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

hawk2012 hawk2... at gmail.com
Fri Jul 25 17:36:29 CEST 2008


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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