[Users] Possible performance issue

Mon Oct 7 11:55:05 CDT 2019

Hello Vaishak,

you options do not include optimization parameters ie:

CXX_OPTIMISE_FLAGS=

does not set any optimization options which means that g++ will compile
as if -O0 was used.

Please change the option list that you are using to make sure that:

CXX_OPTIMISE_FLAGS=-O3
C_OPTIMISE_FLAGS=-O3
F90_OPTIMISE_FLAGS=-O3
F77_OPTIMISE_FLAGS=-O3

are set. If you are sure that login node and compute node are the same
architecture you should also add "-march=native" to these options.

You may also consider using the Intel compiler (icc, icpc,
ifort) instead of gcc (gcc, g++, gfortran) which may (or may not) give
faster execution.

For example the file 

https://bitbucket.org/simfactory/simfactory2/src/master/mdb/optionlists/stampede2-skx.cfg

shows the settings used to compile for the SkyLake nodes of the
Stampede2 cluster at TACC using the Intel compiler.

I noticed that you are using a self-compiled MPI stack.

Usually on clusters the admins will provide an MPI stack optimized for
the cluster hardware (eg to make sure Infiniband interconnects are used
rather than Ethernet). I would expect better performance using those
than using a self-compiled MPI stack (the Intel MPI stack will do in
that respect since it is always provided by the admins and never
self-compiled). Details on how to use it depend on the cluster and you
would have to consult the cluster websites and / or the output of the
cluster's mpicc -showme:compile and mpicc -showme:link commands (for
OpenMPI mvapich and intel-mpi have similar options) to find out which
libraries the official mpi compiler wrapper would use.

Yours,
Roland

> Dear Sir,
> 
> Please find the config-info file attached herewith...
> 
> 
> Yours,
> 
> Vaishak
> 
> On Mon, Oct 7, 2019 at 7:56 PM Haas, Roland <rhaas at illinois.edu> wrote:
> 
> > Hello Vaishak,
> >
> > hmm, still very slow.
> >
> > One question that I forgot to ask before: did you make sure to build
> > and optimized Cactus executable (setting OPTIMISE=yes, DEBUG=no to
> > ensure that you have -O2 or -O3 optimisation settings enabled)?
> >
> > Ideally if you could send the file configs/sim/config-info that would
> > tell me.
> >
> > Yours,
> > Roland
> >
> > > Dear Sir,
> > >
> > > I am a little worried about the performance because this is a new cluster
> > > we have and it is supposed to be performing well. I am inclined to think
> > > that some libraries/compiler options / settings might be the bottleneck.
> > >
> > >
> > > I am presently running two simulations, both using the same parameter
> > file
> > > GW150914.rpar.
> > >
> > > The first one is using mpich-3.3.1, the same as in the simulation
> > mentioned
> > > in the previous thread. I am using one node consisting of 2*16 cores, and
> > > 32 mpiprocs.
> > >
> > > The second one is using openmpi-3.1.2 with openmp. It uses 128 procs,
> > > distributed among 16 mpiprocs and 8 openmp threads per mpiproc. Since I
> > > have 32 PPN, it is launching 4 mpiprocs per node.
> > >
> > > I am herewith attaching the carpet-timing..asc file from both these runs.
> > >
> > > Thanking you
> > >
> > > Regards,
> > > Vaishak
> > >
> > >
> > > On Fri, Oct 4, 2019 at 8:05 PM Haas, Roland <rhaas at illinois.edu> wrote:
> > >
> > > > Hello Vaishak,
> > > >
> > > > I do not see anything obviously wrong with the setup.
> > > >
> > > > It uses 128 MPI ranks for the 4 nodes which fits with there being 2x16
> > > > cores per node.
> > > >
> > > > Lookin at the timer tree output at iteration 1024 (search for
> > > > "gettimeof " and you will find the spot) out of 5977s spend during
> > > > Evolve about 2143s were spent in "syncs" which is communication and
> > > > about the same amount of time in "thorns" that is doing computation.
> > > > While this ratio is not great (spending more time sending data than
> > > > doing computation) it is also not unheard of.
> > > >
> > > > Getting the original output files for the gallery data from Zenodo
> > > > (link is on the gallery page):
> > > >
> > > > wget
> > > > https://zenodo.org/record/155394/files/GW150914_28.tar.xz?download=1
> > > >
> > > > you can see (in GW150914_28/output-0000/GW150914_28.out) that that one
> > > > took about 137s for syncs and 198s for thorns, so the same ratio but
> > > > about a factor of 10 faster.
> > > >
> > > > I am reaching for straws here, but sometimes having too many MPI ranks
> > > > can be detrimental if there is not enough work to split up (OpenMP can
> > > > be a bit more forgiving in that respect, the original gallery run
> > > > used 120 cores on 10 nodes using 6 OpenMP threads per MPI rank).
> > > >
> > > > Since each node has lots of RAM (more than the 96GB required to run the
> > > > simulation), can you try and see what would happen if you were to run
> > > > on only a single node?
> > > >
> > > > Also if you could add the parameter:
> > > >
> > > > Carpet::output_timers_every = 1024
> > > >
> > > > then provide the files carpet-timing-statistics*.asc that would let us
> > > > know in even more detail where the time is spent.
> > > >
> > > > Running for a short time (2048 iterations) is enough to get data to
> > > > compare.
> > > >
> > > > Yours,
> > > > Roland
> > > >
> > > > > Dear All,
> > > > >
> > > > > I am running the simulation GW150914 using the parameter file
> > available
> > > > at
> > > > > the ETK gallery at (GW150914-ETK gallery
> > > > > <https://einsteintoolkit.org/gallery/bbh/index.html>) using 128
> > cores.
> > > > >
> > > > > Each compute node consists of 2 X 16 Cores Intel SkyLake ( Intel(R)
> > > > Xeon(R)
> > > > > Gold 6142 CPU @ 2.60GHz) and 384 GB RAM .  I have compiled and am
> > running
> > > > > Einstein Toolkit without OpenMP and using mpich-3.3.1.
> > > > >
> > > > >
> > > > > The issue is that the simulation seems to be running at a very slow
> > pace.
> > > > > The number of physical time per hour that it is completing is only
> > about
> > > > > 1.3 units. At this rate to complete 1700 units, it would take about
> > 54
> > > > > days, in contrast to 2.8 days on (Intel(R) Xeon(R) CPU E5-2630 v3 @
> > > > > 2.40GHz) as per the details at the example run of GW150914 available
> > at
> > > > the
> > > > > gallery (GW150914-ETK gallery
> > > > > <https://einsteintoolkit.org/gallery/bbh/index.html>).
> > > > >
> > > > > I have also tried using intel mpi (impi) but with simular results.
> > > > >
> > > > > I am also attaching the out file from the simulation.
> > > > >
> > > > > Looking forward to your inputs.
> > > > >
> > > > >
> > > > > Thanks and regards,
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Vaishak P
> > > > >
> > > > > PhD Scholar,
> > > > > Shyama Prasad Mukherjee Fellow
> > > > > Inter-University Center for Astronomy and Astrophysics (IUCAA)
> > > > > Pune, India
> > > >
> > > >
> > > >
> > > > --
> > > > My email is as private as my paper mail. I therefore support encrypting
> > > > and signing email messages. Get my PGP key from http://pgp.mit.edu .
> > > >
> > >
> > >
> >
> >
> >
> > --
> > My email is as private as my paper mail. I therefore support encrypting
> > and signing email messages. Get my PGP key from http://pgp.mit.edu .
> >
> 
> 

-- 
My email is as private as my paper mail. I therefore support encrypting
and signing email messages. Get my PGP key from http://pgp.mit.edu .
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/pgp-signature
Size: 833 bytes
Desc: OpenPGP digital signature
Url : http://lists.einsteintoolkit.org/pipermail/users/attachments/20191007/99cbad03/attachment-0001.bin 