On Thu, 6 Jun 2013, Michele Rosso wrote: > Thanks Satish, now the compilation goes smooth, despite a warning during the > configuration step: > > =============================================================================== > Warning: PETSC_ARCH from environment does not match command-line > or name of script. > Warning: Using from command-line or name of script: > arch-test-cray, ignoring environment: interlagos > =============================================================================== > > I still have a problem though: when I compile my code the following warning > is issued: > > /u/sciteam/mrosso/LIBS/petsc-3.4.0/arch-test-cray/lib/libpetsc.a(dlimpl.o): In > function `PetscDLOpen': > /mnt/a/u/sciteam/mrosso/LIBS/petsc-3.4.0/src/sys/dll/dlimpl.c:109: warning: > Using 'dlopen' in statically linked applications requires at runtime the > shared libraries from the glibc version used for linking > /u/sciteam/mrosso/LIBS/petsc-3.4.0/arch-test-cray/lib/libpetsc.a(send.o): In > function `PetscOpenSocket': > /mnt/a/u/sciteam/mrosso/LIBS/petsc-3.4.0/src/sys/classes/viewer/impls/socket/send.c:97: > warning: Using 'gethostbyname' in statically linked applications requires at > runtime the shared libraries from the glibc version used for linking > > and the run stops because of the following error: > > libhugetlbfs: ERROR: RTLD_NEXT used in code not dynamically loaded
Do you get this error with PETSc examples as well? http://www.nersc.gov/users/computational-systems/hopper/running-jobs/trouble-shooting/ says: >>> Make sure to load the craype-hugepages2m module. <<< Satish > > Thanks again for your help. > > Michele > > > On Thu, 6 Jun 2013, Michele Rosso wrote: > > > > > Hi Satish, > > > > > > I tried what you suggested: > > > > > > #!/usr/bin/python > > > if __name__ == '__main__': > > > import sys > > > import os > > > sys.path.insert(0, os.path.abspath('config')) > > > import configure > > > configure_options = [ > > > 'PETSC_DIR=/u/sciteam/mrosso/LIBS/petsc-3.4.0', > > > '--with-cc=cc', > > > '--with-clib-autodetect=0', > > > '--with-cxx=CC', > > > '--with-cxxlib-autodetect=0', > > > '--with-fc=ftn', > > > '--with-fortranlib-autodetect=0', > > > '--with-x=0', > > > '--with-debgging=0', > > > '--COPTFLAGS=-O3', > > > '--FOPTFLAGS=-O3', > > > 'FFLAGS=-F -em', > > > 'LIBS=-L/opt/cray/cce/8.1.7/CC/x86-64/lib/x86-64/ -lcray-c++ -rts > > you have an extra space here ^ It > > should be -lcray-c++-rt > > > > Satish > > > > > > > -lcraystdc++ -lsupc++ -lgcc_eh', > > > 'PETSC_ARCH=arch-test-cray', > > > ] > > > configure.petsc_configure(configure_options) > > > > > > but now I receive another error: > > > > > > "C compiler you provided with -with-cc=cc does not work" > > > > > > I attached the log file. Thanks for your help. > > > > > > Michele > > > > > > > > > On 06/05/2013 02:15 PM, Satish Balay wrote: > > > > Sorry my configure cmd file was from an older test case for c++. > > > > > > > > Do you need c++ build of PETSc? If not - suggest removing > > > > --with-clanguage=C++ option. > > > > > > > > [Majority of use cases should not need --with-clanguage=C++ - even if > > > > user code is using PETSc from C++] > > > > > > > > If c++ is needed - you can try adding: CXXCPPFLAGS='-h gnu' > > > > > > > > Satish > > > > > > > > On Wed, 5 Jun 2013, Michele Rosso wrote: > > > > > > > > > Thank you Satish for your help. > > > > > I followed you instructions, but I am getting some errors during the > > > > > compilation. > > > > > I attached the python script I used to configure PETSc, and the logs > > > > > for > > > > > both > > > > > configure and make. > > > > > > > > > > > > > > > Michele > > > > > > > > > > On 05/31/2013 05:08 PM, Satish Balay wrote: > > > > > > The following is my configure command to build PETSc on a cray with > > > > > > cray compilers: > > > > > > > > > > > > $ cat reconfigure-arch-test-cray.py > > > > > > #!/usr/bin/python > > > > > > if __name__ == '__main__': > > > > > > import sys > > > > > > import os > > > > > > sys.path.insert(0, os.path.abspath('config')) > > > > > > import configure > > > > > > configure_options = [ > > > > > > '--with-cc=cc', > > > > > > '--with-clanguage=C++', > > > > > > '--with-clib-autodetect=0', > > > > > > '--with-cxx=CC', > > > > > > '--with-cxxlib-autodetect=0', > > > > > > '--with-fc=ftn', > > > > > > '--with-fortranlib-autodetect=0', > > > > > > '--with-x=0', > > > > > > 'FFLAGS=-F -em', > > > > > > 'LIBS=-L/opt/cray/cce/8.1.4/CC/x86-64/lib/x86-64/ > > > > > > -lcray-c++-rts > > > > > > -lcraystdc++ -lsupc++ -lgcc_eh', > > > > > > 'PETSC_ARCH=arch-test-cray', > > > > > > ] > > > > > > configure.petsc_configure(configure_options) > > > > > > <<<<<<<<< > > > > > > > > > > > > And you might have to look for the recommended optimization flags - > > > > > > and > > > > > > use > > > > > > with: > > > > > > --with-debgging=0 COPTFLAGS= FOPTFLAGS= CXXOPTFLAGS= etc. > > > > > > > > > > > > And on BlueWaters - you would have to remove the following lines > > > > > > from > > > > > > PETSC_ARCH/include/petscconf.h [before runing 'make all' to build > > > > > > the > > > > > > libraries] > > > > > > > > > > > > #ifndef PETSC_HAVE_GETPWUID > > > > > > #define PETSC_HAVE_GETPWUID 1 > > > > > > #endif > > > > > > <<<<< > > > > > > > > > > > > Satish > > > > > > > > > > > > On Fri, 31 May 2013, Michele Rosso wrote: > > > > > > > > > > > > > Thanks, but I'd rather use Cray since only a small part of my code > > > > > > > relies > > > > > > > on > > > > > > > PETSc and, as suggested by the BW staff, > > > > > > > Cray-compiled code performs generally better on Cray system. > > > > > > > > > > > > > > Michele > > > > > > > > > > > > > > On 05/31/2013 02:57 PM, Jed Brown wrote: > > > > > > > > Michele Rosso <[email protected]> writes: > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > > > > > I confirm that > > > > > > > > > > > > > > > > > > -pc_type gamg -pc_mg_cycle_type v > > > > > > > > > -pc_gamg_agg_nsmooths 1 > > > > > > > > > > > > > > > > > > produces the correct shift in PETSc 3.4. > > > > > > > > > So my problem is solved. I will upgrade to 3.4 in my > > > > > > > > > productive > > > > > > > > > machine installation. > > > > > > > > > It is a Cray machine (Blue Waters). Assuming I want to use the > > > > > > > > > Cray > > > > > > > > > compiler, which options should I use for ./configure > > > > > > > > > for the installation. > > > > > > > > Or the Intel compiler or GCC. PETSc should run at similar speed > > > > > > > > with > > > > > > > > any. IIRC, Cray recommends the Intel compiler on their machines > > > > > > > > with > > > > > > > > Intel CPUs. There are examples in config/examples/. > > > > > > > > > > > > >
