[Wien] inefficiency of lapw2 on clusters

Mon Dec 28 10:22:37 CET 2020

Thank you for your quick response. I believe that is the key to the
problem. So with larger vector files, the lapw2 will run slower in my
situation. That makes sense.

Peter Blaha <pblaha at theochem.tuwien.ac.at> 于2020年12月28日周一 下午4:38写道：

> This points to a fileserver/network problem on your cluster.
>
> On a big cluster one usually has a home-directory on a fileserver drive,
> which is mounted over a network (eg. NFS, HPFS,..) on all nodes. While
> this is very convenient, it is on many systems also a huge bottleneck.
> Either the fileserver breaks down due to too many simultaneously
> requests or the network does not have sufficient band width.
>
> You probably have set the SCRATCH variable to your working directory
> "./", which means that the large case.vector* files are stored in your
> working directory, leading to the bad performance of lapw2.
>
> On most clusters there is a local scratch or tmp directory (files exist
> only on this node) and when setting your SCRATCH variable to this, the
> slow lapw2 should be gone.
>
> In addition, I see that also lapw1 gets only 90% of a core. I recommend
> setting OMP_NUM_THREADS=2 and spanning only 4 k-parallel jobs in
> parallel (I assume you have a node with 8 cores).
>
>
> On 12/28/20 9:14 AM, Fan wrote:
> > Dear wien2k users,
> >
> > I am trying to run wien2k on clusters, but I encountered a very strange
> > issue that the performance of lapw2 is very inefficient. For example,
> >
> >
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------
> >  >   lapw1  -dn -p       (15:27:45) starting parallel lapw1 at Mon Dec
> > 28 15:27:46 CST 2020
> > ->  starting parallel LAPW1 jobs at Mon Dec 28 15:27:46 CST 2020
> > running LAPW1 in parallel mode (using .machines.help)
> > 8 number_of_parallel_jobs
> >       f02n10(58) 178.212u 3.134s 3:15.91 92.57%      0+0k 0+0io 0pf+0w
> >       f02n10(58) 180.210u 3.011s 3:19.46 91.86%      0+0k 0+0io 0pf+0w
> >       f02n10(58) 183.239u 3.019s 3:22.73 91.87%      0+0k 0+0io 0pf+0w
> >       f02n10(57) 181.113u 2.884s 3:20.20 91.90%      0+0k 0+0io 0pf+0w
> >       f02n10(57) 178.433u 2.965s 3:18.85 91.22%      0+0k 0+0io 0pf+0w
> >       f02n10(57) 151.420u 2.756s 2:48.26 91.63%      0+0k 0+0io 0pf+0w
> >       f02n10(57) 183.799u 3.065s 3:22.58 92.24%      0+0k 0+0io 0pf+0w
> >       f02n10(57) 185.867u 3.109s 3:27.50 91.07%      0+0k 0+0io 0pf+0w
> >     Summary of lapw1para:
> >     f02n10        k=459   user=1422.29    wallclock=1575.49
> > 1.034u 1.698s 3:30.15 1.2%      0+0k 472+128io 2pf+0w
> >  >   lapw2 -up -p        (15:31:16) running LAPW2 in parallel mode
> >        f02n10 37.680u 1.597s 6:32.94 10.00% 0+0k 0+0io 0pf+0w
> >        f02n10 38.841u 1.682s 7:07.57 9.48% 0+0k 0+0io 0pf+0w
> >        f02n10 38.611u 1.727s 6:51.53 9.80% 0+0k 0+0io 0pf+0w
> >        f02n10 38.715u 1.728s 6:48.76 9.89% 0+0k 0+0io 0pf+0w
> >        f02n10 37.847u 1.639s 7:01.08 9.38% 0+0k 0+0io 0pf+0w
> >        f02n10 38.170u 1.709s 6:45.01 9.85% 0+0k 0+0io 0pf+0w
> >        f02n10 39.261u 1.727s 7:01.11 9.73% 0+0k 0+0io 0pf+0w
> >        f02n10 39.772u 1.765s 7:04.40 9.79% 0+0k 0+0io 0pf+0w
> >
> >
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------
> > As you can see the cpu utilizations are much lower than that of lapw1,
> > which made lawp2 more time-consuming than lapw1. MPI parallelization
> > performed even worse.
> >
> > More strangely, it seems to be case-dependent. For TiC and some other
> > systems, it works fine. I also tried other nodes, the problem still
> > persists, however in my local workstation everything went well.
> >
> > The version of wien2k is 19.2 compiled with intel icc and ifort without
> > any errors. MPI, FFTW, and ELPA are all available.
> >
> >   Any suggestion will be appreciated.
> >
> > Fan
> >
> >
> >
> >
> >
> > _______________________________________________
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> > Wien at zeus.theochem.tuwien.ac.at
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> >
>
> --
>
>                                        P.Blaha
> --------------------------------------------------------------------------
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300             FAX: +43-1-58801-165982
> Email: blaha at theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at/TC_Blaha
> --------------------------------------------------------------------------
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