[CP2K:7579] terrible performance across infiniband
Cohen, Ronald
rco... at carnegiescience.edu
Tue Mar 22 16:29:19 UTC 2016
So what was expected when I ran this test? THanks!
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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