Différences

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

--- hypre_patches [2009/07/16 10:00] – créée gerard
+++ hypre_patches [2017/08/25 09:56] (Version actuelle) – modification externe 127.0.0.1
@@ Ligne 1: / Ligne 1: @@
+  * le configure cree le fichier Makefile.config depuis le template Makefile.config.in dans le répertoire config
+  * après exécution de configure, on modifie le fichier Makefile.config pour qu'il prenne en compte la sunperf
+  * <del>et on modifie le script babel-runtime/libtool pour supprimer ''-z text'' à l'édition de liens</del>
+  * {{do_work.sh|script}} pour recompiler hypre
 ====== détection architecture ======
   * fait par le script src/tarch, mais ne donne pas le meme resultat sur sparc et amd64. On fait la modif suivante:
@@ Ligne 21: / Ligne 26: @@
 </code>
+====== ld: fatal: relocations remain against allocatable but non-writable sections ======
+on peut reproduire cette erreur avec les 2 lignes suivantes:
+<code>
+> pwd
+/local/apps/src/hypre-2.0.0/src/babel-runtime/sidl
+mpcc -DHAVE_CONFIG_H -I. -I. -I. -I/usr/include/libxml2 -I/usr/java/include -I/usr/java/include/solaris -I./../sidlx -dalign -xlic_lib=sunperf -I/opt/SUNWhpc/HPC6.0/include -xmodel=medium -m64 -D_REENTRANT -c sidl_BaseClass_Impl.c  -KPIC -DPIC -o .libs/sidl_BaseClass_Impl.o
+/usr/ccs/bin/ld -G -z text -h libsidl-1.0.0.so -o .libs/libsidl-1.0.0.so    .libs/sidl_BaseClass_Impl.o \
+ -R/opt/SUNWhpc/HPC6.0/lib/amd64 -R/usr/lib -L/opt/SUNWhpc/HPC6.0/lib/amd64 -ldl -L/usr/lib -lxml2 -lz -lm -lsocket -lnsl -lpthread -lc
+Text relocation remains                         referenced
+    against symbol                  offset      in file
+sidl_BaseInterface_deleteRef        0x215       .libs/sidl_BaseClass_Impl.o
+sidl_BaseInterface_deleteRef        0x651       .libs/sidl_BaseClass_Impl.o
+sidl_BaseClass_deleteRef            0x558       .libs/sidl_BaseClass_Impl.o
+sidl_BaseInterface_addRef           0x6e8       .libs/sidl_BaseClass_Impl.o
+ld: fatal: relocations remain against allocatable but non-writable sections
+</code>
+et la faire disparaître si on supprime ''-z text'', mais est ce normal? voir [[http://dlc.sun.com/pdf/819-5263/819-5263.pdf|3.4.182 –ztext]]
+patch
+<del><code>
+> diff -u ../../../src/babel-runtime/m4/libtool.m4.ori ../../../src/babel-runtime/m4/libtool.m4
+--- ../../../src/babel-runtime/m4/libtool.m4.ori        2005-11-14 22:20:09.000000000 +0100
++++ ../../../src/babel-runtime/m4/libtool.m4    2009-07-16 13:43:50.839538559 +0200
+@@ -5845,7 +5845,7 @@
+       ;;
+     solaris*)
+-      _LT_AC_TAGVAR(no_undefined_flag, $1)=' -z text'
++      _LT_AC_TAGVAR(no_undefined_flag, $1)=' -z textoff'
+       if test "$GCC" = yes; then
+        _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+        _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~
+</code></del>
+c'est un bug spécifique à la plateforme x86_64, il faut ajouter un flag d'optimisation (ou -fast par exemple)
+====== checking for Fortran name-mangling scheme... unknown ======
+cette erreur concerne l'interface C-Fortran. Le configure semble trouver que c'est correct 2 fois, et échoue 1 fois.
+\
+Il faut ajouter l'option: ''-ext_names=plain'' pour que le programme de test compile. Mais est ce que c'est à faire tout le temps?
+voir [[http://dlc.sun.com/pdf/819-5262/819-5262.pdf|11.1.4 Underscores in Routine Names]]
+====== Tests avec programme hmm ======
+===== SS12 + HPC 6 =====
+<code>
+nemo-henry% module unload hpc82 ss12u1 ; module load hpc ss12
+nemo-henry% which mpcc
+/opt/SUNWhpc/bin/mpcc
+nemo-henry% make clean
+Nettoyage
+rm -f *.o *.mod *.fig *.vtk;
+nemo-henry% make -f Makefile.hmm hmm
+complete: Command not found
+complete: Command not found
+mpcc -g -O5 -m64  -I/local/apps/lib/amd64/opt0/include -DHAVE_CONFIG_H -DHYPRE_TIMING -c mpi_sol_hypre.c
+mpf90 -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -I/local/apps/lib/amd64/opt0/include -DHAVE_CONFIG_H -DHYPRE_TIMING -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -c mod_dessin.f90
+mpf90 -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -I/local/apps/lib/amd64/opt0/include -DHAVE_CONFIG_H -DHYPRE_TIMING -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -c mod_maillage.f90
+mpf90 -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -I/local/apps/lib/amd64/opt0/include -DHAVE_CONFIG_H -DHYPRE_TIMING -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -c mod_castests.f90
+mpf90 -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -I/local/apps/lib/amd64/opt0/include -DHAVE_CONFIG_H -DHYPRE_TIMING -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -c mod_reslin.f90
+mpf90 -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -I/local/apps/lib/amd64/opt0/include -DHAVE_CONFIG_H -DHYPRE_TIMING -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -c mod_interface_hypre.f90
+mpf90 -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -I/local/apps/lib/amd64/opt0/include -DHAVE_CONFIG_H -DHYPRE_TIMING -g -m64 -O5  -C -Xlist -xcheck=init_local -e -fpp -DHypre  -c hmm.f90
+complete: Command not found
+complete: Command not found
+complete: Command not found
+echo /opt/SUNWhpc/bin
+/opt/SUNWhpc/bin
+mpf90 -o hmm mpi_sol_hypre.o mod_dessin.o mod_maillage.o mod_castests.o mod_reslin.o mod_interface_hypre.o hmm.o -L/local/apps/lib/amd64/opt0/lib -R/local/apps/lib/amd64/opt0/lib -L/local/apps/lib/amd64/opt0/../babel-runtime/sidl/.libs -lbHYPREClient-C -lbHYPREClient-CX -lbHYPREClient-F -lbHYPRE -lsidl -ldl -lxml2 -m64 -g -O5 -m64  -xlic_lib=sunperf -L/opt/SUNWhpc/bin/../lib/amd64 -L/local/apps/lib/amd64/opt0/lib -lHYPRE -lm -L/opt/SUNWhpc/bin/../lib/amd64 -lmpi -lfsu -lsunmath -lm -lmtsk
+nemo-henry% mprun -np 4 hmm
+  Paradigme HFV   (solveur: HYPRE, figures: aucun)
+nutest=   1      typepoly=  -9
+ndiv= 200      nb sommets=    40401      nb rectangles=    40000
+          nb aretes=    80400      nb aretes internes=    79600
+\nRenumerotation des aretes:  8 passages,   5.16E-02 secondes
+\nzeta=  4.999999999999778E-01     aire totale= 1.000000000001004     pas=  7.07E-03
+***Resolution HYPRE (PCG+AMG)*** Iterations = 8, Residu = 5.693808e-08
+ pmin  4.185951532810916E-6 \t\t pmax  0.062498116067422324
+ Erreurs relatives:\n\tL2 p= 4.257483975064142E-5 \t Linf p= 3.607706907963071E-5
+ \tL2 gradp= 1.4012123382881934E-5
+ \ntemps execution 7.2776513
+</code>
+===== SS12u1 + HPC 8.2 =====
+<code>
+nemo-henry% module unload hpc ss12; module load hpc82 ss12u1
+nemo-henry% make clean
+nemo-henry% make -f Makefile.hmm hmm
+nemo-henry% mpirun -np 4 hmm
+[nemo:28041] *** Process received signal ***
+[nemo:28041] Signal: Segmentation Fault (11)
+[nemo:28041] Signal code: Address not mapped (1)
+[nemo:28041] Failing at address: 6e65706f6c64
+[nemo:28044] *** Process received signal ***
+[nemo:28044] Signal: Segmentation Fault (11)
+[nemo:28044] Signal code: Address not mapped (1)
+[nemo:28044] Failing at address: 6e65706f6c64
+[nemo:28047] *** Process received signal ***
+[nemo:28047] Signal: Segmentation Fault (11)
+[nemo:28047] Signal code: Address not mapped (1)
+[nemo:28047] Failing at address: 6e65706f6c64
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x4b9a2
+/lib/amd64/libc.so.1:0xd71b6
+/lib/amd64/libc.so.1:0xcbab2
+x6e65706f6c64 [ Signal 11 (SEGV)]
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x2bcd4
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:lt_dlopenadvise+0x9e
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x33a8b
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x33292
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:mca_base_component_find+0x2c7
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:mca_base_components_open+0x193
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:opal_paffinity_base_open+0xc1
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:opal_init+0x57
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-rte.so.0.0.0:orte_init+0x2a
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi.so.0.0.0:ompi_mpi_init+0x110
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi.so.0.0.0:PMPI_Init+0xcd
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi_f77.so.0.0.0:pmpi_init_+0x28
+/local/henry/droniou_hypre/hmm:MAIN_+0xab
+/local/henry/droniou_hypre/hmm:main+0x3d
+/local/henry/droniou_hypre/hmm:0x2c5dc
+[nemo:28041] *** End of error message ***
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x4b9a2
+/lib/amd64/libc.so.1:0xd71b6
+/lib/amd64/libc.so.1:0xcbab2
+x6e65706f6c64 [ Signal 11 (SEGV)]
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x2bcd4
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:lt_dlopenadvise+0x9e
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x33a8b
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x33292
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:mca_base_component_find+0x2c7
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:mca_base_components_open+0x193
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:opal_paffinity_base_open+0xc1
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:opal_init+0x57
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-rte.so.0.0.0:orte_init+0x2a
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi.so.0.0.0:ompi_mpi_init+0x110
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi.so.0.0.0:PMPI_Init+0xcd
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi_f77.so.0.0.0:pmpi_init_+0x28
+/local/henry/droniou_hypre/hmm:MAIN_+0xab
+/local/henry/droniou_hypre/hmm:main+0x3d
+/local/henry/droniou_hypre/hmm:0x2c5dc
+[nemo:28044] *** End of error message ***
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x4b9a2
+/lib/amd64/libc.so.1:0xd71b6
+/lib/amd64/libc.so.1:0xcbab2
+x6e65706f6c64 [ Signal 11 (SEGV)]
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x2bcd4
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:lt_dlopenadvise+0x9e
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x33a8b
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x33292
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:mca_base_component_find+0x2c7
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:mca_base_components_open+0x193
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:opal_paffinity_base_open+0xc1
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:opal_init+0x57
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-rte.so.0.0.0:orte_init+0x2a
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi.so.0.0.0:ompi_mpi_init+0x110
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi.so.0.0.0:PMPI_Init+0xcd
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi_f77.so.0.0.0:pmpi_init_+0x28
+/local/henry/droniou_hypre/hmm:MAIN_+0xab
+/local/henry/droniou_hypre/hmm:main+0x3d
+/local/henry/droniou_hypre/hmm:0x2c5dc
+[nemo:28047] *** End of error message ***
+[nemo:28050] *** Process received signal ***
+[nemo:28050] Signal: Segmentation Fault (11)
+[nemo:28050] Signal code: Address not mapped (1)
+[nemo:28050] Failing at address: 6e65706f6c64
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x4b9a2
+/lib/amd64/libc.so.1:0xd71b6
+/lib/amd64/libc.so.1:0xcbab2
+x6e65706f6c64 [ Signal 11 (SEGV)]
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x2bcd4
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:lt_dlopenadvise+0x9e
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x33a8b
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:0x33292
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:mca_base_component_find+0x2c7
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:mca_base_components_open+0x193
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:opal_paffinity_base_open+0xc1
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-pal.so.0.0.0:opal_init+0x57
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libopen-rte.so.0.0.0:orte_init+0x2a
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi.so.0.0.0:ompi_mpi_init+0x110
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi.so.0.0.0:PMPI_Init+0xcd
+/opt/SUNWhpc/HPC8.2/sun/lib/amd64/libmpi_f77.so.0.0.0:pmpi_init_+0x28
+/local/henry/droniou_hypre/hmm:MAIN_+0xab
+/local/henry/droniou_hypre/hmm:main+0x3d
+/local/henry/droniou_hypre/hmm:0x2c5dc
+[nemo:28050] *** End of error message ***
+--------------------------------------------------------------------------
+mpirun noticed that process rank 0 with PID 28041 on node nemo exited on signal 11 (Segmentation Fault).
+--------------------------------------------------------------------------
+total processes killed (some possibly by mpirun during cleanup)
+</code>