[petsc-users] Installation question

Pham Pham pvsang002 at gmail.com
Fri May 5 05:45:30 CDT 2017 

*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]$
> > > >
> > >
> > >
> >
>
>
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