Task 182794

Name boinc2docker_8655_1556839439.816882_1
Workunit 82318
Created 2 May 2019, 23:24:02 UTC
Sent 3 May 2019, 10:40:43 UTC
Report deadline 10 May 2019, 10:40:43 UTC
Received 4 May 2019, 3:18:22 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 567
Run time 2 min 51 sec
CPU time 1 min 29 sec
Validate state Valid
Credit 4.65
Device peak FLOPS 12.54 GFLOPS
Application version boinc2docker v1.07 (vbox64_mt)
windows_x86_64
Peak working set size 115.18 MB
Peak swap size 133.14 MB
Peak disk usage 524.69 MB

Stderr output

<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
2019-05-04 13:15:11 (10624): vboxwrapper (7.9.26200): starting
2019-05-04 13:15:11 (10624): Feature: Checkpoint interval offset (35 seconds)
2019-05-04 13:15:11 (10624): Detected: VirtualBox COM Interface (Version: 5.2.8)
2019-05-04 13:15:11 (10624): Detected: Minimum checkpoint interval (600.000000 seconds)
2019-05-04 13:15:11 (10624): Create VM. (boinc_3348d670d4308ed4, slot#22)
2019-05-04 13:15:11 (10624): Updating drive controller type and model for desired configuration.
2019-05-04 13:15:11 (10624): Setting Memory Size for VM. (5584MB)
2019-05-04 13:15:11 (10624): Setting CPU Count for VM. (4)
2019-05-04 13:15:11 (10624): Setting Chipset Options for VM.
2019-05-04 13:15:11 (10624): Setting Boot Options for VM.
2019-05-04 13:15:11 (10624): Enabling VM Network Access.
2019-05-04 13:15:11 (10624): Setting Network Configuration for NAT.
2019-05-04 13:15:11 (10624): Disabling USB Support for VM.
2019-05-04 13:15:11 (10624): Disabling COM Port Support for VM.
2019-05-04 13:15:11 (10624): Disabling LPT Port Support for VM.
2019-05-04 13:15:11 (10624): Disabling Audio Support for VM.
2019-05-04 13:15:11 (10624): Disabling Clipboard Support for VM.
2019-05-04 13:15:11 (10624): Disabling Drag and Drop Support for VM.
2019-05-04 13:15:11 (10624): Adding storage controller(s) to VM.
2019-05-04 13:15:11 (10624): Adding virtual ISO 9660 disk drive to VM. (vm_isocontext.iso)
2019-05-04 13:15:13 (10624): Adding VirtualBox Guest Additions to VM.
2019-05-04 13:15:13 (10624): Adding network bandwidth throttle group to VM. (Defaulting to 1024GB)
2019-05-04 13:15:13 (10624): Enabling shared directory for VM.
2019-05-04 13:15:13 (10624): Starting VM. (boinc_3348d670d4308ed4, slot#22)
2019-05-04 13:15:21 (10624): Guest Log: BIOS: VirtualBox 5.2.8

2019-05-04 13:15:21 (10624): Guest Log: CPUID EDX: 0x178bfbff

2019-05-04 13:15:21 (10624): Guest Log: BIOS: Boot : bseqnr=1, bootseq=0032

2019-05-04 13:15:21 (10624): Guest Log: int13_harddisk: function 02, unmapped device for ELDL=80

2019-05-04 13:15:21 (10624): Guest Log: BIOS: Boot from Hard Disk 0 failed

2019-05-04 13:15:21 (10624): Guest Log: BIOS: Boot : bseqnr=2, bootseq=0003

2019-05-04 13:15:21 (10624): Guest Log: BIOS: Booting from CD-ROM...

2019-05-04 13:15:21 (10624): Successfully started VM. (PID = '5192')
2019-05-04 13:15:21 (10624): Reporting VM Process ID to BOINC.
2019-05-04 13:15:26 (10624): Guest Log: BIOS: KBD: unsupported int 16h function 03

2019-05-04 13:15:26 (10624): Guest Log: BIOS: AX=0305 BX=0000 CX=0000 DX=0000 

2019-05-04 13:15:26 (10624): VM state change detected. (old = 'poweroff', new = 'running')
2019-05-04 13:15:36 (10624): Guest Log: vgdrvHeartbeatInit: Setting up heartbeat to trigger every 2000 milliseconds

2019-05-04 13:15:36 (10624): Guest Log: vboxguest: misc device minor 56, IRQ 20, I/O port d020, MMIO at 00000000f0400000 (size 0x400000)

2019-05-04 13:15:36 (10624): Guest Log: net.ipv4.ip_forward = 1

2019-05-04 13:15:36 (10624): Guest Log: sysctl: cannot stat /proc/sys/net/ipv6/conf/all/forwarding: No such file or directory

2019-05-04 13:15:36 (10624): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-05-04 13:15:36 (10624): Guest Log: sysctl: "cannot stat %s" is an unknown key

2019-05-04 13:15:36 (10624): Guest Log: sysctl: setting key "cannot stat %s": No such file or directory

2019-05-04 13:15:36 (10624): Guest Log: Segmentation fault

2019-05-04 13:15:36 (10624): Guest Log: automount ...

2019-05-04 13:15:36 (10624): Preference change detected
2019-05-04 13:15:36 (10624): Setting CPU throttle for VM. (90%)
2019-05-04 13:15:37 (10624): Setting checkpoint interval to 600 seconds. (Higher value of (Preference: 60 seconds) or (Vbox_job.xml: 600 seconds))
2019-05-04 13:15:42 (10624): Guest Log: Is the disk unpartitioned?, test for the 'boot2docker format-me' string

2019-05-04 13:15:42 (10624): Guest Log: automount over.

2019-05-04 13:15:42 (10624): Guest Log: Setting hostname to boot2docker Done.

2019-05-04 13:15:42 (10624): Guest Log: Sat May  4 13:15:35 UTC 2019 dhcp -------------------------------

2019-05-04 13:15:47 (10624): Guest Log: udevadm settle - timeout of 5 seconds reached, the event queue contains:

2019-05-04 13:15:47 (10624): Guest Log:   /sys/devices/LNXSYSTM:00/LNXSYBUS:00/PNP0A03:00/device:00/PNP0700:00 (1386)

2019-05-04 13:15:47 (10624): Guest Log: Sat May  4 13:15:41 UTC 2019 dhcp -------------------------------

2019-05-04 13:15:47 (10624): Guest Log: VBoxService 5.0.16 r105871 (verbosity: 0) linux.amd64 (Mar  4 2016 17:38:55) release log

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000113 main     Log opened 2019-05-04T13:15:41.745686000Z

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000252 main     OS Product: Linux

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000305 main     OS Release: 4.1.19-boot2docker

2019-05-04 13:15:47 (10624): Guest Log: VBo00:00:00.000378 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-05-04 13:15:47 (10624): Guest Log: Ser00:00:00.000427 main     Executable: /sbin/VBoxService

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000429 main     Process ID: 887v

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000430 main     Package type: LINUX_64BITS_GENERIC

2019-05-04 13:15:47 (10624): Guest Log: ice 5.0.16 r105871 (verbosity: 0) lin00:00:00.001424 main     5.0.16 r105871 started. Verbose level = 0

2019-05-04 13:15:47 (10624): Guest Log: x.amd64 (Mar  4 2016 17:38:55) release log

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.004452 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 13:15:47 (10624): Guest Log: 00:00:00.004535 vminfo   Error: Unable to connect to system D-Bus (1/3): D-Bus not installed

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000113 main     Log opened 2019-05-04T13:15:41.745686000Z

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000252 main     OS Product: Linux

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000305 main     OS Release: 4.1.19-boot2docker

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000378 main     OS Version: #1 SMP Sun Apr 17 19:40:54 UTC 2016

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000427 main     Executable: /sbin/VBoxService

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000429 main     Process ID: 887

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.000430 main     Package type: LINUX_64BITS_GENERIC

2019-05-04 13:15:47 (10624): Guest Log: 00:00:00.001424 main     5.0.16 r105871 started. Verbose level = 0

2019-05-04 13:15:47 (10624): Guest Log: Mounting BOINC shared/...

2019-05-04 13:15:47 (10624): Guest Log: -------------------

2019-05-04 13:15:47 (10624): Guest Log: Sat May  4 03:15:43 UTC 2019

2019-05-04 13:15:52 (10624): Guest Log: 00:00:05.007063 vminfo   Error: Unable to connect to system D-Bus (2/3): D-Bus not installed

2019-05-04 13:15:52 (10624): Guest Log: Sat May  4 03:15:54 UTC 2019

2019-05-04 13:15:52 (10624): Guest Log: 1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default 

2019-05-04 13:15:52 (10624): Guest Log:     link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00

2019-05-04 13:15:52 (10624): Guest Log:     inet 127.0.0.1/8 scope host lo

2019-05-04 13:15:52 (10624): Guest Log:        valid_lft forever preferred_lft forever

2019-05-04 13:15:52 (10624): Guest Log:     inet6 ::1/128 scope host 

2019-05-04 13:15:52 (10624): Guest Log:        valid_lft forever preferred_lft forever

2019-05-04 13:15:52 (10624): Guest Log: 2: dummy0: <BROADCAST,NOARP> mtu 1500 qdisc noop state DOWN group default 

2019-05-04 13:15:52 (10624): Guest Log:     link/ether 2e:74:05:9d:43:59 brd ff:ff:ff:ff:ff:ff

2019-05-04 13:15:52 (10624): Guest Log: 3: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc pfifo_fast state UP group default qlen 1000

2019-05-04 13:15:52 (10624): Guest Log:     link/ether 08:00:27:a9:e7:ef brd ff:ff:ff:ff:ff:ff

2019-05-04 13:15:52 (10624): Guest Log:     inet 10.0.2.15/24 brd 10.0.2.255 scope global eth0

2019-05-04 13:15:52 (10624): Guest Log:        valid_lft forever preferred_lft forever

2019-05-04 13:15:52 (10624): Guest Log:     inet6 fe80::a00:27ff:fea9:e7ef/64 scope link 

2019-05-04 13:15:52 (10624): Guest Log:        valid_lft forever preferred_lft forever

2019-05-04 13:15:52 (10624): Guest Log: -------------------

2019-05-04 13:15:52 (10624): Guest Log: Linking /etc/docker to /var/lib/boot2docker for persistence

2019-05-04 13:15:52 (10624): Guest Log: Waiting for Docker daemon to start...

2019-05-04 13:15:52 (10624): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE

2019-05-04 13:15:52 (10624): Guest Log: Running boinc_app...

2019-05-04 13:15:52 (10624): Guest Log: Importing Docker image from BOINC...

2019-05-04 13:15:57 (10624): Guest Log: 00:00:10.008483 vminfo   Error: Unable to connect to system D-Bus (3/3): D-Bus not installed

2019-05-04 13:17:42 (10624): Guest Log: Prerun diagnostics...

2019-05-04 13:17:42 (10624): Guest Log: REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE

2019-05-04 13:17:42 (10624): Guest Log: carlosred/gromacs   latest              da5fd8ed5910        10 months ago       1.271 GB

2019-05-04 13:17:42 (10624): Guest Log: CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES

2019-05-04 13:17:42 (10624): Guest Log: 1.3G	/var/lib/docker

2019-05-04 13:17:42 (10624): Guest Log:               total        used        free      shared  buff/cache   available

2019-05-04 13:17:42 (10624): Guest Log: Mem:           5408          71        3774        1484        1563        3784

2019-05-04 13:17:42 (10624): Guest Log: Swap:          1300           0        1300

2019-05-04 13:17:42 (10624): Guest Log: Prerun commands...

2019-05-04 13:17:42 (10624): Guest Log: Running... 

2019-05-04 13:17:42 (10624): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-05-04 13:17:42 (10624): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-05-04 13:17:47 (10624): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:17:47 (10624): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:17:47 (10624): Guest Log:  52 80810   52 42220    0     0  37198      0  0:00:02  0:00:01  0:00:01 37198

2019-05-04 13:17:47 (10624): Guest Log: 100 80810  100 80810    0     0  51070      0  0:00:01  0:00:01 --:--:-- 51048

2019-05-04 13:17:47 (10624): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-05-04 13:17:47 (10624): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-05-04 13:17:47 (10624): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:17:47 (10624): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:17:47 (10624): Guest Log: 100  1206  100  1206    0     0   2546      0 --:--:-- --:--:-- --:--:--  2544

2019-05-04 13:17:47 (10624): Guest Log:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

2019-05-04 13:17:47 (10624): Guest Log:                                  Dload  Upload   Total   Spent    Left  Speed

2019-05-04 13:17:47 (10624): Guest Log:   0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

2019-05-04 13:17:47 (10624): Guest Log: 100  3467  100  3467    0     0   4894      0 --:--:-- --:--:-- --:--:--  4896

2019-05-04 13:17:47 (10624): 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 13:17:47 (10624): Guest Log: Postrun commands...

2019-05-04 13:17:47 (10624): Guest Log: boinc_app exited (0)

2019-05-04 13:17:47 (10624): Guest Log: Saving results...

2019-05-04 13:17:47 (10624): Guest Log: em_steep.mdp

2019-05-04 13:17:47 (10624): VM Completion File Detected.
2019-05-04 13:17:47 (10624): Powering off VM.
2019-05-04 13:17:48 (10624): Successfully stopped VM.
2019-05-04 13:17:53 (10624): Deregistering VM. (boinc_3348d670d4308ed4, slot#22)
2019-05-04 13:17:53 (10624): Removing virtual disk drive(s) from VM.
2019-05-04 13:17:53 (10624): Removing network bandwidth throttle group from VM.
2019-05-04 13:17:53 (10624): Removing storage controller(s) from VM.
2019-05-04 13:17:54 (10624): Removing VM from VirtualBox.
13:18:00 (10624): called boinc_finish(0)

</stderr_txt>
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