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Trilinos 101: Getting Started with Trilinos

Trilinos 101: Getting Started with Trilinos. November 7, 2006 8:30-9:30 a.m. Mike Heroux Jim Willenbring. Overview. Trilinos Web Page Obtaining Trilinos Tools for Users Mailman Bugzilla Configuring General configure options Platform and machine specific configure options

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Trilinos 101: Getting Started with Trilinos

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  1. Trilinos 101: Getting Started with Trilinos November 7, 2006 8:30-9:30 a.m. Mike Heroux Jim Willenbring

  2. Overview • Trilinos Web Page • Obtaining Trilinos • Tools for Users • Mailman • Bugzilla • Configuring • General configure options • Platform and machine specific configure options • Troubleshooting • Building and Installing • Testing • Improving Efficiency (of the build process) • Linking to Trilinos Libraries

  3. The Trilinos Home Page http://software.sandia.gov/trilinos/ • Highlights of the web page • Download page • User documentation • Getting started page • Installation guide • User guide • FAQ • Individual package documentation • ‘runtests’ make target documentation • External package capability

  4. Obtaining Trilinos • Instructions for obtaining Trilinos are available in • the Trilinos User Guide http://software.sandia.gov/trilinos/publications.html • the Installation Guide http://software.sandia.gov/trilinos/installation_manual.html • Download from the website http://software.sandia.gov/trilinos/downloads.html • Obtain a copy from the CVS repository • Not available for all users

  5. Tools for Users • Mailman • Users are encouraged to sign up for • Users lists for Trilinos and individual packages of interest • Announce lists for Trilinos and individual packages of interest • See http://software.sandia.gov/mailman/listinfo for the complete list of mail lists • For general questions trilinos-help@software.sandia.gov

  6. Tools for Users (cont.) • Bugzilla http://software.sandia.gov/bugzilla/ • Issue tracking tool • An account is required to file a “bug” • Can be used to report bugs or request new features • Please provide as much detail as possible (For example: Platform, OS, compiler versions, configure options, version of Trilinos, etc.)

  7. Configuring Trilinos • Find an in depth discussion in the Trilinos User Guide http://software.sandia.gov/trilinos/trilinosUserGuide.pdf • Trilinos Installation manual http://software.sandia.gov/trilinos/installation_manual.html

  8. Configuring Trilinos (cont.) • Trilinos uses Autoconf and Automake • Don’t just try “configure, make, make install” • Most platforms need more options • Even if the build is successful, the default set of packages and options probably will not suit your needs • If you don’t want to build everything, then don’t • Takes a long time to configure and build • Run into problems while building a package that is not needed

  9. Configuring Trilinos (cont.) • To see all Trilinos options type • ./configure --help=recursive • General Configure options • Determine which Trilinos packages should be built (--enable-<package_name>) • Consider using --disable-default-packages • Serial or MPI?

  10. Configuring Trilinos (cont.) • Platform and machine specific options • Common options online http://software.sandia.gov/trilinos/configuration_manual.html • Example configure invocation scripts • Examples only – customizations will be necessary • Can be found in the Trilinos directory structure in the Trilinos/sampleScripts/directory • For example redstorm_mpi_reddish1 • Users are encouraged to submit their scripts

  11. Configuring Trilinos (cont.) • Example invoke configure file for reddish: module load PrgEnv-pgimodule load mpich../configure --enable-mpi \CXX=mpicxx CC=mpicc F77=mpif77 \CPPFLAGS="-tp k8-64 -lacml -lpgmp -lpgthread" \--with-blas="-L/usr/pgi-6.0/linux86-64/6.0/lib -lacml -lpgmp -lpgthread" \--with-lapack="-L/usr/pgi-6.0/linux86-64/6.0/lib -lacml" \--enable-ml \--disable-default-packages#The lines before ../configure load the proper environment

  12. Configuring Trilinos (cont.) • Platform and machine specific options module load PrgEnv-pgimodule load mpich../configure --enable-mpi \CXX=mpicxx CC=mpicc F77=mpif77 \CPPFLAGS="-tp k8-64 -lacml -lpgmp -lpgthread" \--with-blas="-L/usr/pgi-6.0/linux86-64/6.0/lib -lacml -lpgmp -lpgthread" \--with-lapack="-L/usr/pgi-6.0/linux86-64/6.0/lib -lacml" \--enable-ml \--disable-default-packages

  13. Configuring Trilinos (cont.) • Troubleshooting • Most errors are due to system configurations • Look for errors in the invoke-configure • Autoconf is not able to detect spelling errors. • Line continuation problems (ex --enable-mpi \) • Look at the correct config.log file (created at configure time) • Default error output is very, very poor – often misleading • The config.log at the Trilinos level is not the correct config.log file. Go to the package level config.log file. For example: configure: error: /bin/sh '../../../packages/epetra/configure' failed for packages/epetra indicates that one should look at packages/epetra/config.log

  14. Troubleshooting using config.log • The config.log file is very long • To find what you need, search for the string “Cache” ## ------------------------ ## ## Cache variables. ## ## ----------------------- ## • The error that caused the configure failure can be found above this point, but typically not directly above

  15. Working Through a config.log File • Here is a common configure error • error: Cannot find lapack library, specify a path using --with-ldflags=-I<DIR> (ex. --with-dlflags=-I/usr/path/lib) or a specific library using --with-lapack=DIR/LIB (ex. --with-lapack=/usr/path/lib/libcxml.a) • Look for last successful configure check • In this case it would be a BLAS check • Directly beneath that check will be the failed check • Could be • Missing library (undefined symbol) • Incorrect path • ??

  16. Building and Installing Trilinos • To build Trilinos type make • To install Trilinos type make install

  17. Testing • Tests can be run individually after compilation • ‘runtests’ make targets http://software.sandia.gov/trilinos/developer/test_harness/runtests_make_target.html • To run the test suite (the tool will only attempt to run tests that were built), after "make“, type make runtests-serial • Can run tests for individual packages

  18. Testing • ‘runtests’ make targets • For MPI use make runtests-mpi • Must specify TRILINOS_MPI_GO in the environment or as an argument to make make runtests-mpi TRILINOS_MPI_GO="'mpiexec -np 2'" • Trilinos/commonTools/test/utilities/runtests –help • Installation Tests • Make a good “linking” test • <prefix>/examples • Not all of these work yet

  19. Improving Efficiency • All of these techniques are discussed in the Trilinos User Guide • Build only the packages that are needed • After Trilinos has been ported to a machine • --disable-tests --disable-examples ---disable-libcheck • Cannot use --disable-libcheck with makefile.export • make –j n • n is the number of jobs to create • Not supported by all versions of “make” • --cache-file=config.cache • Be sure to blow away if errors occur • Can put removal command in invoke-configure

  20. Linking to Trilinos Libraries • Makefile.export system makes linking easy • Files created in the include directory during install • Makefile.export.<package_name> files • Useful macros <PACKAGE_NAME>_INCLUDES <PACKAGE_NAME>_LIBS • Makefile.export.<package_name>.macros files • More macros including <PACKAGE_NAME>_CXXFLAGS <PACKAGE_NAME>_CXX • Use the macros in application makefiles

  21. Linking to Trilinos Libraries • Example: TRILINOS_PREFIX=/common/Trilinos/7.0.2 include $(TRILINOS_PREFIX)/include/Makefile.export.epetra.macros include $(TRILINOS_PREFIX)/include/Makefile.export.epetra INCDIR=$(EPETRA_INCLUDES) LIBDIR=$(EPETRA_LIBS) CXXFLAGS=$(INCDIR) $(EPETRA_CXXFLAGS) $(EPETRA_DEFS) CXX= $(EPETRA_CXX) • Typically must include several Makefile.export files

  22. Common Pitfalls • --with-gnumake • Compiler/library version mismatches • __gxx__personality • gfortran or g77 • Upgrading system and not recompiling 3PL’s • Linking to BLAS/LAPACK • Typo’s in configure arguments

  23. Where to Find Help • Getting started link http://software.sandia.gov/trilinos/getting_started.html • Help link from Trilinos home page http://software.sandia.gov/Trilinos/help.html • Online FAQ section http://software.sandia.gov/trilinos/faq.html • Trilinos User Guide http://software.sandia.gov/trilinos/publications.html

  24. Where to Find Help (cont.) • Submitting a bug report • Please provide as much detail as possible • Attach the appropriate config.log http://software.sandia.gov/trilinos/bug_reports.html • For general questions trilinos-help@software.sandia.gov • Trilinos Home Page http://software.sandia.gov/trilinos

  25. Discussion • Questions, comments?

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