I'm trying to run 'r.fillnulls' and it hangs on one computer but not on another.
On my laptop running Ubuntu 20.04 it runs fine in GRASS 7.8.6. It also runs in a docker container running GRASS 7.8.4.
On our server it just hangs. This is running Ubuntu 18.04 and grass 7.8.2. It also hangs running *the same docker image* Ubuntu 20.04 GRASS 7.8.4
Do you have any suggestions how to debug this? Examining it with top sows it is churning away with 100 % CPU usage. It takes ~5 minutes on my laptop then completes. It never completes on the server (which is much more powerful - it should complete faster).
On Tue, Jan 18, 2022 at 9:23 PM Ken Mankoff <mankoff@gmail.com> wrote:
Hello,
I'm trying to run 'r.fillnulls' and it hangs on one computer but not on another.
On my laptop running Ubuntu 20.04 it runs fine in GRASS 7.8.6. It also runs in a docker container running GRASS 7.8.4.
On our server it just hangs. This is running Ubuntu 18.04 and grass 7.8.2. It also hangs running *the same docker image* Ubuntu 20.04 GRASS 7.8.4
Do you have any suggestions how to debug this?
You can find out the process ID (the columns are
USER PID %CPU %MEM ...
so that it is the number after the user name):
ps aux | grep r.fillnulls
and then run strace on it
strace -p <pid>
The result may be hard to read yet give some insights if it is waiting
for something (e.g., a device) on that machine.
Markus
Examining it with top sows it is churning away with 100 % CPU usage. It takes ~5 minutes on my laptop then completes. It never completes on the server (which is much more powerful - it should complete faster).
I'm out of my depth here. It seems like a similar issue elsewhere may point to SSL library issues or that this is a parent thread waiting on another thread. From https://meenakshi02.wordpress.com/2011/02/02/strace-hanging-at-futex/ and 'ps -efL | grep filln', there is only one other PID. If I strace that, all I see is
I'm out of my depth here. It seems like a similar issue elsewhere may
point to SSL library issues or that this is a parent thread waiting on
another thread. From https://meenakshi02.wordpress.com/2011/02/02/strace-hanging-at-futex/
and 'ps -efL | grep filln', there is only one other PID. If I strace
that, all I see is
At the back r.fillnulls is calling other interpolation modules. Some
of them can run in parallel but they are using implicit approach in
selection of threads to run by detecting number of CPUs. My guess –
for some reason this magick code gets CPU count wrong and thus does
not utilize all CPUs available.
Māris.
otrd., 2022. g. 18. janv., plkst. 23:20 — lietotājs Ken Mankoff
(<mankoff@gmail.com>) rakstīja:
Hi Markus,
> I'm out of my depth here. It seems like a similar issue elsewhere may
> point to SSL library issues or that this is a parent thread waiting on
> another thread. From
> https://meenakshi02.wordpress.com/2011/02/02/strace-hanging-at-futex/
> and 'ps -efL | grep filln', there is only one other PID. If I strace
> that, all I see is
>
> read(3,