I have recently been experiencing a temporary freeze issue that occurs once per each time I boot my computer. This only happens once per boot cycle, not after logging out and back in.

My current specifications are: Debian Jessie x64, 500GB main drive, 1TB home drive

The issue is as follows: After logging, I can perform some actions just fine, such as xcalc or a terminal. However when I launch other applications, the hard drive light goes solid green and there is about a 10 to 20 second freeze. I can move my mouse and even manipulate some windows, but if during this freeze I try to launch a terminal or execute say "ls -l" in an already open terminal, it doesn't respond until after the freeze. Currently it seems like it is network-facing applications that cause the freeze when launched (Firefox, Thunderbird, others as well). dmesg doesn't seem to produce any meaningful output. I have moved the files to another disk (via grub-install, rsync, update grub.cfg/fstab with new UUIDs), booted from it, and still get the same problem. I'm thinking a full re-installation may fix the problem as I haven't re-installed since Lenny, but would like to avoid it.

Does anyone have any suggestions what could be causing this temporary freeze or any workarounds to it?

Thanks in advance.

Try CTRL-ALT-F1 to get a system console and run top to see what's happening.

The top applications during the freeze where:

top
systemd
kthread
thunderbird

During the freeze, none of these took more than 1 CPU I executed "top -n1" several times. Near the last time, Thunderbird was at about 50% CPU usage for a moment, VIRT is about 800000, RES 190000, SHR 70000, but I think this was after everything became responsive again. I have 6 cores and 12G memory.

I also use a bridged setup in that my network interface is br0 with eth0 being enslaved to it. I also have some basic firewall rules enabled at startup. I've had the same setup for a while now, but the issue really only seems to have started when I upgraded to Debian Jessie from Wheezy. I realize it is a different kernel, but even with Wheezy I was using the 3.12 (or something like that) kernel from backports.

OK this is a shot wayyyy into the dark. pcCoder mentions that it is or seems to be network faced ,, ie Thunderbird by his/her guess's.

My thoughts are, and these may be irrelevant:

Are you behind a router or is your Email client looking straight at your ISP's gateway? and are you running the default Firewall "UFW" on your Distro ????

'Sudo ufw status' in terminal window , if active then ok, else ' sudo ufw enable'

if you are not behind a router, I would recommend the Actiontech
series router series as a purchase. you need to be on the LAN side and hard wired to the router to make changes in it as root
trying to change settings over wlan on these units is fruitless , same goes for the WAN side....

Also using Bleachbit to clean out your system of junk, much like CCleaner does on windows, might work wonders here.

Hardening your network with a router if you don't have one is a good first Big step.

Bleachbit will scrub your Email clients caches and hopefully the thing that is trying to call home

Running ClamAV, [ clamTK is the GUI ], on your email cache may also rectify the issue.

One other quick question pcCoder, your bridged network... is that an adhoc style or are you twinning the network with some windows boxes? Asking just because your net-topology here ,I can't quite picture when you say br0 with eth0 is enslaved to it .....

Upgraded to backports kernel 4.1. It seems to have reduced the delay/freeze, but it is still present to some extent.

I am behind a home router that has been flashed with DD-WRT. All WAN management has been disabled.

My system firewall is simply a shell script that applies some iptables rules that is initialized at startup.

The bridged network is basically this:

I no longer think this is a network issue. After logging in to XFCE and opening a terminal, I issue a command to copy a some files from one location to another (cp -ar ~/Temp/dir1 ~/Temp/dir2). This is about 200 or more MB of files. After this happens, the HD light goes solid green again, and when I click on the application launcher (xfce4 whiskermenu), the window pops up but only shows the window face color (gray). After the copy is completed, the window is fully drawn with the menu items for the application launcher. As a result, I'm thinking it could be some hard disk issue instead. But again it only happens once per boot. If I log out and back in, and do the same thing, it does not happen again, until I reboot and do it again. So now I think it could be an HD issue.

I had a very oddball embedded Linux issue. The system was very customized. What would happen is that it would perform logrotate once a day, but it would also do that immediately after boot and the application started up, just how we wrote the code. Turns out the common use case was that the unit was used for a work day. Small surprise there, and then shut down. Promptly the next day it would be started up, and Viola, logrotate would promptly rotate the entire last days' worth of logs and it caused a visible hiccup in performance because these logs were fairly extensive in early development.

Well, we fixed it by changing the size qualification, the rules, removing tons of superfluous log entries, and going to a RAM disk for non-critical stuff we didn't need to keep.

Long way of saying, yeah ... could be the disk. But I'm doubting it's exactly this, however you should see if there are ways to determine what may or may not be writing to the disk shortly after boot.