yade-dev team mailing list archive

[Bruno Chareyre <bruno.chareyre@xxxxxxxxxxx>]

I have ubuntu 12.04 64bits on two machines and I never had the problem
that you have now. Maybe after some updates?...

No we are not compiling openblas from source (I am, in fact, but the
fact that you ask means that you are not compiling it, for sure it is
not done silently).

Openblas is not used unless you simulate fluid coupling with FlowEngine.
You could disable it at compile time to be sure it is not the cause of
your problem. -DYADE_CGAL=OFF should be enough to switch off also
PFVFLOW and LINSOLV, the latest one uses openblas. If switched off, the
library will not be linked. You could even uninstall openblas in your
system to be 100% sure.



Bruno


On 28/02/14 11:47, Eulitz, Alexander wrote:
> yes, and it can be assumed that some modules that are imported in yade could be the reason fort he problem:[1]
>
> "After some more googling I found the answer here.
> It turns out that certain Python modules (numpy, scipy, tables, pandas, skimage...) mess with core affinity on import. As far as I can tell, this problem seems to be specifically caused by them linking against multithreaded OpenBLAS libraries.
> A workaround is to reset the task affinity using
> os.system("taskset -p 0xff %d" % os.getpid())
> With this line pasted in after the module imports, my example now runs on all cores.
> There are also two ways to disable the CPU affinity-resetting behaviour of OpenBLAS itself. At run-time you can use the environment variable OPENBLAS_MAIN_FREE (or GOTOBLAS_MAIN_FREE), for example
> OPENBLAS_MAIN_FREE=1 python myscript.py
> Or alternatively, if you're compiling OpenBLAS from source you can permanently disable it at build-time by editing the Makefile.rule to contain the line
> NO_AFFINITY=1
> "
>
> Are we compiling OpenBLAS from source?
> But even if we are, why does the cpu affinity problem appear even for a built from late 2013 which definitely worked well concerning multicore operation?
> Maybe it was an update oft he openblas modul that was done by apt-get update?
>  
>
> [1] http://stackoverflow.com/questions/15639779/what-determines-whether-different-python-processes-are-assigned-to-the-same-or-d?lq=1 answer#25
>
> -----Ursprüngliche Nachricht-----
> Von: Yade-dev [mailto:yade-dev-bounces+alexander.eulitz=iwf.tu-berlin.de@xxxxxxxxxxxxxxxxxxx] Im Auftrag von Christian Jakob
> Gesendet: Freitag, 28. Februar 2014 10:52
> An: Yade Development Group
> Betreff: [Yade-dev] cpu affinity problem
>
> Hi there,
>
> I just tried to find out what is not working at my machine in parallel mode (using yade -jN). First thing I recognized is different MHz for my CPUs are used:
>
> me@debian ~/YADE/build >less /proc/cpuinfo | grep MHz
> cpu MHz         : 3167.68
> cpu MHz         : 2000.0
> cpu MHz         : 2000.0
> cpu MHz         : 2000.0
> cpu MHz         : 2000.0
> cpu MHz         : 2000.0
> cpu MHz         : 2000.0
> cpu MHz         : 2000.0
>
> I disabled GV1/GV3 and C mode for CPU performance in BIOS:
>
> (I skipped the part where I had to reinstall kde and graphic driver because PC was running for 276 days and there was a kernel update, which broke my graphics module, which leads to black screen when starting kdm, which .... whatever ... )
>
> me@debian ~/YADE/build >less /proc/cpuinfo | grep MHz
> cpu MHz         : 3158.704
> cpu MHz         : 3158.704
> cpu MHz         : 3158.704
> cpu MHz         : 3158.704
> cpu MHz         : 3158.704
> cpu MHz         : 3158.704
> cpu MHz         : 3158.704
> cpu MHz         : 3158.704
>
> But still the same problem occurs (for new and old versions of yade).  
> So I googled that and it seems to be a problem with cpu affinity.
>
> When I run yade -j4 --performance I see 4 PIDs (threads) running at 1 and the same core the whole time (e.g. PID = {11962,11963,11964,11965} in htop).
>
> Then I tried this ...
>
> me@debian ~/YADE/trunk >taskset -c -p 0 11962 pid 11962's current affinity list: 0 pid 11962's new affinity list: 0 me@debian ~/YADE/trunk >taskset -c -p 1 11963 pid 11963's current affinity list: 0 pid 11963's new affinity list: 1 me@debian ~/YADE/trunk >taskset -c -p 2 11964 pid 11964's current affinity list: 0 pid 11964's new affinity list: 2 me@debian ~/YADE/trunk >taskset -c -p 3 11965 pid 11965's current affinity list: 0 pid 11965's new affinity list: 3
>
> and viola, it is working as expected (at least until one run with X balls is finished, after that PID is changing again and all new PIDs switched back on CPU 0).
>
> So my question is:
>
> How can I set cpu affinity? Do you know a fast-and-dirty way to get rid of this?
>
> Thanks in advance,
>
> cheesed off Christian
>
>
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>


-- 
_______________
Bruno Chareyre
Associate Professor
ENSE³ - Grenoble INP
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