[petsc-users] petsc4py help with parallel execution

Balay, Satish balay at mcs.anl.gov
Fri Nov 16 12:13:36 CST 2018 

Likely this build is with gnu compilers.

https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/

The above suggests - the following might work:

'--with-blaslapack-lib=-L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl'

Satish

On Fri, 16 Nov 2018, Balay, Satish via petsc-users wrote:

> On Fri, 16 Nov 2018, Ivan Voznyuk via petsc-users wrote:
> 
> > Hi Satish,
> > Thanks for your reply.
> > 
> > Bad news... I tested 2 solutions that you proposed, none has worked.
> > 
> > 1. --with-blaslapack-dir=/opt/intel/mkl
> > --with-mkl_pardiso-dir=/opt/intel/mkl installed well, without any problems.
> > However, the code is still turning in sequential way.
> 
> Are you using Intel compilers?
> 
> please send configure.log for this.
> 
> Satish
> 
> > 2. When I changed -lmkl_sequential to -lmkl_intel_thread -liomp, he at
> > first did not find the liomp, so I had to create a symbolic link of libiomp5.so
> > to /lib.
> > At the launching of the .py code I had to go with:
> > export
> > LD_PRELOAD=/opt/intel/mkl/lib/intel64/libmkl_core.so:/opt/intel/mkl/lib/intel64/libmkl_sequential.so
> > and
> > export LD_LIBRARY_PATH=/opt/petsc/petsc1/arch-linux2-c-debug/lib/
> > 
> > But still it does not solve the given problem and code is still running
> > sequentially...
> > 
> > May be you have some other ideas?
> > 
> > Thanks,
> > Ivan
> > 
> > 
> > 
> > 
> > On Fri, Nov 16, 2018 at 6:11 PM Balay, Satish <balay at mcs.anl.gov> wrote:
> > 
> > > Yes PETSc prefers sequential MKL - as MPI handles parallelism.
> > >
> > > One way to trick petsc configure to use threaded MKL is to enable pardiso.
> > > i.e:
> > >
> > > --with-blaslapack-dir=/opt/intel/mkl --with-mkl_pardiso-dir=/opt/intel/mkl
> > >
> > >
> > > http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/11/15/configure_master_arch-pardiso_grind.log
> > >
> > > BLAS/LAPACK: -Wl,-rpath,/soft/com/packages/intel/16/u3/mkl/lib/intel64
> > > -L/soft/com/packages/intel/16/u3/mkl/lib/intel64 -lmkl_intel_lp64
> > > -lmkl_core -lmkl_intel_thread -liomp5 -ldl -lpthread
> > >
> > > Or you can manually specify the correct MKL library list [with
> > > threading] via --with-blaslapack-lib option.
> > >
> > > Satish
> > >
> > > On Fri, 16 Nov 2018, Ivan Voznyuk via petsc-users wrote:
> > >
> > > > Hi,
> > > > You were totally right: no miracle, parallelization does come from
> > > > multithreading. We checked Option 1/: played with OMP_NUM_THREADS=1 it
> > > > changed computational time.
> > > >
> > > > So, I reinstalled everything (starting with Ubuntu ending with petsc) and
> > > > configured the following things:
> > > >
> > > > - installed system's ompenmpi
> > > > - installed Intel MKL Blas / Lapack
> > > > - configured PETSC as ./configure --with-cc=mpicc --with-fc=mpif90
> > > > --with-cxx=mpicxx --with-blas-lapack-dir=/opt/intel/mkl/lib/intel64
> > > > --download-scalapack --download-mumps --with-hwloc --with-shared
> > > > --with-openmp=1 --with-pthread=1 --with-scalar-type=complex
> > > > hoping that it would take into account blas multithreading
> > > > - installed petsc4py
> > > >
> > > > However, I do not get any parallelization...
> > > > What I tried to do so far unsuccessfully :
> > > > - play with OMP_NUM_THREADS
> > > > - reinstall the system
> > > > - ldd PETSc.cpython-35m-x86_64-linux-gnu.so yields lld_result.txt (here
> > > > attached)
> > > > I noted that libmkl_sequential.so library there. Do you think this is
> > > > normal?
> > > > - I found a similar problem reported here:
> > > > https://lists.mcs.anl.gov/pipermail/petsc-users/2016-March/028803.html
> > > To
> > > > solve this problem, developers recommended to replace -lmkl_sequential to
> > > > -lmkl_intel_thread options in PETSC_ARCH/lib/conf/petscvariables.
> > > However,
> > > > I did not find something that would be named like this (it might be a
> > > > change of version)
> > > > - Anyway, I replaced lmkl_sequential to lmkl_intel_thread in every file
> > > of
> > > > PETSC, but it changed nothing.
> > > >
> > > > As a result, in the new make.log (here attached ) I have a parameter
> > > > #define PETSC_HAVE_LIBMKL_SEQUENTIAL 1 and option -lmkl_sequential
> > > >
> > > > Do you have any idea of what I should change in the initial options in
> > > > order to obtain the blas multithreding parallelization?
> > > >
> > > > Thanks a lot for your help!
> > > >
> > > > Ivan
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Fri, Nov 16, 2018 at 1:25 AM Dave May <dave.mayhem23 at gmail.com>
> > > wrote:
> > > >
> > > > >
> > > > >
> > > > > On Thu, 15 Nov 2018 at 17:44, Ivan via petsc-users <
> > > > > petsc-users at mcs.anl.gov> wrote:
> > > > >
> > > > >> Hi Stefano,
> > > > >>
> > > > >> In fact, yes, we look at the htop output (and the resulting
> > > computational
> > > > >> time ofc).
> > > > >>
> > > > >> In our code we use MUMPS, which indeed depends on blas / lapack. So I
> > > > >> think this might be it!
> > > > >>
> > > > >> I will definetely check it (I mean the difference between our MUMPS,
> > > > >> blas, lapack).
> > > > >>
> > > > >> If you have an idea of how we can verify on his PC that the source of
> > > his
> > > > >> parallelization does come from BLAS, please do not hesitate to tell
> > > me!
> > > > >>
> > > > >
> > > > > Option 1/
> > > > > * Set this environment variable
> > > > >   export OMP_NUM_THREADS=1
> > > > > * Re-run your "parallel" test.
> > > > > * If the performance differs (job runs slower) compared with your
> > > previous
> > > > > run where you inferred parallelism was being employed, you can safely
> > > > > assume that the parallelism observed comes from threads
> > > > >
> > > > > Option 2/
> > > > > * Re-configure PETSc to use a known BLAS implementation which does not
> > > > > support threads
> > > > > * Re-compile PETSc
> > > > > * Re-run your parallel test
> > > > > * If the performance differs (job runs slower) compared with your
> > > previous
> > > > > run where you inferred parallelism was being employed, you can safely
> > > > > assume that the parallelism observed comes from threads
> > > > >
> > > > > Option 3/
> > > > > * Use a PC which does not depend on BLAS at all,
> > > > > e.g. -pc_type jacobi -pc_type bjacobi
> > > > > * If the performance differs (job runs slower) compared with your
> > > previous
> > > > > run where you inferred parallelism was being employed, you can safely
> > > > > assume that the parallelism observed comes from BLAS + threads
> > > > >
> > > > >
> > > > >
> > > > >> Thanks!
> > > > >>
> > > > >> Ivan
> > > > >> On 15/11/2018 18:24, Stefano Zampini wrote:
> > > > >>
> > > > >> If you say your program is parallel by just looking at the output from
> > > > >> the top command, you are probably linking against a multithreaded blas
> > > > >> library
> > > > >>
> > > > >> Il giorno Gio 15 Nov 2018, 20:09 Matthew Knepley via petsc-users <
> > > > >> petsc-users at mcs.anl.gov> ha scritto:
> > > > >>
> > > > >>> On Thu, Nov 15, 2018 at 11:59 AM Ivan Voznyuk <
> > > > >>> ivan.voznyuk.work at gmail.com> wrote:
> > > > >>>
> > > > >>>> Hi Matthew,
> > > > >>>>
> > > > >>>> Does it mean that by using just command python3 simple_code.py
> > > (without
> > > > >>>> mpiexec) you *cannot* obtain a parallel execution?
> > > > >>>>
> > > > >>>
> > > > >>> As I wrote before, its not impossible. You could be directly calling
> > > > >>> PMI, but I do not think you are doing that.
> > > > >>>
> > > > >>>
> > > > >>>> It s been 5 days we are trying to understand with my colleague how
> > > he
> > > > >>>> managed to do so.
> > > > >>>> It means that by using simply python3 simple_code.py he gets 8
> > > > >>>> processors workiing.
> > > > >>>> By the way, we wrote in his code few lines:
> > > > >>>> rank = PETSc.COMM_WORLD.Get_rank()
> > > > >>>> size = PETSc.COMM_WORLD.Get_size()
> > > > >>>> and we got rank = 0, size = 1
> > > > >>>>
> > > > >>>
> > > > >>> This is MPI telling you that you are only running on 1 processes.
> > > > >>>
> > > > >>>
> > > > >>>> However, we compilator arrives to KSP.solve(), somehow it turns on 8
> > > > >>>> processors.
> > > > >>>>
> > > > >>>
> > > > >>> Why do you think its running on 8 processes?
> > > > >>>
> > > > >>>
> > > > >>>> This problem is solved on his PC in 5-8 sec (in parallel, using
> > > *python3
> > > > >>>> simple_code.py*), on mine it takes 70-90 secs (in sequantial, but
> > > with
> > > > >>>> the same command *python3 simple_code.py*)
> > > > >>>>
> > > > >>>
> > > > >>> I think its much more likely that there are differences in the solver
> > > > >>> (use -ksp_view to see exactly what solver was used), then
> > > > >>> to think it is parallelism. Moreover, you would never ever ever see
> > > that
> > > > >>> much speedup on a laptop since all these computations
> > > > >>> are bandwidth limited.
> > > > >>>
> > > > >>>   Thanks,
> > > > >>>
> > > > >>>      Matt
> > > > >>>
> > > > >>>
> > > > >>>> So, conclusion is that on his computer this code works in the same
> > > way
> > > > >>>> as scipy: all the code is executed in sequantial mode, but when it
> > > comes to
> > > > >>>> solution of system of linear equations, it runs on all available
> > > > >>>> processors. All this with just running python3 my_code.py (without
> > > any
> > > > >>>> mpi-smth)
> > > > >>>>
> > > > >>>> Is it an exception / abnormal behavior? I mean, is it something
> > > > >>>> irregular that you, developers, have never seen?
> > > > >>>>
> > > > >>>> Thanks and have a good evening!
> > > > >>>> Ivan
> > > > >>>>
> > > > >>>> P.S. I don't think I know the answer regarding Scipy...
> > > > >>>>
> > > > >>>>
> > > > >>>> On Thu, Nov 15, 2018 at 2:39 PM Matthew Knepley <knepley at gmail.com>
> > > > >>>> wrote:
> > > > >>>>
> > > > >>>>> On Thu, Nov 15, 2018 at 8:07 AM Ivan Voznyuk <
> > > > >>>>> ivan.voznyuk.work at gmail.com> wrote:
> > > > >>>>>
> > > > >>>>>> Hi Matthew,
> > > > >>>>>> Thanks for your reply!
> > > > >>>>>>
> > > > >>>>>> Let me precise what I mean by defining few questions:
> > > > >>>>>>
> > > > >>>>>> 1. In order to obtain a parallel execution of simple_code.py, do I
> > > > >>>>>> need to go with mpiexec python3 simple_code.py, or I can just
> > > launch
> > > > >>>>>> python3 simple_code.py?
> > > > >>>>>>
> > > > >>>>>
> > > > >>>>> mpiexec -n 2 python3 simple_code.py
> > > > >>>>>
> > > > >>>>>
> > > > >>>>>> 2. This simple_code.py consists of 2 parts: a) preparation of
> > > matrix
> > > > >>>>>> b) solving the system of linear equations with PETSc. If I launch
> > > mpirun
> > > > >>>>>> (or mpiexec) -np 8 python3 simple_code.py, I suppose that I will
> > > basically
> > > > >>>>>> obtain 8 matrices and 8 systems to solve. However, I need to
> > > prepare only
> > > > >>>>>> one matrix, but launch this code in parallel on 8 processors.
> > > > >>>>>>
> > > > >>>>>
> > > > >>>>> When you create the Mat object, you give it a communicator (here
> > > > >>>>> PETSC_COMM_WORLD). That allows us to distribute the data. This is
> > > all
> > > > >>>>> covered extensively in the manual and the online tutorials, as
> > > well as the
> > > > >>>>> example code.
> > > > >>>>>
> > > > >>>>>
> > > > >>>>>> In fact, here attached you will find a similar code
> > > (scipy_code.py)
> > > > >>>>>> with only one difference: the system of linear equations is
> > > solved with
> > > > >>>>>> scipy. So when I solve it, I can clearly see that the solution is
> > > obtained
> > > > >>>>>> in a parallel way. However, I do not use the command mpirun (or
> > > mpiexec). I
> > > > >>>>>> just go with python3 scipy_code.py.
> > > > >>>>>>
> > > > >>>>>
> > > > >>>>> Why do you think its running in parallel?
> > > > >>>>>
> > > > >>>>>   Thanks,
> > > > >>>>>
> > > > >>>>>      Matt
> > > > >>>>>
> > > > >>>>>
> > > > >>>>>> In this case, the first part (creation of the sparse matrix) is
> > > not
> > > > >>>>>> parallel, whereas the solution of system is found in a parallel
> > > way.
> > > > >>>>>> So my question is, Do you think that it s possible to have the
> > > same
> > > > >>>>>> behavior with PETSC? And what do I need for this?
> > > > >>>>>>
> > > > >>>>>> I am asking this because for my colleague it worked! It means
> > > that he
> > > > >>>>>> launches the simple_code.py on his computer using the command
> > > python3
> > > > >>>>>> simple_code.py (and not mpi-smth python3 simple_code.py) and he
> > > obtains a
> > > > >>>>>> parallel execution of the same code.
> > > > >>>>>>
> > > > >>>>>> Thanks for your help!
> > > > >>>>>> Ivan
> > > > >>>>>>
> > > > >>>>>>
> > > > >>>>>> On Thu, Nov 15, 2018 at 11:54 AM Matthew Knepley <
> > > knepley at gmail.com>
> > > > >>>>>> wrote:
> > > > >>>>>>
> > > > >>>>>>> On Thu, Nov 15, 2018 at 4:53 AM Ivan Voznyuk via petsc-users <
> > > > >>>>>>> petsc-users at mcs.anl.gov> wrote:
> > > > >>>>>>>
> > > > >>>>>>>> Dear PETSC community,
> > > > >>>>>>>>
> > > > >>>>>>>> I have a question regarding the parallel execution of petsc4py.
> > > > >>>>>>>>
> > > > >>>>>>>> I have a simple code (here attached simple_code.py) which
> > > solves a
> > > > >>>>>>>> system of linear equations Ax=b using petsc4py. To execute it,
> > > I use the
> > > > >>>>>>>> command python3 simple_code.py which yields a sequential
> > > performance. With
> > > > >>>>>>>> a colleague of my, we launched this code on his computer, and
> > > this time the
> > > > >>>>>>>> execution was in parallel. Although, he used the same command
> > > python3
> > > > >>>>>>>> simple_code.py (without mpirun, neither mpiexec).
> > > > >>>>>>>>
> > > > >>>>>>> I am not sure what you mean. To run MPI programs in parallel, you
> > > > >>>>>>> need a launcher like mpiexec or mpirun. There are Python
> > > programs (like
> > > > >>>>>>> nemesis) that use the launcher API directly (called PMI), but
> > > that is not
> > > > >>>>>>> part of petsc4py.
> > > > >>>>>>>
> > > > >>>>>>>   Thanks,
> > > > >>>>>>>
> > > > >>>>>>>      Matt
> > > > >>>>>>>
> > > > >>>>>>>> My configuration: Ubuntu x86_64 Ubuntu 16.04, Intel Core i7,
> > > PETSc
> > > > >>>>>>>> 3.10.2, PETSC_ARCH=arch-linux2-c-debug, petsc4py 3.10.0 in
> > > virtualenv
> > > > >>>>>>>>
> > > > >>>>>>>> In order to parallelize it, I have already tried:
> > > > >>>>>>>> - use 2 different PCs
> > > > >>>>>>>> - use Ubuntu 16.04, 18.04
> > > > >>>>>>>> - use different architectures (arch-linux2-c-debug,
> > > > >>>>>>>> linux-gnu-c-debug, etc)
> > > > >>>>>>>> - ofc use different configurations (my present config can be
> > > found
> > > > >>>>>>>> in make.log that I attached here)
> > > > >>>>>>>> - mpi from mpich, openmpi
> > > > >>>>>>>>
> > > > >>>>>>>> Nothing worked.
> > > > >>>>>>>>
> > > > >>>>>>>> Do you have any ideas?
> > > > >>>>>>>>
> > > > >>>>>>>> Thanks and have a good day,
> > > > >>>>>>>> Ivan
> > > > >>>>>>>>
> > > > >>>>>>>> --
> > > > >>>>>>>> Ivan VOZNYUK
> > > > >>>>>>>> PhD in Computational Electromagnetics
> > > > >>>>>>>>
> > > > >>>>>>>
> > > > >>>>>>>
> > > > >>>>>>> --
> > > > >>>>>>> What most experimenters take for granted before they begin their
> > > > >>>>>>> experiments is infinitely more interesting than any results to
> > > which their
> > > > >>>>>>> experiments lead.
> > > > >>>>>>> -- Norbert Wiener
> > > > >>>>>>>
> > > > >>>>>>> https://www.cse.buffalo.edu/~knepley/
> > > > >>>>>>> <http://www.cse.buffalo.edu/~knepley/>
> > > > >>>>>>>
> > > > >>>>>>
> > > > >>>>>>
> > > > >>>>>> --
> > > > >>>>>> Ivan VOZNYUK
> > > > >>>>>> PhD in Computational Electromagnetics
> > > > >>>>>> +33 (0)6.95.87.04.55
> > > > >>>>>> My webpage <https://ivanvoznyukwork.wixsite.com/webpage>
> > > > >>>>>> My LinkedIn <http://linkedin.com/in/ivan-voznyuk-b869b8106>
> > > > >>>>>>
> > > > >>>>>
> > > > >>>>>
> > > > >>>>> --
> > > > >>>>> What most experimenters take for granted before they begin their
> > > > >>>>> experiments is infinitely more interesting than any results to
> > > which their
> > > > >>>>> experiments lead.
> > > > >>>>> -- Norbert Wiener
> > > > >>>>>
> > > > >>>>> https://www.cse.buffalo.edu/~knepley/
> > > > >>>>> <http://www.cse.buffalo.edu/~knepley/>
> > > > >>>>>
> > > > >>>>
> > > > >>>>
> > > > >>>> --
> > > > >>>> Ivan VOZNYUK
> > > > >>>> PhD in Computational Electromagnetics
> > > > >>>> +33 (0)6.95.87.04.55
> > > > >>>> My webpage <https://ivanvoznyukwork.wixsite.com/webpage>
> > > > >>>> My LinkedIn <http://linkedin.com/in/ivan-voznyuk-b869b8106>
> > > > >>>>
> > > > >>>
> > > > >>>
> > > > >>> --
> > > > >>> What most experimenters take for granted before they begin their
> > > > >>> experiments is infinitely more interesting than any results to which
> > > their
> > > > >>> experiments lead.
> > > > >>> -- Norbert Wiener
> > > > >>>
> > > > >>> https://www.cse.buffalo.edu/~knepley/
> > > > >>> <http://www.cse.buffalo.edu/~knepley/>
> > > > >>>
> > > > >>
> > > >
> > > >
> > >
> > >
> > 
> > 
>

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