[petsc-users] Installation question

Matthew Knepley knepley at gmail.com
Fri May 5 11:26:25 CDT 2017 

On Fri, May 5, 2017 at 10:18 AM, Pham Pham <pvsang002 at gmail.com> 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 <balay at mcs.anl.gov> 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 at 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 <balay at mcs.anl.gov>
>> 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
>> > > > petsc-maint at mcs.anl.gov
>> > > > ************************************************************
>> ********
>> > > >
>> > > > Please explain what is happening?
>> > > >
>> > > > Thank you very much.
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > On Wed, Apr 19, 2017 at 11:43 PM, Satish Balay <balay at mcs.anl.gov>
>> > > 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 at 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 at atlas7-c10 petsc-3.7.5]$
>> > > > > > [mpepvs at 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
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