On Fri, May 5, 2017 at 10:18 AM, Pham Pham <[email protected]> wrote:
> Hi Satish, > > It runs now, and shows a bad speed up: > Please help to improve this. > http://www.mcs.anl.gov/petsc/documentation/faq.html#computers The short answer is: You cannot improve this without buying a different machine. This is a fundamental algorithmic limitation that cannot be helped by threads, or vectorization, or anything else. Matt > Thank you. > > > > > On Fri, May 5, 2017 at 10:02 PM, Satish Balay <[email protected]> wrote: > >> With Intel MPI - its best to use mpiexec.hydra [and not mpiexec] >> >> So you can do: >> >> make PETSC_DIR=/home/svu/mpepvs/petsc/petsc-3.7.5 >> PETSC_ARCH=arch-linux-cxx-opt MPIEXEC=mpiexec.hydra test >> >> >> [you can also specify --with-mpiexec=mpiexec.hydra at configure time] >> >> Satish >> >> >> On Fri, 5 May 2017, Pham Pham wrote: >> >> > *Hi,* >> > *I can configure now, but fail when testing:* >> > >> > [mpepvs@atlas7-c10 petsc-3.7.5]$ make >> > PETSC_DIR=/home/svu/mpepvs/petsc/petsc-3.7.5 >> PETSC_ARCH=arch-linux-cxx-opt >> > test Running test examples to verify correct installation >> > Using PETSC_DIR=/home/svu/mpepvs/petsc/petsc-3.7.5 and >> > PETSC_ARCH=arch-linux-cxx-opt >> > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 >> MPI >> > process >> > See http://www.mcs.anl.gov/petsc/documentation/faq.html >> > mpiexec_atlas7-c10: cannot connect to local mpd >> (/tmp/mpd2.console_mpepvs); >> > possible causes: >> > 1. no mpd is running on this host >> > 2. an mpd is running but was started without a "console" (-n option) >> > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 >> MPI >> > processes >> > See http://www.mcs.anl.gov/petsc/documentation/faq.html >> > mpiexec_atlas7-c10: cannot connect to local mpd >> (/tmp/mpd2.console_mpepvs); >> > possible causes: >> > 1. no mpd is running on this host >> > 2. an mpd is running but was started without a "console" (-n option) >> > Possible error running Fortran example src/snes/examples/tutorials/ex5f >> > with 1 MPI process >> > See http://www.mcs.anl.gov/petsc/documentation/faq.html >> > mpiexec_atlas7-c10: cannot connect to local mpd >> (/tmp/mpd2.console_mpepvs); >> > possible causes: >> > 1. no mpd is running on this host >> > 2. an mpd is running but was started without a "console" (-n option) >> > Completed test examples >> > ========================================= >> > Now to evaluate the computer systems you plan use - do: >> > make PETSC_DIR=/home/svu/mpepvs/petsc/petsc-3.7.5 >> > PETSC_ARCH=arch-linux-cxx-opt streams >> > >> > >> > >> > >> > *Please help on this.* >> > *Many thanks!* >> > >> > >> > On Thu, Apr 20, 2017 at 2:02 AM, Satish Balay <[email protected]> >> wrote: >> > >> > > Sorry - should have mentioned: >> > > >> > > do 'rm -rf arch-linux-cxx-opt' and rerun configure again. >> > > >> > > The mpich install from previous build [that is currently in >> > > arch-linux-cxx-opt/] >> > > is conflicting with --with-mpi-dir=/app1/centos6.3/gnu/mvapich2-1.9/ >> > > >> > > Satish >> > > >> > > >> > > On Wed, 19 Apr 2017, Pham Pham wrote: >> > > >> > > > I reconfigured PETSs with installed MPI, however, I got serous >> error: >> > > > >> > > > **************************ERROR***************************** >> ******** >> > > > Error during compile, check arch-linux-cxx-opt/lib/petsc/c >> onf/make.log >> > > > Send it and arch-linux-cxx-opt/lib/petsc/conf/configure.log to >> > > > [email protected] >> > > > ************************************************************ >> ******** >> > > > >> > > > Please explain what is happening? >> > > > >> > > > Thank you very much. >> > > > >> > > > >> > > > >> > > > >> > > > On Wed, Apr 19, 2017 at 11:43 PM, Satish Balay <[email protected]> >> > > wrote: >> > > > >> > > > > Presumably your cluster already has a recommended MPI to use >> [which is >> > > > > already installed. So you should use that - instead of >> > > > > --download-mpich=1 >> > > > > >> > > > > Satish >> > > > > >> > > > > On Wed, 19 Apr 2017, Pham Pham wrote: >> > > > > >> > > > > > Hi, >> > > > > > >> > > > > > I just installed petsc-3.7.5 into my university cluster. When >> > > evaluating >> > > > > > the computer system, PETSc reports "It appears you have 1 >> node(s)", I >> > > > > donot >> > > > > > understand this, since the system is a multinodes system. Could >> you >> > > > > please >> > > > > > explain this to me? >> > > > > > >> > > > > > Thank you very much. >> > > > > > >> > > > > > S. >> > > > > > >> > > > > > Output: >> > > > > > ========================================= >> > > > > > Now to evaluate the computer systems you plan use - do: >> > > > > > make PETSC_DIR=/home/svu/mpepvs/petsc/petsc-3.7.5 >> > > > > > PETSC_ARCH=arch-linux-cxx-opt streams >> > > > > > [mpepvs@atlas7-c10 petsc-3.7.5]$ make >> > > > > > PETSC_DIR=/home/svu/mpepvs/petsc/petsc-3.7.5 >> > > > > PETSC_ARCH=arch-linux-cxx-opt >> > > > > > streams >> > > > > > cd src/benchmarks/streams; /usr/bin/gmake --no-print-directory >> > > > > > PETSC_DIR=/home/svu/mpepvs/petsc/petsc-3.7.5 >> > > > > PETSC_ARCH=arch-linux-cxx-opt >> > > > > > streams >> > > > > > /home/svu/mpepvs/petsc/petsc-3.7.5/arch-linux-cxx-opt/bin/mpicxx >> -o >> > > > > > MPIVersion.o -c -Wall -Wwrite-strings -Wno-strict-aliasing >> > > > > > -Wno-unknown-pragmas -fvisibility=hidden -g -O >> > > > > > -I/home/svu/mpepvs/petsc/petsc-3.7.5/include >> > > > > > -I/home/svu/mpepvs/petsc/petsc-3.7.5/arch-linux-cxx-opt/include >> > > > > > `pwd`/MPIVersion.c >> > > > > > Running streams with >> > > > > > '/home/svu/mpepvs/petsc/petsc-3.7.5/arch-linux-cxx-opt/bin/mpiexec >> ' >> > > > > using >> > > > > > 'NPMAX=12' >> > > > > > Number of MPI processes 1 Processor names atlas7-c10 >> > > > > > Triad: 9137.5025 Rate (MB/s) >> > > > > > Number of MPI processes 2 Processor names atlas7-c10 atlas7-c10 >> > > > > > Triad: 9707.2815 Rate (MB/s) >> > > > > > Number of MPI processes 3 Processor names atlas7-c10 atlas7-c10 >> > > > > atlas7-c10 >> > > > > > Triad: 13559.5275 Rate (MB/s) >> > > > > > Number of MPI processes 4 Processor names atlas7-c10 atlas7-c10 >> > > > > atlas7-c10 >> > > > > > atlas7-c10 >> > > > > > Triad: 14193.0597 Rate (MB/s) >> > > > > > Number of MPI processes 5 Processor names atlas7-c10 atlas7-c10 >> > > > > atlas7-c10 >> > > > > > atlas7-c10 atlas7-c10 >> > > > > > Triad: 14492.9234 Rate (MB/s) >> > > > > > Number of MPI processes 6 Processor names atlas7-c10 atlas7-c10 >> > > > > atlas7-c10 >> > > > > > atlas7-c10 atlas7-c10 atlas7-c10 >> > > > > > Triad: 15476.5912 Rate (MB/s) >> > > > > > Number of MPI processes 7 Processor names atlas7-c10 atlas7-c10 >> > > > > atlas7-c10 >> > > > > > atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 >> > > > > > Triad: 15148.7388 Rate (MB/s) >> > > > > > Number of MPI processes 8 Processor names atlas7-c10 atlas7-c10 >> > > > > atlas7-c10 >> > > > > > atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 >> > > > > > Triad: 15799.1290 Rate (MB/s) >> > > > > > Number of MPI processes 9 Processor names atlas7-c10 atlas7-c10 >> > > > > atlas7-c10 >> > > > > > atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 >> atlas7-c10 >> > > > > > Triad: 15671.3104 Rate (MB/s) >> > > > > > Number of MPI processes 10 Processor names atlas7-c10 >> atlas7-c10 >> > > > > > atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 >> atlas7-c10 >> > > > > > atlas7-c10 atlas7-c10 >> > > > > > Triad: 15601.4754 Rate (MB/s) >> > > > > > Number of MPI processes 11 Processor names atlas7-c10 >> atlas7-c10 >> > > > > > atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 >> atlas7-c10 >> > > > > > atlas7-c10 atlas7-c10 atlas7-c10 >> > > > > > Triad: 15434.5790 Rate (MB/s) >> > > > > > Number of MPI processes 12 Processor names atlas7-c10 >> atlas7-c10 >> > > > > > atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 >> atlas7-c10 >> > > > > > atlas7-c10 atlas7-c10 atlas7-c10 atlas7-c10 >> > > > > > Triad: 15134.1263 Rate (MB/s) >> > > > > > ------------------------------------------------ >> > > > > > np speedup >> > > > > > 1 1.0 >> > > > > > 2 1.06 >> > > > > > 3 1.48 >> > > > > > 4 1.55 >> > > > > > 5 1.59 >> > > > > > 6 1.69 >> > > > > > 7 1.66 >> > > > > > 8 1.73 >> > > > > > 9 1.72 >> > > > > > 10 1.71 >> > > > > > 11 1.69 >> > > > > > 12 1.66 >> > > > > > Estimation of possible speedup of MPI programs based on Streams >> > > > > benchmark. >> > > > > > It appears you have 1 node(s) >> > > > > > Unable to plot speedup to a file >> > > > > > Unable to open matplotlib to plot speedup >> > > > > > [mpepvs@atlas7-c10 petsc-3.7.5]$ >> > > > > > [mpepvs@atlas7-c10 petsc-3.7.5]$ >> > > > > > >> > > > > >> > > > > >> > > > >> > > >> > > >> > >> >> > -- 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
