em_steep.mdp -c methane_water.gro -p topol.top -o min_thing.tpr

2019-05-04 13:17:37 (6780): Guest Log: Postrun commands...

2019-05-04 13:17:37 (6780): Guest Log: boinc_app exited (0)

2019-05-04 13:17:37 (6780): Guest Log: Saving results...

2019-05-04 13:17:37 (6780): Guest Log: em_steep.mdp

2019-05-04 13:17:37 (6780): VM Completion File Detected.
2019-05-04 13:17:37 (6780): Powering off VM.
2019-05-04 13:17:39 (6780): Successfully stopped VM.
2019-05-04 13:17:44 (6780): Deregistering VM. (boinc_344782e0542d1081, slot#51)
2019-05-04 13:17:44 (6780): Removing virtual disk drive(s) from VM.
2019-05-04 13:17:44 (6780): Removing network bandwidth throttle group from VM.
2019-05-04 13:17:44 (6780): Removing storage controller(s) from VM.
2019-05-04 13:17:44 (6780): Removing VM from VirtualBox.
13:17:49 (6780): called boinc_finish(0)

</stderr_txt>
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