[petsc-users] petsc configuer time

[Barry Smith]

On Mar 13, 2014, at 4:03 PM, Dharmendar Reddy <dharmareddy84 at gmail.com> wrote:

> 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.

   It is many many smallish file loads back and forth during configure that can make it slow. This “machine” I take it is not yours but is some community workstation you wish to use? Do df / on it to see what filesystems are available and how much space they have. For example I did

~/Src/petsc  barry/add-snes-get-final-function-value $ df /
Filesystem   512-blocks      Used Available Capacity  iused    ifree %iused  Mounted on
/dev/disk0s2  975425848 398228040 576685808    41% 49842503 72085726   41%   /

and see I have tons of space available on /dev/disk0s2 so I do 

cd / 

and can look at what I might be able to use.

You may need to ask the system administrator of the machine to give you a directory on the machine that has lots of free space to use to work with PETSc.

Or are there are other workstations connected to the same fileserver that you could try and might be faster?

I personally do all development on my laptop because I hate waiting around for slow filesystems.

  Barry




> 

> 
> 
> 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)
>>