[CP2K:7586] terrible performance across infiniband

Cohen, Ronald rco... at carnegiescience.edu
Tue Mar 22 17:48:20 UTC 2016
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So I must be using IB but just getting poor performance. Attached is the
output of ompi_info --all  . The problem I have is there is essentially no
admin who is available, and I don't have root access.  Thank you again!


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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>>>>>>>>> Visit this group at https://groups.google.com/group/cp2k.
>>>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>>>
>>>>>>>> --
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>>>>>>>>
>>>>>>>
>>>>>>> --
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>>>>>>>
>>>>>> --
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>>>>>>
>>>>>> --
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>>>>>>
>>>>>
>>>>> --
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>>>>>
>>>>
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>>>>
>>>
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>>
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>
> --
> You received this message because you are subscribed to a topic in the
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