Task 182806

Name boinc2docker_8874_1556839442.838315_1
Workunit 82324
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, 3:23:37 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 567
Run time 2 min 44 sec
CPU time 1 min 37 sec
Validate state Valid
Credit 4.19
Device peak FLOPS 12.54 GFLOPS
Application version boinc2docker v1.07 (vbox64_mt)
windows_x86_64
Peak working set size 103.09 MB
Peak swap size 133.01 MB
Peak disk usage 524.69 MB

Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
2019-05-04 13:20:35 (5212): vboxwrapper (7.9.26200): starting
2019-05-04 13:20:35 (5212): Feature: Checkpoint interval offset (312 seconds)
2019-05-04 13:20:35 (5212): Detected: VirtualBox COM Interface (Version: 5.2.8)
2019-05-04 13:20:35 (5212): Detected: Minimum checkpoint interval (600.000000 seconds)
2019-05-04 13:20:35 (5212): Create VM. (boinc_4c535a0ecbf94bd5, slot#22)
2019-05-04 13:20:35 (5212): Updating drive controller type and model for desired configuration.
2019-05-04 13:20:36 (5212): Setting Memory Size for VM. (5584MB)
2019-05-04 13:20:36 (5212): Setting CPU Count for VM. (4)
2019-05-04 13:20:36 (5212): Setting Chipset Options for VM.
2019-05-04 13:20:36 (5212): Setting Boot Options for VM.
2019-05-04 13:20:36 (5212): Enabling VM Network Access.
2019-05-04 13:20:36 (5212): Setting Network Configuration for NAT.
2019-05-04 13:20:36 (5212): Disabling USB Support for VM.
2019-05-04 13:20:36 (5212): Disabling COM Port Support for VM.
2019-05-04 13:20:36 (5212): Disabling LPT Port Support for VM.
2019-05-04 13:20:36 (5212): Disabling Audio Support for VM.
2019-05-04 13:20:36 (5212): Disabling Clipboard Support for VM.
2019-05-04 13:20:36 (5212): Disabling Drag and Drop Support for VM.
2019-05-04 13:20:36 (5212): Adding storage controller(s) to VM.
2019-05-04 13:20:36 (5212): Adding virtual ISO 9660 disk drive to VM. (vm_isocontext.iso)
2019-05-04 13:20:36 (5212): Adding VirtualBox Guest Additions to VM.
2019-05-04 13:20:36 (5212): Adding network bandwidth throttle group to VM. (Defaulting to 1024GB)
2019-05-04 13:20:36 (5212): Enabling shared directory for VM.
2019-05-04 13:20:36 (5212): Starting VM. (boinc_4c535a0ecbf94bd5, slot#22)
2019-05-04 13:20:44 (5212): Guest Log: BIOS: VirtualBox 5.2.8

2019-05-04 13:20:44 (5212): Guest Log: CPUID EDX: 0x178bfbff

2019-05-04 13:20:44 (5212): Guest Log: BIOS: Boot : bseqnr=1, bootseq=0032

2019-05-04 13:20:44 (5212): Guest Log: int13_harddisk: function 02, unmapped device for ELDL=80

2019-05-04 13:20:44 (5212): Guest Log: BIOS: Boot from Hard Disk 0 failed

2019-05-04 13:20:44 (5212): Guest Log: BIOS: Boot : bseqnr=2, bootseq=0003

2019-05-04 13:20:44 (5212): Guest Log: BIOS: Booting from CD-ROM...

2019-05-04 13:20:44 (5212): Successfully started VM. (PID = '10900')
2019-05-04 13:20:44 (5212): Reporting VM Process ID to BOINC.
2019-05-04 13:20:49 (5212): Guest Log: BIOS: KBD: unsupported int 16h function 03

2019-05-04 13:20:49 (5212): Guest Log: BIOS: AX=0305 BX=0000 CX=0000 DX=0000 

2019-05-04 13:20:49 (5212): VM state change detected. (old = 'poweroff', new = 'running')
2019-05-04 13:20:59 (5212): Preference change detected
2019-05-04 13:20:59 (5212): Setting CPU throttle for VM. (90%)
2019-05-04 13:20:59 (5212): Setting checkpoint interval to 600 seconds. (Higher value of (Preference: 60 seconds) or (Vbox_job.xml: 600 seconds))
2019-05-04 13:21:09 (5212): Guest Log: net.ipv4.ip_forward = 1

2019-05-04 13:21:09 (5212): Guest Log: sysctl: cannot stat /proc/sys/net/ipv6/conf/all/forwarding: No such file or directory

2019-05-04 13:21:09 (5212): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-05-04 13:21:09 (5212): Guest Log: sysctl: "cannot stat %s" is an unknown key

2019-05-04 13:21:09 (5212): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-05-04 13:21:09 (5212): Guest Log: Segmentation fault

2019-05-04 13:21:09 (5212): Guest Log: automount ...

2019-05-04 13:21:09 (5212): Guest Log: vgdrvHeartbeatInit: Setting up heartbeat to trigger every 2000 milliseconds

2019-05-04 13:21:09 (5212): Guest Log: vboxguest: misc device minor 56, IRQ 20, I/O port d020, MMIO at 00000000f0400000 (size 0x400000)

2019-05-04 13:21:09 (5212): Guest Log: Is the disk unpartitioned?, test for the 'boot2docker format-me' string

2019-05-04 13:21:09 (5212): Guest Log: automount over.

2019-05-04 13:21:09 (5212): Guest Log: Setting hostname to boot2docker Done.

2019-05-04 13:21:09 (5212): Guest Log: Sat May  4 13:21:06 UTC 2019 dhcp -------------------------------

2019-05-04 13:21:14 (5212): Guest Log: udevadm settle - timeout of 5 seconds reached, the event queue contains:

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1103)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00 (1335)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:00 (1336)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:01 (1337)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:02 (1338)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXCPU:03 (1339)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00 (1340)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00/input/input0 (1341)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXPWRBN:00/input/input0/event0 (1342)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00 (1343)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00/input/input1 (1344)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSLPBN:00/input/input1/event1 (1345)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00 (1346)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00 (1347)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/ACPI0003:00 (1348)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/ACPI0003:00/power_supply/AC (1349)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00 (1350)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/device:01 (1351)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/input/input6 (1352)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/LNXVIDEO:00/input/input6/event5 (1353)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0400:00 (1354)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0400:01 (1355)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:00 (1356)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:01 (1357)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:02 (1358)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0501:03 (1359)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0C02:00 (1360)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP0C0A:00 (1361)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/PNP8390:00 (1362)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00 (1363)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/APP0001:00 (1364)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0000:00 (1365)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0100:00 (1366)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0103:00 (1367)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0200:00 (1368)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0303:00 (1369)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1370)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0B00:00 (1371)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0F03:00 (1372)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:02 (1373)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:00 (1374)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:01 (1375)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:02 (1376)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0C0F:03 (1377)

2019-05-04 13:21:14 (5212): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:01 (1378)

2019-05-04 13:21:14 (5212): Guest Log: Sat May  4 13:21:12 UTC 2019 dhcp -------------------------------

2019-05-04 13:21:14 (5212): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.000087 main     Log opened 2019-05-04T13:21:12.676411000Z

2019-05-04 13:21:14 (5212): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.000087 main     Log opened 2019-05-04T13:21:12.676411000Z

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.003516 main     OS Product: Linux

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.003516 main     OS Product: Linux

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.004716 main     OS Release: 4.1.19-boot2docker

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.004716 main     OS Release: 4.1.19-boot2docker

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.006050 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.006050 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.007660 main     Executable: /sbin/VBoxService

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.007663 main     Process ID: 944

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.007664 main     Package type: LINUX_64BITS_GENERIC

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.007660 main     Executable: /sbin/VBoxService

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.007663 main     Process ID: 944

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.007664 main     Package type: LINUX_64BITS_GENERIC

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.014532 main     5.0.16 r105871 started. Verbose level = 0

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.014532 main     5.0.16 r105871 started. Verbose level = 0

2019-05-04 13:21:14 (5212): Guest Log: 00:00:00.020134 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 13:21:14 (5212): Guest Log: 00:00:00.020214 vminfo   Error: Unable to connect to system D-Bus (1/3): D-Bus not installed

2019-05-04 13:21:14 (5212): Guest Log: Mounting BOINC shared/...

2019-05-04 13:21:19 (5212): Guest Log: -------------------

2019-05-04 13:21:19 (5212): Guest Log: Sat May  4 03:21:15 UTC 2019

2019-05-04 13:21:19 (5212): Guest Log: 00:00:05.023540 vminfo   Error: Unable to connect to system D-Bus (2/3): D-Bus not installed

2019-05-04 13:21:24 (5212): Guest Log: Sat May  4 03:21:25 UTC 2019

2019-05-04 13:21:24 (5212): Guest Log: 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default 

2019-05-04 13:21:24 (5212): Guest Log:     link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00

2019-05-04 13:21:24 (5212): Guest Log:     inet 127.0.0.1/8 scope host lo

2019-05-04 13:21:24 (5212): Guest Log:        valid_lft forever preferred_lft forever

2019-05-04 13:21:24 (5212): Guest Log:     inet6 ::1/128 scope host 

2019-05-04 13:21:24 (5212): Guest Log:        valid_lft forever preferred_lft forever

2019-05-04 13:21:24 (5212): Guest Log: 2: dummy0: <BROADCAST,NOARP> mtu 1500 qdisc noop state DOWN group default 

2019-05-04 13:21:24 (5212): Guest Log:     link/ether f6:99:89:1f:2e:82 brd ff:ff:ff:ff:ff:ff

2019-05-04 13:21:24 (5212): Guest Log: 3: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc pfifo_fast state UP group default qlen 1000

2019-05-04 13:21:24 (5212): Guest Log:     link/ether 08:00:27:2a:d0:cc brd ff:ff:ff:ff:ff:ff

2019-05-04 13:21:24 (5212): Guest Log:     inet 10.0.2.15/24 brd 10.0.2.255 scope global eth0

2019-05-04 13:21:24 (5212): Guest Log:        valid_lft forever preferred_lft forever

2019-05-04 13:21:24 (5212): Guest Log:     inet6 fe80::a00:27ff:fe2a:d0cc/64 scope link 

2019-05-04 13:21:24 (5212): Guest Log:        valid_lft forever preferred_lft forever

2019-05-04 13:21:24 (5212): Guest Log: -------------------

2019-05-04 13:21:24 (5212): Guest Log: Linking /etc/docker to /var/lib/boot2docker for persistence

2019-05-04 13:21:24 (5212): Guest Log: Waiting for Docker daemon to start...

2019-05-04 13:21:24 (5212): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE

2019-05-04 13:21:24 (5212): Guest Log: Running boinc_app...

2019-05-04 13:21:24 (5212): Guest Log: Importing Docker image from BOINC...

2019-05-04 13:21:24 (5212): Guest Log: 00:00:10.024753 vminfo   Error: Unable to connect to system D-Bus (3/3): D-Bus not installed

2019-05-04 13:23:00 (5212): Guest Log: Prerun diagnostics...

2019-05-04 13:23:00 (5212): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE

2019-05-04 13:23:00 (5212): Guest Log: carlosred/gromacs   latest              da5fd8ed5910        10 months ago       1.271 GB

2019-05-04 13:23:00 (5212): Guest Log: CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES

2019-05-04 13:23:00 (5212): Guest Log: 1.3G	/var/lib/docker

2019-05-04 13:23:00 (5212): Guest Log:               total        used        free      shared  buff/cache   available

2019-05-04 13:23:00 (5212): Guest Log: Mem:           5408          72        3772        1484        1563        3783

2019-05-04 13:23:00 (5212): Guest Log: Swap:          1300           0        1300

2019-05-04 13:23:00 (5212): Guest Log: Prerun commands...

2019-05-04 13:23:00 (5212): Guest Log: Running... 

2019-05-04 13:23:00 (5212): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-05-04 13:23:00 (5212): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-05-04 13:23:05 (5212): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:23:05 (5212): Guest Log:   0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0

2019-05-04 13:23:05 (5212): Guest Log:  69 80810   69 56340    0     0  28485      0  0:00:02  0:00:01  0:00:01 28483

2019-05-04 13:23:05 (5212): Guest Log: 100 80810  100 80810    0     0  36210      0  0:00:02  0:00:02 --:--:-- 36221

2019-05-04 13:23:05 (5212): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-05-04 13:23:05 (5212): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-05-04 13:23:05 (5212): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:23:05 (5212): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:23:05 (5212): Guest Log: 100  1206  100  1206    0     0   1642      0 --:--:-- --:--:-- --:--:--  1643

2019-05-04 13:23:05 (5212): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-05-04 13:23:05 (5212): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-05-04 13:23:05 (5212): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:23:05 (5212): Guest Log: 100  3467  100  3467    0     0   4668      0 --:--:-- --:--:-- --:--:--  4672

2019-05-04 13:23:05 (5212): Guest Log: /bin/bash: line 1:    17 Illegal instruction     gmx grompp -f em_steep.mdp -c methane_water.gro -p topol.top -o min_thing.tpr

2019-05-04 13:23:05 (5212): Guest Log: Postrun commands...

2019-05-04 13:23:05 (5212): Guest Log: boinc_app exited (0)

2019-05-04 13:23:05 (5212): Guest Log: Saving results...

2019-05-04 13:23:05 (5212): Guest Log: em_steep.mdp

2019-05-04 13:23:05 (5212): VM Completion File Detected.
2019-05-04 13:23:05 (5212): Powering off VM.
2019-05-04 13:23:06 (5212): Successfully stopped VM.
2019-05-04 13:23:11 (5212): Deregistering VM. (boinc_4c535a0ecbf94bd5, slot#22)
2019-05-04 13:23:11 (5212): Removing virtual disk drive(s) from VM.
2019-05-04 13:23:11 (5212): Removing network bandwidth throttle group from VM.
2019-05-04 13:23:11 (5212): Removing storage controller(s) from VM.
2019-05-04 13:23:12 (5212): Removing VM from VirtualBox.
13:23:17 (5212): called boinc_finish(0)

</stderr_txt>
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