[petsc-users] petsc configuer time

[Dharmendar Reddy]

The issue was due to python. It is not the python from Enthought, but
the python which was installed in another custom software which was in
the path.
Now the configure takes about 20 minutes  before it begins installing
the packages.

Thanks
Reddy

On Thu, Mar 13, 2014 at 6:12 PM, Dharmendar Reddy
<dharmareddy84 at gmail.com> wrote:
> I was suspecting python may be the cause,
> I am using: Enthought Canopy Python 2.7.3 | 64-bit | (default, Aug  8
> 2013, 05:43:23)
>
> I will try other approaches.
>
> Thanks
> Reddy
>
>
> On Thu, Mar 13, 2014 at 6:04 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>> Hm - configure should first print the 'executing' message - and then
>> run the command.
>>
>> If its hanging at 'pusing language' message - I'm not sure what the
>> cause is.
>>
>> Perhaps the python stdout-buffer-flush is off-sync. [and its icc/ifort
>> thats hanging]. Or there is a problem with python on this machine?
>>
>> 2 things you can try to confirm.
>>
>> 1. run configure with gcc/gfortran and see if thats quicker.
>> If so - then intel compilers are the cause for slowdown.
>>
>> 2. Try configure with the option --useThreads=0 and see if this makes a difference.
>> [or tray a different python]
>>
>> Satish
>>
>> On Thu, 13 Mar 2014, Dharmendar Reddy wrote:
>>
>>> I see that at every pushing language, the screen statys there for a
>>> while and the compile execute commands quickly appear and go....
>>>
>>>
>>> On Thu, Mar 13, 2014 at 4:23 PM, Balay, Satish <balay at mcs.anl.gov> wrote:
>>> > You can try "  tail -f configure.log" to see where  its hanging during the
>>> > run
>>> >
>>> > Intel compilers can hang waiting for response from license server.
>>> >
>>> > Satish
>>> > ________________________________
>>> > From: Dharmendar Reddy
>>> > Sent: 3/13/2014 2:03 PM
>>> > To: Smith, Barry F.
>>> > Cc: PETSc users list
>>> > Subject: Re: [petsc-users] petsc configuer time
>>> >
>>> > Yes, my home directory is mounted on nfs. And i have configured and
>>> > installed petsc many times on my laptop and TACC stampede (which also
>>> > has my home directory mounted on network file system).  But the
>>> > particular computer that i am working on now has been extremely slow
>>> > when it comes to petsc configure. Any suggestions on how i can fix
>>> > this ? I do not have a choice of not having my home on nfs.
>>> >
>>> >
>>> > Otherwise, i do not see big disk i/o impact even when i visualize
>>> > large ( > 100 MB ) files for visualization.
>>> >
>>> >
>>> >
>>> > On Thu, Mar 13, 2014 at 3:55 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>> >>
>>> >>    The long time is pretty much always due to a slow file system (it takes
>>> >> about 3 minutes with my laptop using the local disk) but on a desktop
>>> >> machine using a network file system it can take up to 20 minutes.  We
>>> >> generally always build on a local disk; since disk space is so cheap now
>>> >> pretty much any machine has gigabytes free of disk space that you can use to
>>> >> build on.
>>> >>
>>> >>    I think two hours is totally unacceptably long. What type of system are
>>> >> you building on and where is the file system? My guess is /home/reddy is off
>>> >> on some slow filesystem away from the machine you are compiling on.
>>> >>
>>> >>    Barry
>>> >>
>>> >> On Mar 13, 2014, at 3:29 PM, Dharmendar Reddy <dharmareddy84 at gmail.com>
>>> >> wrote:
>>> >>
>>> >>> Hello,
>>> >>>         How long does it take to configure petsc ? I understand that
>>> >>> it depends on the options, but i am find the particular version i have
>>> >>> is taking very long time (nearly 2 hours) before it begins configuring
>>> >>> packages.
>>> >>>
>>> >>> I am using intel MPI and intel compilers.
>>> >>>
>>> >>> I am using the following config opts:
>>> >>> PETSC_VERSION   = petsc-3.4.3
>>> >>> MPICC=mpiicc
>>> >>> MPIF90=mpiifort
>>> >>> MPICXX=mpiicpc
>>> >>> COMPILERS = --with-cc="$(MPICC)" --with-fc="$(MPIF90)"
>>> >>> --with-cxx="$(MPICXX)" COPTFLAGS="$(O_LEVEL)" CXXOPTFLAGS="$(O_LEVEL)"
>>> >>> FOPTFLAGS="$(O_LEVEL)"
>>> >>> # COMPILERS = --with-mpi-dir=$(MPI_HOME)
>>> >>>
>>> >>> BLAS_LAPACK     = $(PETSC_BLAS_LAPACK_DIR)
>>> >>> PETSCExtPackagePath = /home/reddy/libs/petsc
>>> >>> METISPATH=$(PETSCExtPackagePath)/metis-5.0.2-p3.tar.gz
>>> >>> MUMPSPATH=$(PETSCExtPackagePath)/MUMPS_4.10.0-p3.tar.gz
>>> >>> PARMETISPATH=$(PETSCExtPackagePath)/parmetis-4.0.2-p5.tar.gz
>>> >>> SUPERLUPATH=$(PETSCExtPackagePath)/superlu_dist_3.3.tar.gz
>>> >>> SCALPACKINC=$(MKLHOME)/include
>>> >>> SCALPACKLIB="$(MKLROOT)/lib/intel64/libmkl_scalapack_lp64.a
>>> >>> -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a
>>> >>> $(MKLROOT)/lib/intel64/libmkl_core.a
>>> >>> $(MKLROOT)/lib/intel64/libmkl_sequential.a -Wl,--end-group
>>> >>> $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a -lpthread -lm"
>>> >>> #BLACSINC=$(MKLHOME)/include
>>> >>> #BLACSLIB=$(MKLHOME)/lib/intel64/libmkl_blacs_intelmpi_lp64.a
>>> >>> confOptsCommon = --with-x=0 --with-make-np=12 --with-hdf5
>>> >>> --with-hdf5-dir=$(HDF5_DIR) --with-single-library=0  --with-pic=1
>>> >>> --with-shared-libraries=0 --with-blas-lapack-dir=$(BLAS_LAPACK)
>>> >>> --with-clanguage=C++ --with-fortran --with-debugging=1 $(COMPILERS)
>>> >>> --download-metis=$(METISPATH) --download-parmetis=$(PARMETISPATH)
>>> >>> --download-superlu_dist=$(SUPERLUPATH) --download-mumps=$(MUMPSPATH)
>>> >>> --with-scalapack-include=$(SCALPACKINC)
>>> >>> --with-scalapack-lib=$(SCALPACKLIB)
>>> >>> #--with-blacs-include=$(BLACSINC) --with-blacs-lib=$(BLACSLIB)
>>> >>>
>>> >>> ### configure command
>>> >>> ./configure --with-scalar-type=real $(confOptsCommon)
>>> >>
>>>
>>