20min to get to installing packages is still a lot. The other issues discussed in this thread could be the cause [intel compilers, search path on nfs, build on nfs]
Satish On Thu, 13 Mar 2014, Dharmendar Reddy wrote: > 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 > <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> > >>> >> 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) > >>> >> > >>> > >> >
