[petsc-users] Installation question

Fri May 5 09:02:53 CDT 2017

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/conf/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]$
> > > > >
> > > >
> > > >
> > >
> >
> >
> 