[CP2K:7587] terrible performance across infiniband

Glen MacLachlan mac... at gwu.edu
Tue Mar 22 19:07:04 UTC 2016


Hi Ron,

I think this is sort of off topic for the CP2K folks and more along the
lines of OpenMPI but I'm happy to continue the discussion -- I'm afraid
they might ask us to take it elsewhere though.

So you want to do a couple of things

   1.  vary the number of tasks and look for scaling -- you need to do this
   across multiple nodes to see what affect infiniband is having -- I assume
   you know how to ask your scheduler to distribute the tasks across multiple
   nodes.
   2. look for the throughput that you expect to be getting from your
   infiniband fabric. Did you mention what inifiniband you are running? qdr?
   fdr? You can compare the NPB benchmarks for your ib and ethernet networks.
   Do you know what your ethernet network throughput is? gigE? 10gig? You may
   want to have a look at this benchmark report that used NPB and NWChem,
   among others:
   http://www.dell.com/Downloads/Global/Power/ps1q10-20100215-Mellanox.pdf

Also, not having an admin handy or root access is not to bad of an
impediment. You can stand up your own instance of openmpi without special
privileges. Before you start chasing too many benchmarks (which can be
difficult to resist) you may want to spin up your own OpenMPI instance and
see if you can beat the ethernet performance.

By the way, when you type ifconfig do you see an interface that looks like
ib0 or ib1 or something like that?

Best,
Glen

==========================================
Glen MacLachlan, PhD
*HPC Specialist  *
*for Physical Sciences &*

*Professorial Lecturer, Data Sciences*

Office of Technology Services
The George Washington University
725 21st Street
Washington, DC 20052
Suite 211, Corcoran Hall

==========================================




On Tue, Mar 22, 2016 at 1:05 PM, Cohen, Ronald <rco... at carnegiescience.edu>
wrote:

> Dear Glen,
>
> I made NPB. Which test do you recommend me running? I have run several and
> it is not clear what to look for.
>
> Sincerely,
>
> Ron
>
>
> ---
> Ronald Cohen
> Geophysical Laboratory
> Carnegie Institution
> 5251 Broad Branch Rd., N.W.
> Washington, D.C. 20015
> rco... at carnegiescience.edu
> office: 202-478-8937
> skype: ronaldcohen
> https://twitter.com/recohen3
> https://www.linkedin.com/profile/view?id=163327727
>
> On Tue, Mar 22, 2016 at 12:33 PM, Glen MacLachlan <mac... at gwu.edu> wrote:
>
>> Check with your admin to see what networks are available but if you
>> disable tcp using mpirun --mca btl ^tcp then you should be giving MPI no
>> choice but to use IB. You can also increase the verbosity by adding --mca
>> btl_openib_verbose 1.
>>
>> Also, did you run ompi_info --all as Andreas suggested?
>>
>> Best,
>> Glen
>>
>> ==========================================
>> Glen MacLachlan, PhD
>> *HPC Specialist  *
>> *for Physical Sciences &*
>>
>> *Professorial Lecturer, Data Sciences*
>>
>> Office of Technology Services
>> The George Washington University
>> 725 21st Street
>> Washington, DC 20052
>> Suite 211, Corcoran Hall
>>
>> ==========================================
>>
>>
>>
>>
>> On Tue, Mar 22, 2016 at 11:21 AM, Cohen, Ronald <
>> rco... at carnegiescience.edu> wrote:
>>
>>> OK, I ran xhpl with those flags and got the same 1 GF performance as
>>> without. So I guess my openmpi is not using ib. I wonder how to turn that
>>> on! My config.log for the build seems to show that it found infiniband. I
>>> attached it in case you have time to look. Thank you so much!
>>>
>>> Ron
>>>
>>>
>>> ---
>>> Ronald Cohen
>>> Geophysical Laboratory
>>> Carnegie Institution
>>> 5251 Broad Branch Rd., N.W.
>>> Washington, D.C. 20015
>>> rco... at carnegiescience.edu
>>> office: 202-478-8937
>>> skype: ronaldcohen
>>> https://twitter.com/recohen3
>>> https://www.linkedin.com/profile/view?id=163327727
>>>
>>> On Tue, Mar 22, 2016 at 12:12 PM, Glen MacLachlan <mac... at gwu.edu>
>>> wrote:
>>>
>>>> Yeah, the ^ is a regular expression character that means ignore what
>>>> comes after -- think of it as a negation.
>>>>
>>>> Best,
>>>> Glen
>>>>
>>>> ==========================================
>>>> Glen MacLachlan, PhD
>>>> *HPC Specialist  *
>>>> *for Physical Sciences &*
>>>>
>>>> *Professorial Lecturer, Data Sciences*
>>>>
>>>> Office of Technology Services
>>>> The George Washington University
>>>> 725 21st Street
>>>> Washington, DC 20052
>>>> Suite 211, Corcoran Hall
>>>>
>>>> ==========================================
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Mar 22, 2016 at 11:04 AM, Cohen, Ronald <
>>>> rco... at carnegiescience.edu> wrote:
>>>>
>>>>> Thank you so much. It is a bit difficult because I did not set up this
>>>>> machine and do not have root access, but I know it is a mess. I backed up
>>>>> to just try the HPL benchmark.
>>>>> I am finding 100 GFLOPS one node performance on N=2000 and 16 cores,
>>>>> and 1.5 GFLOPS using two nodes, 8 cores per node. So there is definately
>>>>> something really wrong. I need to getthis working before I can worry about
>>>>> threads or cp2k.
>>>>> Was that a caret in your command above:
>>>>>
>>>>> mpirun --mca btl ^tcp
>>>>>
>>>>> ?
>>>>>
>>>>> I looked through my openmpi build and it seems to have found the
>>>>> infiniband includes such as they exist on the machine, but I could not the
>>>>> expected mxm or Mellanox drivers anywhere on the machine.
>>>>>
>>>>> I am CCing Peter Fox, the person who volunteers his time for this
>>>>> machine, and who has root access!
>>>>>
>>>>> Sincerely,
>>>>>
>>>>> Ron
>>>>>
>>>>>
>>>>> ---
>>>>> Ronald Cohen
>>>>> Geophysical Laboratory
>>>>> Carnegie Institution
>>>>> 5251 Broad Branch Rd., N.W.
>>>>> Washington, D.C. 20015
>>>>> rco... at carnegiescience.edu
>>>>> office: 202-478-8937
>>>>> skype: ronaldcohen
>>>>> https://twitter.com/recohen3
>>>>> https://www.linkedin.com/profile/view?id=163327727
>>>>>
>>>>> On Tue, Mar 22, 2016 at 10:32 AM, Glen MacLachlan <mac... at gwu.edu>
>>>>> wrote:
>>>>>
>>>>>> Hi Ron,
>>>>>>
>>>>>> There's a chance that OpenMPI wasn't configured to use IB properly.
>>>>>> Why don't you disable tcp and see if you are using IB?  It's easy
>>>>>>
>>>>>> mpirun --mca btl ^tcp ...
>>>>>>
>>>>>>
>>>>>> Regarding OpenMP:
>>>>>> I'm not sure we're converging on the same discussion anymore but
>>>>>> setting OMP_NUM_THREADS=1 does *not* disable multithreading overhead
>>>>>> -- you need to compile without the fopenmp to get a measure of true single
>>>>>> thread performance.
>>>>>>
>>>>>>
>>>>>> Best,
>>>>>> Glen
>>>>>>
>>>>>> ==========================================
>>>>>> Glen MacLachlan, PhD
>>>>>> *HPC Specialist  *
>>>>>> *for Physical Sciences &*
>>>>>>
>>>>>> *Professorial Lecturer, Data Sciences*
>>>>>>
>>>>>> Office of Technology Services
>>>>>> The George Washington University
>>>>>> 725 21st Street
>>>>>> Washington, DC 20052
>>>>>> Suite 211, Corcoran Hall
>>>>>>
>>>>>> ==========================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Mon, Mar 21, 2016 at 5:05 PM, Ronald Cohen <
>>>>>> rco... at carnegiescience.edu> wrote:
>>>>>>
>>>>>>> According to my experience in general, or the cp2k web pages in
>>>>>>> particular that is not the case.  Please see the performance page for
>>>>>>> cp2k.  The problem I am sure now is with the openmpi build not using the
>>>>>>> proper infiniband libraries or drivers.
>>>>>>>
>>>>>>> Thank you!
>>>>>>>
>>>>>>> Ron
>>>>>>>
>>>>>>> Sent from my iPad
>>>>>>>
>>>>>>> On Mar 21, 2016, at 5:36 PM, Glen MacLachlan <mac... at gwu.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>> It's hard to talk about the performance when you set OMP_NUM_THREADS
>>>>>>> = 1 because there is so much overhead associated with OpenMP that launching
>>>>>>> 1 thread almost always is a performance killer. In fact, OMP_NUM_THREADS=1
>>>>>>> never rivals single-threaded performance-wise because of that overhead. No
>>>>>>> one ever sets  OMP_NUM_THREADS=1 unless they are playing around...We never
>>>>>>> do that in production jobs. How about when you scale up to 4 or 8 threads?
>>>>>>>
>>>>>>> Glen
>>>>>>>
>>>>>>> P.S. I see you're in DC...so am I. I support CP2K for the chemists
>>>>>>> at GWU. Hope you aren't using Metro to get around the DMV :p
>>>>>>> On Mar 21, 2016 5:11 PM, "Cohen, Ronald" <rco... at carnegiescience.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Yes I am using hybrid mode. But even if I set OMP_NUM_THREADS=1
>>>>>>>> performance is terrible.
>>>>>>>>
>>>>>>>> ---
>>>>>>>> Ronald Cohen
>>>>>>>> Geophysical Laboratory
>>>>>>>> Carnegie Institution
>>>>>>>> 5251 Broad Branch Rd., N.W.
>>>>>>>> Washington, D.C. 20015
>>>>>>>> rco... at carnegiescience.edu
>>>>>>>> office: 202-478-8937
>>>>>>>> skype: ronaldcohen
>>>>>>>> https://twitter.com/recohen3
>>>>>>>> https://www.linkedin.com/profile/view?id=163327727
>>>>>>>>
>>>>>>>> On Mon, Mar 21, 2016 at 5:04 PM, Glen MacLachlan <mac... at gwu.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Are you conflating MPI with OpenMP? OMP_NUM_THREADS sets the
>>>>>>>>> number of threads used by OpenMP and OpenMP doesn't work on a distributed
>>>>>>>>> memory environment unless you piggyback on MPI which would be a hybrid use
>>>>>>>>> and I'm not sure CP2K ever worked optimally in hybrid mode or at least
>>>>>>>>> that's what I've gotten from reading the comments on the source code.
>>>>>>>>>
>>>>>>>>> As for MPI, are you sure your MPI stack was compiled with IB
>>>>>>>>> bindings? I had similar issues and the problem was that I wasn't actually
>>>>>>>>> using IB. If you can, disable eth and leave only IB and see what happens.
>>>>>>>>>
>>>>>>>>> Glen
>>>>>>>>> On Mar 21, 2016 4:48 PM, "Ronald Cohen" <
>>>>>>>>> rco... at carnegiescience.edu> wrote:
>>>>>>>>>
>>>>>>>>>> On the dco machine deepcarbon I find decent single node mpi
>>>>>>>>>> performnace, but running on the same number of processors across two nodes
>>>>>>>>>> is terrible, even with the infiniband interconect. This is the cp2k  H2O-64
>>>>>>>>>> benchmark:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 16 cores on 1 node: total time 530 seconds
>>>>>>>>>>  SUBROUTINE                       CALLS  ASD         SELF TIME
>>>>>>>>>>      TOTAL TIME
>>>>>>>>>>                                 MAXIMUM       AVERAGE  MAXIMUM
>>>>>>>>>>  AVERAGE  MAXIMUM
>>>>>>>>>>  CP2K                                 1  1.0    0.015    0.019
>>>>>>>>>>  530.306  530.306
>>>>>>>>>>  -
>>>>>>>>>>               -
>>>>>>>>>>  -                         MESSAGE PASSING PERFORMANCE
>>>>>>>>>>               -
>>>>>>>>>>  -
>>>>>>>>>>               -
>>>>>>>>>>
>>>>>>>>>>  -------------------------------------------------------------------------------
>>>>>>>>>>
>>>>>>>>>>  ROUTINE             CALLS  TOT TIME [s]  AVE VOLUME [Bytes]
>>>>>>>>>>  PERFORMANCE [MB/s]
>>>>>>>>>>  MP_Group                5         0.000
>>>>>>>>>>  MP_Bcast             4103         0.029              44140.
>>>>>>>>>>         6191.05
>>>>>>>>>>  MP_Allreduce        21860         7.077                263.
>>>>>>>>>>            0.81
>>>>>>>>>>  MP_Gather              62         0.008                320.
>>>>>>>>>>            2.53
>>>>>>>>>>  MP_Sync                54         0.001
>>>>>>>>>>  MP_Alltoall         19407        26.839             648289.
>>>>>>>>>>          468.77
>>>>>>>>>>  MP_ISendRecv        21600         0.091              94533.
>>>>>>>>>>        22371.25
>>>>>>>>>>  MP_Wait            238786        50.545
>>>>>>>>>>  MP_comm_split          50         0.004
>>>>>>>>>>  MP_ISend            97572         0.741             239205.
>>>>>>>>>>        31518.68
>>>>>>>>>>  MP_IRecv            97572         8.605             239170.
>>>>>>>>>>         2711.98
>>>>>>>>>>  MP_Memory          167778        45.018
>>>>>>>>>>
>>>>>>>>>>  -------------------------------------------------------------------------------
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> on 16 cores on 2 nodes: total time 5053 seconds !!
>>>>>>>>>>
>>>>>>>>>> SUBROUTINE                       CALLS  ASD         SELF TIME
>>>>>>>>>>    TOTAL TIME
>>>>>>>>>>                                 MAXIMUM       AVERAGE  MAXIMUM
>>>>>>>>>>  AVERAGE  MAXIMUM
>>>>>>>>>>  CP2K                                 1  1.0    0.311    0.363
>>>>>>>>>> 5052.904 5052.909
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> -------------------------------------------------------------------------------
>>>>>>>>>>  -
>>>>>>>>>>               -
>>>>>>>>>>  -                         MESSAGE PASSING PERFORMANCE
>>>>>>>>>>               -
>>>>>>>>>>  -
>>>>>>>>>>               -
>>>>>>>>>>
>>>>>>>>>>  -------------------------------------------------------------------------------
>>>>>>>>>>
>>>>>>>>>>  ROUTINE             CALLS  TOT TIME [s]  AVE VOLUME [Bytes]
>>>>>>>>>>  PERFORMANCE [MB/s]
>>>>>>>>>>  MP_Group                5         0.000
>>>>>>>>>>  MP_Bcast             4119         0.258              43968.
>>>>>>>>>>          700.70
>>>>>>>>>>  MP_Allreduce        21892      1546.186                263.
>>>>>>>>>>            0.00
>>>>>>>>>>  MP_Gather              62         0.049                320.
>>>>>>>>>>            0.40
>>>>>>>>>>  MP_Sync                54         0.071
>>>>>>>>>>  MP_Alltoall         19407      1507.024             648289.
>>>>>>>>>>            8.35
>>>>>>>>>>  MP_ISendRecv        21600         0.104              94533.
>>>>>>>>>>        19656.44
>>>>>>>>>>  MP_Wait            238786       513.507
>>>>>>>>>>  MP_comm_split          50         4.096
>>>>>>>>>>  MP_ISend            97572         1.102             239206.
>>>>>>>>>>        21176.09
>>>>>>>>>>  MP_IRecv            97572         2.739             239171.
>>>>>>>>>>         8520.75
>>>>>>>>>>  MP_Memory          167778        18.845
>>>>>>>>>>
>>>>>>>>>>  -------------------------------------------------------------------------------
>>>>>>>>>>
>>>>>>>>>> Any ideas? The code was built with the latest gfortran and I
>>>>>>>>>> built all of the dependencies, using this arch file.
>>>>>>>>>>
>>>>>>>>>> CC   = gcc
>>>>>>>>>> CPP  =
>>>>>>>>>> FC   = mpif90
>>>>>>>>>> LD   = mpif90
>>>>>>>>>> AR   = ar -r
>>>>>>>>>> PREFIX   = /home/rcohen
>>>>>>>>>> FFTW_INC   = $(PREFIX)/include
>>>>>>>>>> FFTW_LIB   = $(PREFIX)/lib
>>>>>>>>>> LIBINT_INC = $(PREFIX)/include
>>>>>>>>>> LIBINT_LIB = $(PREFIX)/lib
>>>>>>>>>> LIBXC_INC  = $(PREFIX)/include
>>>>>>>>>> LIBXC_LIB  = $(PREFIX)/lib
>>>>>>>>>> GCC_LIB = $(PREFIX)/gcc-trunk/lib
>>>>>>>>>> GCC_LIB64  = $(PREFIX)/gcc-trunk/lib64
>>>>>>>>>> GCC_INC = $(PREFIX)/gcc-trunk/include
>>>>>>>>>> DFLAGS  = -D__FFTW3 -D__LIBINT -D__LIBXC2\
>>>>>>>>>>     -D__LIBINT_MAX_AM=7 -D__LIBDERIV_MAX_AM1=6 -D__MAX_CONTR=4\
>>>>>>>>>>     -D__parallel -D__SCALAPACK -D__HAS_smm_dnn -D__ELPA3
>>>>>>>>>> CPPFLAGS   =
>>>>>>>>>> FCFLAGS = $(DFLAGS) -O2 -ffast-math -ffree-form
>>>>>>>>>> -ffree-line-length-none\
>>>>>>>>>>     -fopenmp -ftree-vectorize -funroll-loops\
>>>>>>>>>>     -mtune=native  \
>>>>>>>>>>      -I$(FFTW_INC) -I$(LIBINT_INC) -I$(LIBXC_INC)
>>>>>>>>>> -I$(MKLROOT)/include \
>>>>>>>>>>      -I$(GCC_INC)
>>>>>>>>>> -I$(PREFIX)/include/elpa_openmp-2015.11.001/modules
>>>>>>>>>> LIBS    =  \
>>>>>>>>>>     $(PREFIX)/lib/libscalapack.a
>>>>>>>>>> $(PREFIX)/lib/libsmm_dnn_sandybridge-2015-11-10.a \
>>>>>>>>>>     $(FFTW_LIB)/libfftw3.a\
>>>>>>>>>>     $(FFTW_LIB)/libfftw3_threads.a\
>>>>>>>>>>     $(LIBXC_LIB)/libxcf90.a\
>>>>>>>>>>     $(LIBXC_LIB)/libxc.a\
>>>>>>>>>>     $(PREFIX)/lib/liblapack.a  $(PREFIX)/lib/libtmglib.a
>>>>>>>>>> $(PREFIX)/lib/libgomp.a  \
>>>>>>>>>>     $(PREFIX)/lib/libderiv.a $(PREFIX)/lib/libint.a
>>>>>>>>>>  -lelpa_openmp -lgomp -lopenblas
>>>>>>>>>> LDFLAGS = $(FCFLAGS)  -L$(GCC_LIB64) -L$(GCC_LIB)
>>>>>>>>>> -static-libgfortran -L$(PREFIX)/lib
>>>>>>>>>>
>>>>>>>>>> It was run with  OMP_NUM_THREADS=2 on the two nodes and  OMP_NUM_THREADS=1
>>>>>>>>>> on the one node.
>>>>>>>>>> Running with  OMP_NUM_THREADS=1 on two nodes .
>>>>>>>>>>
>>>>>>>>>> I am now checking whether OMP_NUM_THREADS=1 on two nodes is
>>>>>>>>>> faster than OMP_NUM_THREADS=2 , but I do not think so.
>>>>>>>>>>
>>>>>>>>>> Ron Cohen
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
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>>>>>
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