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dune [2010/06/30 07:10] – créée gerarddune [2014/12/29 09:21] – [nouvelle version de solver-bench (0.45) plus slepc] gerard
Ligne 11: Ligne 11:
 [devel1@octopus ~/src]$ ./dune-common-2.0/bin/dunecontrol all [devel1@octopus ~/src]$ ./dune-common-2.0/bin/dunecontrol all
 [devel1@octopus dune]$ ./dune-common-2.0/bin/dunecontrol --opts=config.opts all [devel1@octopus dune]$ ./dune-common-2.0/bin/dunecontrol --opts=config.opts all
 +
 +</code>
 +
 +====== installer une nouvelle version de solver-bench ======
 +  * dans ''/local/apps/src/dune''
 +  * déplacer l'ancienne version
 +  * récuperer le fichier do_work.sh
 +  * ne pas oublier de rajouter **-lmpi** dans **LIBS** (voir ci-dessous)
 +
 +====== benchmark ======
 +  * R.K a installé /local/apps/src/dune/solver-bench-0.1beta
 +  * recopié ce dossier dans /home/henry/projects/
 +  * dans solver-bench-0.1beta/src, il y a un programme de bench :
 +<code>
 +[henry@octopus src]$ ./benchruntime 
 +Usage: ./benchruntime <datafile.xdr> < UMFPACK = 0 | ISTL-CG = 1 | ISTL-BiCGstab = 2 | OEM-CG = 3 | OEM-GMRES = 4 > 
 +
 +Residual: euclidian = 1.21829e-29  infinity = 1.77636e-15
 +
 +ERROR: UMFPack not available, re-configure with --with-umfpack=PATH_TO_UMFPACK!! 
 +UMFPACK:  Final errors: euclidian = 0.493997  infinity = 0.561107
 +Solution needed 0 seconds. 
 +
 +</code>
 +avec un autre solveur et une autre matrice:
 +<code>
 +[henry@octopus src]$ ./benchruntime ../../herbin/AKWAK/APPS/TROISD/resultats/matrixfile_1 2
 +Residual: euclidian = 2.43625e-17  infinity = 3.3555e-09
 +Reduction to achieve: 3.10816e-19
 +=== BiCGSTABSolver
 + Iter          Defect            Rate
 +    0          8.85338
 +  0.5          4.34976         0.491311
 +    1         0.477752         0.109834
 +  1.5         0.328951         0.688539
 +    2       0.00710675        0.0216043
 +  2.5       0.00885003           1.2453
 +    3       0.00118422          0.13381
 +  3.5      0.000483821         0.408555
 +    4       2.3323e-05        0.0482058
 +  4.5      4.16061e-06         0.178391
 +    5      1.17866e-06         0.283291
 +  5.5      7.05524e-07          0.59858
 +    6      7.83043e-09        0.0110987
 +  6.5      6.49605e-10         0.082959
 +    7      9.89328e-11         0.152297
 +  7.5       1.2981e-11          0.13121
 +    8      1.51537e-12         0.116738
 +  8.5      1.62378e-13         0.107154
 +    9      3.17988e-14         0.195832
 +  9.5      1.81317e-15        0.0570202
 +   10       2.7893e-16         0.153835
 + 10.5      1.04694e-17        0.0375342
 +   11      2.14529e-18          0.20491
 +=== rate=0.0203082, T=0, TIT=0, IT=11
 +Difference : 2.91461e-09
 +ISTL-BiCGstab:  Final errors: euclidian = 8.49496e-18  infinity = 1.88764e-09
 +Solution needed 0 seconds. 
 +
 +</code>
 +
 +===== avec umfpack =====
 +  * ajouter umfpack avec le script fourni par R.K. : [[umfpack_installer.sh]]
 +  * umfpack s'installe dans le répertoire courant: /local/apps/src/dune/UMFPACK, en version 5.4.0
 +  * on recompile dune et le module solver-bench avec umfpack
 +  * on vérifie que c'est pris en compte:
 +<code>
 +[henry@octopus src]$ ./benchruntime ../../herbin/AKWAK/APPS/TROISD/resultats/matrixfile_1 0
 +Residual: euclidian = 2.43625e-17  infinity = 3.3555e-09
 +nR = 93 nC = 93 nZ = 1467
 +Rows offset is 0
 +Overall time for UMFPACK solve: 0.001
 +UMFPACK:  Final errors: euclidian = 17.687  infinity = 0.996845
 +Solution needed 0 seconds.
 +
 +</code>
 +
 +
 +====== petsc ======
 +<code>
 +[devel1@octopus petsc-3.1-p4]$ export PETSC_DIR=$PWD                            
 +[devel1@octopus petsc-3.1-p4]$ ./config/configure.py --with-cc=gcc --with-fc=gfortran
 +...
 +Compilers:
 +  C Compiler:         gcc  -Wall -Wwrite-strings -Wno-strict-aliasing -g3 
 +  Fortran Compiler:   gfortran  -Wall -Wno-unused-variable -g  
 +Linkers:
 +  Static linker:   /usr/bin/ar cr
 +X11:
 +  Includes: 
 +  Library:  -lX11
 +BLAS/LAPACK: -llapack -lblas
 +PETSc:
 +  PETSC_ARCH: linux-gnu-c-debug
 +  PETSC_DIR: /local/apps/src/petsc-3.1-p4
 +  Clanguage: C
 +  Scalar type: real
 +  Precision: double
 +  Memory alignment: 16
 +  shared libraries: disabled
 +  dynamic libraries: disabled
 +xxx=========================================================================xxx
 +   Configure stage complete. Now build PETSc libraries with:
 +   make PETSC_DIR=/local/apps/src/petsc-3.1-p4 PETSC_ARCH=linux-gnu-c-debug all
 +xxx=========================================================================xxx
 +[devel1@octopus petsc-3.1-p4]$      
 +
 +[devel1@octopus petsc-3.1-p4]$ make PETSC_DIR=/local/apps/src/petsc-3.1-p4 PETSC_ARCH=linux-gnu-c-debug test
 +Running test examples to verify correct installation
 +C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process
 +Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process
 +Completed test examples
 +    
 +</code>
 +
 +===== nouvelle version de solver-bench (0.45) plus slepc =====
 +<note>L'exemple ci-dessous est avec le mode debug, voir les fichiers do_work.sh pour le code optimisé</note>
 +
 +<code>
 +bash-3.2$ ./config/configure.py --with-mpi=0
 +bash-3.2$ make PETSC_DIR=/local/apps/src/dune/petsc-3.1-p5 PETSC_ARCH=linux-gnu-c-debug all
 +bash-3.2$ make PETSC_DIR=/local/apps/src/dune/petsc-3.1-p5 PETSC_ARCH=linux-gnu-c-debug test
 +
 +bash-3.2$ export PETSC_DIR=/local/apps/src/dune/petsc-3.1-p5
 +bash-3.2$ export PETSC_ARCH=linux-gnu-c-debug
 +bash-3.2$ export SLEPC_DIR=/local/apps/src/dune/slepc-3.1-p4
 +bash-4.2$ cd ../slepc-3.1-p4
 +bash-3.2$ ./configure 
 +bash-3.2$ make
 +bash-3.2$ make test
 +Running test examples to verify correct installation
 +C/C++ example src/examples/ex1 run successfully with 1 MPI process
 +Fortran example src/examples/ex1f run successfully with 1 MPI process
 +Completed test examples
 +
 +</code>
 +
 +après, on essaie:
 +<code>
 +bash-3.2$ ./installdune.sh solver-comp
 +
 +
 +but i saw in the messages that petsc and slepc weren't found:
 +
 +Found the following Dune-components: 
 +
 +----------------------------------------
 +
 +dune-common.............: yes (/local/apps/src/dune/Dune) version 2.0
 +dune-istl...............: yes (/local/apps/src/dune/Dune) version 2.0
 +BLAS....................: yes
 +METIS...................: no
 +MPI.....................: no
 +PETSC...................: no
 +ParMETIS................: no
 +SLEPC...................: no
 +SuperLU-DIST............: no
 +SuperLU.................: no
 +UMFPACK.................: yes (/local/apps/src/dune/UMFPACK)
 +
 +----------------------------------------
 +
 +See ./configure --help and config.log for reasons why a component wasn't found
 +</code>
 +si on édite config.log:
 +<code>
 +./configure CXX=g++ CXXFLAGS=-O3 -funroll-loops -finline-functions -DNDEBUG \
 +--prefix=/local/apps/src/dune/Dune \
 +--enable-parallel \
 +--disable-documentation --disable-compilercheck --disable-mpiruntest \
 +--with-umfpack=/local/apps/src/dune/UMFPACK \
 +--with-dune-common=/local/apps/src/dune/Dune --with-dune-istl=/local/apps/src/dune/Dune
 +
 +</code>
 +
 +alors que pour la derneire version:
 +<code>
 +./configure CXX=g++ CXXFLAGS="-O3 -funroll-loops -finline-functions -DNDEBUG" \
 +--prefix=/local/apps/src/dune/Dune \
 +--disable-documentation --disable-compilercheck --disable-mpiruntest \
 +--with-umfpack=/local/apps/src/dune/UMFPACK \
 +--with-petsc=/local/apps/src/petsc-3.1-p5 \
 +--with-dune-common=/local/apps/src/dune/Dune \
 +--with-dune-istl=/local/apps/src/dune/Dune \
 +CPPFLAGS="-I/local/apps/src/petsc-3.1-p5/linux-gnu-c-debug/include -I/usr/lib/openmpi/1.4-gcc/include" \
 +LDFLAGS="-L/local/apps/src/petsc-3.1-p5/linux-gnu-c-debug/lib" 
 +</code>
 +
 +et ca passe donc avec la ligne:
 +<code>
 +./configure CXX=g++ CXXFLAGS="-O3 -funroll-loops -finline-functions -DNDEBUG" --prefix=/local/apps/src/dune/Dune --disable-documentation --disable-compilercheck --disable-mpiruntest --with-umfpack=/local/apps/src/dune/UMFPACK --with-petsc=/local/apps/src/dune/petsc-3.1-p5 --with-dune-common=/local/apps/src/dune/Dune --with-dune-istl=/local/apps/src/dune/Dune CPPFLAGS="-I/local/apps/src/dune/petsc-3.1-p5/linux-gnu-c-debug/include -I/usr/lib/openmpi/1.4-gcc/include" LDFLAGS="-L/local/apps/src/dune/petsc-3.1-p5/linux-gnu-c-debug/lib" 
 +
 +</code>
 +ne pas oublier l'include openmpi, car il a besin de mpi.h alors qu'on a demande de compiler petsc sans mpi
 +
 +pour rajouter slepc:
 +<code>
 +./configure CXX=g++ CXXFLAGS="-O3 -funroll-loops -finline-functions -DNDEBUG" \
 +--prefix=/local/apps/src/dune/Dune \
 +--disable-documentation --disable-compilercheck --disable-mpiruntest \
 +--with-umfpack=/local/apps/src/dune/UMFPACK \
 +--with-petsc=/local/apps/src/dune/petsc-3.1-p5 \
 +--with-dune-common=/local/apps/src/dune/Dune \
 +--with-dune-istl=/local/apps/src/dune/Dune \
 +--with-slepc=/local/apps/src/dune/slepc-3.1-p4/linux-gnu-c-debug \
 +--with-slepc-includedir=/local/apps/src/dune/slepc-3.1-p4/include \
 +--with-slepc-libdir=/local/apps/src/dune/slepc-3.1-p4/linux-gnu-c-debug/lib \
 +CPPFLAGS="-I/local/apps/src/dune/petsc-3.1-p5/linux-gnu-c-debug/include -I/usr/lib/openmpi/1.4-gcc/include -I/local/apps/src/dune/slepc-3.1-p4/include" \
 +LDFLAGS="-L/local/apps/src/dune/petsc-3.1-p5/linux-gnu-c-debug/lib -L/usr/lib64/openmpi/1.4-gcc/lib" \
 +LIBS="-lmpi -lX11"
 +
 +...
 +Found the following Dune-components: 
 +
 +----------------------------------------
 +
 +dune-common.............: yes (/local/apps/src/dune/Dune) version 2.0
 +dune-istl...............: yes (/local/apps/src/dune/Dune) version 2.0
 +BLAS....................: yes
 +METIS...................: no
 +MPI.....................: no
 +PETSC...................: yes (/local/apps/src/dune/petsc-3.1-p5)
 +ParMETIS................: no
 +SLEPC...................: yes (/local/apps/src/dune/slepc-3.1-p4/linux-gnu-c-debug)
 +SuperLU-DIST............: no
 +SuperLU.................: no
 +UMFPACK.................: yes (/local/apps/src/dune/UMFPACK)
 +
 +----------------------------------------
 +
 +See ./configur
 +</code>
 +
 +<note important>Attention, cette compilation échoue, il faut enlever LIBS, lancer le configure, et hacker manuellement les 2 Makefile pour rajouter ces libs!</note>
 +<code>
 +bash-3.2$ diff /tmp/Makefile src/Makefile
 +225c225
 +< LIBS =    -L/local/apps/src/dune/Dune/lib -ldunecommon   -L/local/apps/src/dune/Dune/lib -ldunecommon ${DUNEMPILIBS}   -L/local/apps/src/dune/Dune/lib -ldunecommon  -L/local/apps/src/dune/Dune/lib -ldunecommon    -lm  -lumfpack -lamd -lpetsc -lslepc -llapack -lblas
 +---
 +> LIBS =    -L/local/apps/src/dune/Dune/lib -ldunecommon   -L/local/apps/src/dune/Dune/lib -ldunecommon ${DUNEMPILIBS}   -L/local/apps/src/dune/Dune/lib -ldunecommon  -L/local/apps/src/dune/Dune/lib -ldunecommon    -lm  -lumfpack -lamd -lpetsc -lslepc -llapack -lblas -lmpi
  
 </code> </code>
  • dune.txt
  • Dernière modification : 2017/08/25 09:56
  • de 127.0.0.1