Ubuntu – Process hangs before termination with ubuntu 18.04

18.04processstrace

When using ABAQUS 6.14 (but also ABAQUS 2018) on ubuntu 18.04 everything seems to work fine except the termination of the standard process (the process started when performing an implicit analysis — if you are not familiar with this it doesn't matter).

The analysis indeed works as one can also see in a log file (the .sta file, for those who are familiar with abaqus) the message THE ANALYSIS HAS COMPLETED SUCCESSFULLY. The output database contains the analysis results. However, after the analysis has been completed, the process standard remains in a sleeping status using 0% CPU and keeping the same amount of RAM as when it was running.

From strace I get:

[pid 23191] close(8)                    = 0
[pid 23185] <... select resumed> )      = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> )      = 0 (Timeout)
[pid 23193] futex(0x7f3acd917db0, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 23191] futex(0x7f3acd917db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
[pid 23193] <... futex resumed> )       = 0
[pid 23191] <... futex resumed> )       = -1 EAGAIN (Resource temporarily unavailable)
[pid 23191] futex(0x7f3acd917db0, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23191] munmap(0x7f3ab130b000, 327680) = 0
[pid 23191] munmap(0x7f3ab136b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab16db000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0fbb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0ddb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab0a0b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab03fb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab050b000, 1114112) = 0
[pid 23191] munmap(0x7f3ab00cb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab02eb000, 1114112) = 0
[pid 23191] munmap(0x7f3ab14eb000, 1114112) = 0
[pid 23191] futex(0x7f3ab8a5dd44, FUTEX_WAIT_PRIVATE, 8, NULL) = -1 EAGAIN (Resource temporarily unavailable)
[pid 23191] futex(0x7f3ab8a5dd44, FUTEX_WAIT_PRIVATE, 12, NULL <unfinished ...>
[pid 23193] <... select resumed> )      = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> )      = 0 (Timeout)
[pid 23185] select(10, [5 6 8 9], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23193] <... select resumed> )      = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> )      = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> )      = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> )      = 0 (Timeout)
[pid 23185] select(10, [5 6 8 9], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23193] <... select resumed> )      = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>
[pid 23185] <... select resumed> )      = 0 (Timeout)
[pid 23185] select(0, NULL, NULL, NULL, {tv_sec=0, tv_usec=50000} <unfinished ...>
[pid 23193] <... select resumed> )      = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000}) = 0 (Timeout)
[pid 23193] select(7, [4 5 6], NULL, NULL, {tv_sec=0, tv_usec=20000} <unfinished ...>

Like if the two processes were in a deadlock state. Moreover, the commands

pid -p 7002

and

pid -p 7010

do give an empty output. The dirs /proc/7002 and /proc/7010 do not exist.

The only abaqus-related processes executing are

david  6995  0.0  0.1 295428 51388 pts/0    S    17:00   0:00 /opt/abaqus/6.14-1/code/bin/python /opt/abaqus/6.14-1
david  6998  0.0  0.2 368744 97948 pts/0    S    17:00   0:00 /opt/abaqus/6.14-1/code/bin/python std_inst.com
david  7001  0.1  0.0 122076 20096 pts/0    Sl   17:00   0:03 /opt/abaqus/6.14-1/code/bin/eliT_DriverLM -job std_in
david  7008  0.4  0.5 735812 185364 pts/0   Sl   17:00   0:07 /opt/abaqus/6.14-1/code/bin/standard -standard -acade

On ubuntu 16.04 the exact same version works like a charm. Here the same strace on ubuntu 16.04 (with the same kernel version as my 18.04, i.e. 4.15.0-29):

3890  close(8)                          = 0
3892  <... select resumed> )            = 0 (Timeout)
3892  futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3890  futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892  <... futex resumed> )             = -1 EAGAIN (Resource temporarily unavailable)
3892  futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3890  futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892  <... futex resumed> )             = -1 EAGAIN (Resource temporarily unavailable)
3892  futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
3890  futex(0x7f29e43e1db0, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
3892  <... futex resumed> )             = 0
3890  <... futex resumed> )             = -1 EAGAIN (Resource temporarily unavailable)
3890  futex(0x7f29e43e1db0, FUTEX_WAKE_PRIVATE, 1) = 0
3892  select(7, [4 5 6], NULL, NULL, {0, 20000} <unfinished ...>
3890  munmap(0x7f29c7adb000, 327680)    = 0
3890  munmap(0x7f29c7b3b000, 1114112)   = 0
3890  munmap(0x7f29c7eab000, 1114112)   = 0
3890  munmap(0x7f29c778b000, 1114112)   = 0
3890  munmap(0x7f29c75ab000, 1114112)   = 0
3890  munmap(0x7f29c71db000, 1114112)   = 0
3890  munmap(0x7f29c6bcb000, 1114112)   = 0
3890  munmap(0x7f29c6cdb000, 1114112)   = 0
3890  munmap(0x7f29c689b000, 1114112)   = 0
3890  munmap(0x7f29c6abb000, 1114112)   = 0
3890  munmap(0x7f29c7cbb000, 1114112)   = 0
3890  exit_group(0)                     = ?
3891  +++ exited with 0 +++
3893  +++ exited with 0 +++
3892  +++ exited with 0 +++
3890  +++ exited with 0 +++
3880  <... wait4 resumed> [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0, NULL) = 3890
3880  --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=3890, si_uid=1000, si_status=0, si_utime=107, si_stime=7} ---

Has someone a good idea how to solve this? Or in which direction should I investigate further.

Best Answer

Dassaults System published a bug-fix this month:

You need to update to Abaqus 2018 to Abaqus 2018-HF16 from https://software.3ds.com/ more details can be found at https://github.com/willfurnass/abaqus-2017-centos-7-singularity/issues/5#issue-713025844

I tried it with updating Abaqus 2020 to Abaqus 2020-HF5 and it worked for Ubuntu 20.04 as well as Fedora 32.

System Monitor

This can be found in System > Administration

account

You can also create a keyboard shortcut for this in this article.

Once the GUI launches you can select the Processes tab which will list all the running processes. Sort by the CPU column to find the most CPU intensive task

cpu

Lastly you can right click that task and choose to end it, stop it, or kill it. Killing it will immediately stop and remove that process from the system.

kill

Command-Line

If you have a terminal open you can simply type top this will list all the running processes similar to that of the Processes tab in the GUI

top

Within top it is CPU sorted by default - so the top most CPU intensive tasks are at the top. At anytime you can press the letter k to kill a process

Simply type the PID of the process you wish to kill and press enter. It will ask for a Kill signal to send. To kill the process nicely use the default 15 - to kill it right away "Do not pass go, do not collect $200" use 9.

sigkill

The process will then be terminated.

If you are experiencing sluggish interface you can try to SSH in remotely if that is enabled - or switch to a virtual console via Ctrl+Alt+F# Where F# is a Function Key (F3, F4, F5, etc). To return to the Desktop environment switch to either F7 or F8 depending on your version of Ubuntu.

Ubuntu – Ubuntu 18.04 LTS hangs up every time with AMD GPU

June 14, 2018 Update

Based on this ArchLinux forum thread it appears you need to add:

amdgpu.dc=0

to your /etc/default/grub LINUX line after quiet splash. Then run sudo update-grub.

Being a new install of Ubuntu 18.04 you are one of the lucky ones that can use journalctl to look at the last boot (which locked up). Use:

journalctl -b-1

Then press the End key to jump to EOF (End Of File). In my successful last boot it says:

Jun 10 16:18:51 alien systemd[1]: Unmounting /mnt/d...
Jun 10 16:18:51 alien systemd[1]: Unmounted /run/user/1000.
Jun 10 16:18:51 alien systemd[1]: Unmounted /media/rick/Ubuntu 18.04 LTS amd64.
Jun 10 16:18:51 alien systemd[1]: Unmounted /boot/efi.
Jun 10 16:18:51 alien ntfs-3g[648]: Unmounting /dev/nvme0n1p8 (Shared_WSL+Linux)
Jun 10 16:18:51 alien ntfs-3g[648]: Permissions cache : 21 writes, 4033288 reads, 99.9% hits
Jun 10 16:18:51 alien systemd[1]: Unmounted /media/rick/casper-rw.
Jun 10 16:18:51 alien systemd[1]: Unmounted /mnt/e.
Jun 10 16:18:51 alien ntfs-3g[736]: Unmounting /dev/sda3 (HGST_Win10)
Jun 10 16:18:51 alien ntfs-3g[736]: Permissions cache : 754 writes, 4108560 reads, 99.9% hits
Jun 10 16:18:51 alien ntfs-3g[637]: Unmounting /dev/nvme0n1p4 (NVMe_Win10)
Jun 10 16:18:51 alien ntfs-3g[637]: Permissions cache : 987 writes, 4983239 reads, 99.9% hits
Jun 10 16:18:51 alien systemd[1]: Unmounted /mnt/d.
Jun 10 16:18:51 alien systemd[1]: Unmounted /mnt/c.
Jun 10 16:18:51 alien systemd[1]: Reached target Unmount All Filesystems.
Jun 10 16:18:51 alien systemd[1]: Stopped target Local File Systems (Pre).
Jun 10 16:18:51 alien systemd[1]: Stopped Remount Root and Kernel File Systems.
Jun 10 16:18:51 alien systemd[1]: Stopped Create Static Device Nodes in /dev.
Jun 10 16:18:51 alien systemd[1]: Reached target Shutdown.
Jun 10 16:18:51 alien systemd[1]: Reached target Final Step.
Jun 10 16:18:51 alien systemd[1]: dev-disk-by\x2dpartlabel-Basic\x5cx20data\x5cx20partition.device: Dev dev-
Jun 10 16:18:51 alien systemd[1]: Received SIGRTMIN+20 from PID 18665 (plymouthd).
Jun 10 16:18:51 alien systemd[1]: Started Show Plymouth Reboot Screen.
Jun 10 16:18:51 alien systemd[1]: Starting Reboot...
Jun 10 16:18:51 alien systemd[1]: Shutting down.
Jun 10 16:18:51 alien kernel: systemd-shutdow: 36 output lines suppressed due to ratelimiting
Jun 10 16:18:51 alien systemd-shutdown[1]: Sending SIGTERM to remaining processes...
Jun 10 16:18:51 alien dnsmasq[1393]: exiting on receipt of SIGTERM
Jun 10 16:18:51 alien systemd-journald[288]: Journal stopped
lines 46804-46832/46832 (END)

In yours you need to look for error messages.

You may have to use the Page Up key to see them.

When you have found what you are looking for (or have given up looking) press Q to exit.

If overheating was causing the shutdown you can install Intel Powerclamp: Stop cpu from overheating

Besides lm-sensors you can get temperature readings for all thermal zones directly from the command line using this one-liner:

$ paste <(cat /sys/class/thermal/thermal_zone*/type) <(cat /sys/class/thermal/thermal_zone*/temp) | column -s $'\t' -t | sed 's/\(.\)..$/.\1°C/'

INT3400 Thermal  20.0°C
SEN1             44.0°C
SEN2             52.0°C
SEN3             64.0°C
SEN4             59.0°C
B0D4             73.0°C
pch_skylake      76.5°C
x86_pkg_temp     73.0°C

Reported in Celsius and drop the last three zeros.

Best Answer

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System Monitor

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Ubuntu – Ubuntu 18.04 LTS hangs up every time with AMD GPU

June 14, 2018 Update

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