[CP2K:7589] terrible performance across infiniband

Cohen, Ronald rco... at carnegiescience.edu
Tue Mar 22 19:09:19 UTC 2016
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Yes, thank you so much. Basically I am getting mud even with 2 nodes, so
using more could not be better. I understand it is off topic, so won't
bother you. I have to get this working before I can worry about cp2k
performance!

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 3:07 PM, Glen MacLachlan <mac... at gwu.edu> wrote:

> 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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>>>>>>>>>>
>>>>>>>>>
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>>>>>>>>
>>>>>>>
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>>>>>
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