[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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>>>>>
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