Processes getting wedged in "U" (uninterruptible wait) state after Security Update 2020-003

[Franco Vaccari]

I add to my previous description that on my system, SIP is enabled (just checked with csrutil status), but maybe turning it off will work…

Do you see any error message in console when you launch a process and it get stuck?

Ciao

Franco

> On 29 May 2020, at 02:27, Prokash Sinha <prokashs at gmail.com> wrote:
> 
> Hi Greg !
> 
> If you still have the recent update ( meaning you did not revert yet
> ), perhaps you can try into recovery boot ( At boot time  Command + R
> ). When you get to recover mode, somewhere in Utilities, you will see
> the terminal -- try disabling it  ( $csrutil disable, then reboot ).
> 
> Yes, the security updates are gradually being pushed to MacOS since
> 10.12 ( before that time, hardly much security was there ). So
> sandboxing, CSR, and a whole lot of authorization related stuff (
> coming from BSD, after Darwinised).
> 
> I think if you disable CSR, it would work ( macports, brew, and other
> common utilities can fail, and any binaries in 32 bit will cause havoc
> ).  Try finding the binary ( Bundle Types ) specially inside of your
> macports directory ( somewhere /usr/... ).  $file <filename>. or some
> command.
> 
> Usually all these 3rd party packages being updated to 64 bits.
> 
> Hope it helps!
> ~pro
> 
> On Thu, May 28, 2020 at 5:10 PM Franco Vaccari <vaccari at units.it> wrote:
>> 
>> Hi Greg…
>> 
>> I’m on 10.14.6 and I installed the security update on my MacBook Pro (Retina Mid 2012).  Didn’t face any problem with MacPorts. I don’t use the same ports you are mentioning, but I’ve just installed htop to give it a try, and here it works.
>> 
>> I’m sorry I can’t help more than this, but at least you know it’s not a general problem, and there must be something specific that went broken on your Mini…
>> 
>> Ciao
>> 
>> Franco
>> 
>>> On 29 May 2020, at 01:25, Greg Earle <earle at isolar.DynDNS.ORG> wrote:
>>> 
>>> Hi all,
>>> 
>>> Kind of a long shot here, but given the level of Mac expertise on this list ...
>>> 
>>> At work I have a production Mac mini running macOS Mojave 10.14.6.  It ran perfectly fine - with several MacPorts ports in regular use - until last night.
>>> 
>>> I made the mistake of installing Security Update 2020-003.
>>> 
>>> After the reboot I started noticing things going haywire quickly.
>>> 
>>> - Servers that were running but not listening on their usual ports (or at all)
>>> 
>>> - Servers that were running normally but could not be killed (not even kill -9)
>>> 
>>> - Processes (including MacPorts apps) that get wedged as soon as they run
>>> 
>>> The common thread through all these is that the processes - whether you tried to kill them or run them from scratch - all get wedged in "U" (uninterruptible wait) state.  (Nothing is NFS or CIFS mounted so I doubt it's due to disk I/O.)
>>> 
>>> For example:
>>> 
>>> A COTS product we have uses Postgres as the back-end database; the Postgres server starts at boot time, but it doesn't bind to its normal listening port.  If I try to kill the process, it wedges - just like these other ones do.
>>> 
>>> If I try to run MacPorts' "htop" port ("/opt/local/bin/htop") - it immediately wedges.  I can't even run it under "dtruss" - I get no output at all, like as if it never even gets off the ground to run.
>>> 
>>> (Strangely, the normal system "top" runs fine and doesn't wedge - it also shows these processes as being in "stuck" state, as expected.)
>>> 
>>> If I try to restart MacPorts' Xymon monitoring port (which has several persistent processes started at boot time), one of them, "xymonlaunch", won't quit and it gets wedged in "U" state.
>>> 
>>> I was able to use "gcore" to get a core dump of one of the wedged processes, but when I tried to use the MacPorts "gdb" (/opt/local/bin/ggdb) to examine it, you guessed it ... instantly wedged.
>>> 
>>> In fact, pretty much EVERYTHING in the MacPorts "/opt/local/bin" directory is wedging on me at startup!  I'm completely baffled at this point.
>>> 
>>> Tried running the MacPorts "tree" and "openssl" next.  Stuck.
>>> 
>>> The list of wedged processes is getting impressive:
>>> 
>>> --
>>> whdmac:~ root# top -l 1 | egrep STATE\|stuck | sed -e 's/stuck.*/stuck/g' -e 's/STATE.*/STATE/g' -e 's/     //g'
>>> Processes: 152 total, 2 running, 5 stuck
>>> PID   COMMAND    %CPU TIME     #TH #WQ #PORTS MEM  PURG CMPRS PGRP PPID STATE
>>> 993   openssl     0.0  00:00.00 1   0   0     8192B+ 0B 0B    993  1    stuck
>>> 973   tree        0.0  00:00.00 1   0   0     8192B+ 0B 0B    973  445  stuck
>>> 956   htop        0.0  00:00.00 1   0   0     8192B+ 0B 0B    956  1    stuck
>>> 261   xymonlaunch 0.0  00:00.00 1   0   0     8192B+ 0B 0B    246  246  stuck
>>> 100   dbus-daemon 0.0  00:00.00 1   0   0     8192B+ 0B 0B    100  1    stuck
>>> --
>>> 
>>> I'm resigned to probably having to boot it into Recovery Mode and restore the system from a pre-Security Update 2020-003 Time Machine backup, but I thought I'd run it up the flagpole here first just to see if I was the only person in the world experiencing this.  Maybe this Mac is possessed ...
>>> 
>>>              - Greg
>>