Différences

Ci-dessous, les différences entre deux révisions de la page.

--- dune [2010/06/30 07:10] – créée gerard
+++ dune [2017/08/25 09:56] (Version actuelle) – modification externe 127.0.0.1
@@ Ligne 1: / Ligne 1: @@
   * [[http://dune.mathematik.uni-freiburg.de/download.html]]
   * [[http://www.dune-project.org/doc/installation-notes.html]]
+====== recompilation de solver-bench sur judith (CentOS7) ======
+dune sur judith, ne pas oublier:
+<code>
+[root@judith ~]# yum groupinstall 'Development Tools'
+</code>
+  * dans /local/apps/src/dune
+  * dernière version du solver-bench: 0.70
+  * a besoin de : (voir config.log)
+<code>
+--with-umfpack=/local/apps/src/dune/UMFPACK
+--with-petsc=/local/apps/src/dune/petsc-3.1-p5
+--with-dune-istl=/local/apps/src/dune/Dune
+--with-slepc=/local/apps/src/dune/slepc-3.1-p4/linux-gnu-c-opt
+</code>
+si on essaie de recompiler UMFPACK en utilisant le script de RK: ./umfpack_installer.sh
+<code>
+./umfpack_simple: error while loading shared libraries: libgfortran.so.1: cannot open shared object file: No such file or directory
+</code>
+et:
+<code>
+[root@judith ~]# yum provides "*/libgfortran.so.1"
+compat-libgfortran-41-4.1.2-44.el7.i686 : Compatibility Fortran 95 runtime
+                                        : library version 4.1.2
+Repo        : base
+Matched from:
+Filename    : /usr/lib/libgfortran.so.1
+</code>
+on installe cette lib:
+<code>
+[root@judith ~]# yum install compat-libgfortran-41-4.1.2-44.el7
+</code>
+et on lance l'install, voir umfpack_installer.LOG, qui montre plein de différences sur les résultats obtenus, est ce que c'est génant?
+\\
+autre erreur, le do_work.sh ne passe pas à cause du compilo fortran qui n'accepte plus le -R alors qu'avant, il signalait juste l'erreur mais créeait quand même l'exécutable. On enlève le -R de LD_FLAGS
+et ça passe:
+<code>
+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-opt)
+SuperLU-DIST............: no
+SuperLU.................: no
+UMFPACK.................: yes
+</code>
+ensuite, on lance le make
+\\
+autre erreur:
+<code>
+/local/apps/src/dune/Dune/include/dune/common/nullptr.hh:25:24: error: conflicting declaration ‘typedef class dune_nullptr_t nullptr_t’
+ typedef dune_nullptr_t nullptr_t;
+                        ^
+In file included from /local/apps/src/dune/UMFPACK/AMD/Include/amd.h:45:0,
+                 from /local/apps/src/dune/UMFPACK/UMFPACK/Include/umfpack.h:91,
+                 from umfpack.hh:34,
+                 from mymatrix.hh:78,
+                 from benchmarkruntime.cc:35:
+/usr/lib/gcc/x86_64-redhat-linux/4.8.2/include/stddef.h:432:29: error: ‘nullptr_t’ has a previous declaration as ‘typedefstd::nullptr_t nullptr_t’
+   typedef decltype(nullptr) nullptr_t;
+</code>                             ^
+<del>on va essayer de commenter le typedef dans /local/apps/src/dune/Dune/include/dune/common/nullptr.hh</del> on va ajouter -DHAVE_NULLPTR au compilo
+ça passe, mais il y a un autre problème à l'édition de liens du à petsc qui n'a pas été recompilé
+on essaie de recompiler petsc, et RK a fourni le script
+install_petsc_slepc.sh avec all comme argument
+ça passe toujours pas, on essaie autrement (voir wiki)
+<code>
+bash-4.2$ export PETSC_DIR=$PWD
+bash-4.2$ ./config/configure.py --with-cc=gcc --with-fc=gfortran --with-mpi=0
+...
+Compilers:
+  C Compiler:         gcc  -Wall -Wwrite-strings -Wno-strict-aliasing -g3
+  Fortran Compiler:   gfortran  -Wall -Wno-unused-variable -g
+Linkers:
+  Static linker:   /bin/ar cr
+  Dynamic linker:   /bin/ar
+X11:
+  Includes:
+  Library:  -lX11
+BLAS/LAPACK: -llapack -lblas
+PETSc:
+  PETSC_ARCH: linux-gnu-c-debug
+  PETSC_DIR: /local/apps/src/dune/petsc-3.1-p5
+  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/dune/petsc-3.1-p5 PETSC_ARCH=linux-gnu-c-debug all
+xxx=========================================================================xxx
+</code>
+il faut aussi ajouter la lib mpi et
+Different compiler and linker combinations require different flags. -R works for many GNU compiler and linker combinations, but not all compilers and linkers. In some cases, you may have to instead tell the compiler to pass the -rpath flag to the linker. One typical way to do this is with -Wl,-rpath,/usr/local/lib.
+dans LD_FLAGS dans do_work.sh
+pour compiler solver-bench, il a fallu aussi lancer certaines lignes du makefile à la main, ce qui est passé alors que depuis le makefile non
+<code>
+libtool: link: gfortran -g -O2 -Wl,-rpath -Wl,/usr/lib64/openmpi/lib --tag=CXX -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -o fortrantest example_F.o writexdr.o -Wl,-rpath -Wl,/usr/lib64/openmpi/lib  -L/local/apps/src/dune/petsc-3.1-p5/linux-gnu-c-opt/lib -L/usr/lib64/openmpi/lib -L/local/apps/src/dune/slepc-3.1-p4/linux-gnu-c-opt/lib -L/local/apps/src/dune/petsc-3.1-p5/lib -L/local/apps/src/dune/UMFPACK/UMFPACK/Lib -L/local/apps/src/dune/UMFPACK/AMD/Lib -L/local/apps/src/dune/Dune/lib -lslepc -lpetsc /local/apps/src/dune/Dune/lib/libdunecommon.a -lumfpack -lamd -lm -lmpi -llapack -lblas
+gfortran: error: unrecognized command line option '--tag=CXX'
+make[2]: *** [fortrantest] Error 1
+make[2]: Leaving directory `/local/apps/src/dune/solver-bench-0.70/examples'
+</code>
+il faut aller dans le Makefile du dossier examples/ et virer --tag=CXX des lignes LD...., avec la nouvelle verson du compilo gfortran ça passe sans problème
+on vérifie sur un des benches:
+<code>
+---------------------------------------------------------
+RESULTS for `LS-FVM_test1_dkershaw16.xdr'
+---------------------------------------------------------
+Contributor and scheme: LS-FVM
+Test: 1
+Mesh: dkershaw16
+---------------------------------------------------------
+Problem size:
+) unknowns:                   4096
+) non-zero Matrix entries:    97336
+) entries in blocks of size:  1
+Solver + Preconditioner: ISTL-CG + ILU (0) (relax. 1)
+Reduction to achieve: 1e-10
+Number of iterations: 409601
+Residual : || b - Ax ||_inf                = 2.04981
+rel. Res.: || b - Ax ||_inf / || b ||_inf  = 2.32316
+Computed eigenvalues values: lambda_max = -11.2098, lambda_min = -0.00820027
+Estimated condition number:  lambda_max/lambda_min = 1367
+CPU time to solve in seconds: 101.545
+Memory used in MB: 4.74609 (program internal)
+Memory used in MB: 7.9375 (rusage.ru_maxrss)
+---------------------------------------------------------
+</code>
+à comparer avec [[http://solqual.latp.univ-provence.fr/ref_bench/a5fe7a76a75737a80d2c42e7d64b68e3/]], qui montre qu'on a gagné un facteur 3!
+| CPU time to solve in seconds| 369.315 | 101.545 |
 ====== installation sur octopus ======
@@ Ligne 11: / Ligne 154: @@
 [devel1@octopus ~/src]$ ./dune-common-2.0/bin/dunecontrol 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
+          8.85338
+.5          4.34976         0.491311
+         0.477752         0.109834
+.5         0.328951         0.688539
+       0.00710675        0.0216043
+.5       0.00885003           1.2453
+       0.00118422          0.13381
+.5      0.000483821         0.408555
+       2.3323e-05        0.0482058
+.5      4.16061e-06         0.178391
+      1.17866e-06         0.283291
+.5      7.05524e-07          0.59858
+      7.83043e-09        0.0110987
+.5      6.49605e-10         0.082959
+      9.89328e-11         0.152297
+.5       1.2981e-11          0.13121
+      1.51537e-12         0.116738
+.5      1.62378e-13         0.107154
+      3.17988e-14         0.195832
+.5      1.81317e-15        0.0570202
+       2.7893e-16         0.153835
+.5      1.04694e-17        0.0375342
+      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
+c225
+< 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>