Why my cp2k.popt is running much slower than cp2k.sopt?

hawk2012 hawk2... at gmail.com
Fri Jul 25 17:38:33 CEST 2008


correction:
"it toook 158 seconds to finish the test job with 4 CPUs while it only
took 85 seconds to finish the
same job with 8 CPUs."

On Jul 25, 10:36 am, hawk2012 <hawk2... at gmail.com> wrote:
> Thank you for your help.
> The machine I used to test cp2k is a SMP machine with 8 cores running
> on CentOS5.0. So, there is no network bottleneck problem and no TCP/IP
> connection latency. On the same machine I tested another parallel MD
> program(a simple MD program for LJ potential) and found that the
> parallel efficiency is almost linear (it toook 158 seconds to finish
> the test job with 4 CPUs while it only took 85 seconds to finish the
> same job).
>
> On Jul 24, 4:22 pm, Axel <akoh... at gmail.com> wrote:
>
> > > It seems that the MPI performace is really bad. It spent a lot of time
> > > in calling MP_Allreduce and MP_Wait. For cp2k.sopt it took only 162
>
> > right this is what is needed. a lot. and this is why cp2k needs
> > a very fast and low latency network and a good MPI implementation.
>
> > > seconds to finish the job while it took 3010 seconds to finish the
> > > same job. There must be something wrong the executable cp2k.popt since
> > > my other parallel executable can be run using the same /home/mpich.g95/
> > > bin/mpirun with normal performance.  Any suggestions?
>
> > before discussing any cp2k related issues. you should first
> > check how well your MPI setup works _at all_. i suspect there
> > is a much lower lying problem than cp2k and its requirements.
>
> > most MPI packages come with some benchmark examples to measure
> > performance and latencies. i suggest to try those first and
> > check how well your setup works and compare it to similar
> > set ups. it would help a _lot_ if you give a sufficiently detailed
> > account of your hardware when discussing performance. please
> > see earlier discussions on the subject.
>
> > if collective operations and barriers are giving you problems
> > than your may not be using your machine correctly or have not
> > set it up correctly. they should also matter a lot in case of
> > using TCP/IP connections for parallel computation which incur
> > large latency penalties due to the TCP/IP encoding. the fact
> > that you are using MPICH doesn't help as well, since its
> > collectives, especially in version 1.x.x, are supposed to be
> > pretty inefficient.
>
> > what is worrying me even more is the fact that you seem to be
> > running your tests as root. this goes against about everything
> > i've learned during my carreer about good computer use practices.
>
> > basically the root account should only used if it cannot be avoided.
> > to give an example: on our own local clusters (where i do maintain
> > MPI, compilers, libraries and most applications including cp2k)
> > i don't even _know_ the root password (and don't _want_ to, since
> > this way, it is close to impossible to mess up the machines by
> > accident or carelessness).
>
> > cheers,
> >     axel.


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