**PELICANS** ====== isis 4.1.0 ====== ===== serveur judith ===== * /local/apps/isis-4.1.0 * le répertoire doc est recopié sur le serveur web, et donc accessible sur https://www.i2m.univ-amu.fr/support/pelicans/ * pour l'utiliser [henry@judith ~]$ source /local/apps/isis-4.1.0/bin/init.csh [henry@judith ~]$ isis_run -h * on peut lancer l'itnerface graphique **xisis** * pour accéder au tutoriel depuis xisis, aller dans Preferences, pdf-open, et remplacer acroread par evince ===== version parallèle ===== ==== openmpi ==== installé par centos -> 1.6.4 (3.el7) ==== metis ==== * Warning: install METIS as a dynamic library ( in METIS directory, make COPTIONS=-fPIC ) * modifier Makefile.in * /local/apps/metis-4.0.3 * dans Lib/proto.h, on commente les déclarations de drand48, srand48 et ilog2 sinon pelicans/isis ne compilera pas [devel1@judith ~/metis-4.0.3]$ make | & tee MAKE.LOG ==== pelicans sans metis ==== [devel1@judith ~/isis-4.1.0]$ diff PELICANS/etc/extra-Linux.mak-ori PELICANS/etc/extra-Linux.mak 10c10 < WITH_MPI = 0 --- > WITH_MPI = 1 148c148 < MPIRUN = /home/semar/pelican/ExternalPackages/Linux/openmpi/bin/mpirun --- > MPIRUN = /usr/lib64/openmpi/bin/mpirun 155,156c155,156 < CPPFLAGS += -I$(MPIPATH)/include < MPIPATH = $(EXTRA_LIBS_DIR)/openmpi --- > CPPFLAGS += -I/usr/include/openmpi-x86_64 -I$(MPIPATH)/include > MPIPATH = /usr/lib64/openmpi [devel1@judith ~/isis-4.1.0]$ make install | & tee INSTALL.LOG ... -------------------------------------------------- | Test is successful -------------------------------------------------- ************************************************** * number of successful tests: 214 * number of ambiguous tests: 0 * number of failing tests: 0 ************************************************** *** Elapsed time in second: user 0.084841 **** * target test_install completed **************************************** make[1]: Leaving directory `/local/apps/isis-4.1.0/ISIS' on passe les tests MPI [devel1@judith ~/isis-4.1.0]$ source /local/apps/isis-4.1.0/bin/init.csh [devel1@judith ~/isis-4.1.0]$ make test_MPI ... **************************************** make[1]: Leaving directory `/local/apps/isis-4.1.0/ISIS' ================================================================================= Test MPI ================================================================================= *** Operating system: Linux *** Executable: /local/apps/isis-4.1.0/ISIS/lib/Linux-gcc/opt0.exe *** Data file: /local/apps/isis-4.1.0/PELICANS/etc/ExternalAPI/MPI/tests_enabling/data.pel *** PELICANS library compiler : gcc compilation date : Nov 29 2014 compilation level : opt0 ---------------------------------------------------- | Unit tests performed on class PEL_Expression : ==================================================== | ... MPI_enabling_test kind : OK | ... MPI_enabling_test evaluation : OK ==================================================== | End of 2 tests of class PEL_Expression in 2.4e-05 s ---------------------------------------------------- ---- Success of all unit tests ---- *** Elapsed time in second: user 0.00017 ==== pelicans avec metis ==== [devel1@judith ~/isis-4.1.0]$ diff PELICANS/etc/extra-Linux.mak-ori PELICANS/etc/extra-Linux.mak 10c10 < WITH_MPI = 0 --- > WITH_MPI = 1 24c24 < WITH_METIS = 0 --- > WITH_METIS = 1 148c148 < MPIRUN = /home/semar/pelican/ExternalPackages/Linux/openmpi/bin/mpirun --- > MPIRUN = /usr/lib64/openmpi/bin/mpirun 155,156c155,156 < CPPFLAGS += -I$(MPIPATH)/include < MPIPATH = $(EXTRA_LIBS_DIR)/openmpi --- > CPPFLAGS += -I/usr/include/openmpi-x86_64 -I$(MPIPATH)/include > MPIPATH = /usr/lib64/openmpi 236c236 < METISPATH = $(EXTRA_LIBS_DIR)/metis --- > METISPATH = /local/apps/metis-4.0.3 et on lance la compilation [devel1@judith ~/isis-4.1.0]$ make install | & tee INSTALL.LOG ================================================================================= Configuration file ================================================================================= Hostname: judith.cmi.univ-mrs.fr Compiler: gcc Architecture-Makefile searched in: /local/apps/isis-4.1.0/PELICANS/etc judith.cmi.univ-mrs.fr-gcc judith.cmi.univ-mrs.fr-undef Linux_3.10.0-gcc * Linux-gcc /local/apps/isis-4.1.0/PELICANS/etc/Linux-gcc.mak undef-gcc Linux_3.10.0-undef Linux-undef Extra-Makefile searched in: /local/apps/isis-4.1.0/PELICANS/etc judith.cmi.univ-mrs.fr-gcc judith.cmi.univ-mrs.fr-undef Linux_3.10.0-gcc Linux-gcc undef-gcc Linux_3.10.0-undef * Linux-undef /local/apps/isis-4.1.0/PELICANS/etc/extra-Linux.mak Compiler Architecture name: Linux-gcc External libraries: MPI: enabled JAVA: disabled METIS: enabled ================================================================================= Installing PELICANS, level=opt0 ================================================================================= ... | Test is successful -------------------------------------------------- -------------------------------------------------- | ISIS/IHM/samples/WallConduction/DoRun -------------------------------------------------- | Test is successful -------------------------------------------------- ************************************************** * number of successful tests: 214 * number of ambiguous tests: 0 * number of failing tests: 0 ************************************************** *** Elapsed time in second: user 0.068729 **** * target test_install completed **************************************** make[1]: Leaving directory `/local/apps/isis-4.1.0/ISIS' ==== Test parallèle (tutorial) ==== on modifie le data.pel, comme indiqué dans le tutorial (p72): [ghenry@holopherne RoomFire]$ grep parallel *.pel data.pel:execution_mode="parallel" [ghenry@holopherne RoomFire]$ grep splitt *.pel data.pel:splitting_strategy="METIS" et on lance le calcul, sur une machine qui a 30 slots (CentOS 7, openmpi openmpi-1.6.4-3): [ghenry@holopherne RoomFire]$ which mpirun /usr/lib64/openmpi/bin/mpirun [ghenry@holopherne RoomFire]$ isis_run data.pel resu -np 2 Process #0 : launched on holopherne.cmi.univ-mrs.fr (79758). Process #1 : launched on holopherne.cmi.univ-mrs.fr (79759). Process #1 : terminated. Process #0 : terminated. Process #0 : launched on holopherne.cmi.univ-mrs.fr (79766). Process #1 : launched on holopherne.cmi.univ-mrs.fr (79767). terminate called after throwing an instance of 'PEL_Exceptions::InternalError' -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 79767 on node holopherne.cmi.univ-mrs.fr exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- ce bug est dû à une mauvaise version du fichier ''CALIFS/packages/simulators/heat_transfer/src/IS_Enthalpy.cc''. On le remplace, puis: make APPLI0 et ça passe ====== pelicans ====== sur octopus: CentOS, 64bits Le couplage à MUMPS (+mpi) est dispo dans PELICANS. A Cadarache, ils utilisent les librairies suivantes pour linker avec PELICANS : CPPFLAGS += -I$(MUMPS)/include LIBPATH += $(MUMPS)/lib SCALAP = -L$(SCALAPACK)/lib -lscalapack -lblacs -lblacsF77 -lblacsC -lblacs -lblacsF77 -lblacsC LIBBLAS = -lblas -llapack -lmpi_f77 -lmpi_f90 LDLIBS += -ldmumps -lmumps_common ${SCALAP} ${LIBBLAS} -lpord /usr/lib/libscalapack.so.1 /usr/lib/libmpiblacs.so.1 /usr/lib/libmpiblacsCinit.so.1 /usr/lib/libmpiblacsCinit.so.1.0.0 /usr/lib/libmpiblacsF77init.so.1 /usr/lib/libmpiblacsF77init.so.1.0.0 /usr/lib64/libblas.so.3 /usr/lib/liblapack.so.3.0.3 /usr/lib64/liblapack.so.3 sur nemo: solaris 10, amd64 ====== 9 jan 09 utilisation de stlport4 ====== pour contourner le problème suivant avec la librairie standard ancienne: "/local/henry/PelicansSVN/PDEsolver/src/PDE_BasisFunctionCell.cc", line 205: Error: Could not find a match for std::count(PDE_BasisFunctionCell**, PDE_BasisFunctionCell**, PDE_BasisFunctionCell*) needed in PDE_BasisFunctionCell::set_child_parent_relationship(PDE_BasisFunctionCell*, double, bool). __modifications de SunOS-CC.mak__ 24c24 < CXXFLAGS += $(OPT) -KPIC --- > CXXFLAGS += $(OPT) -KPIC -library=stlport4 35c35 < LDLIBSSO = -lCstd -lCrun --- > LDLIBSSO = -library=stlport4 -lCrun ensuite, il faut faire un certain nombre de modifs sur les sources, essentiellement pour ajouter "using namespace std;" [[http://www.latp.univ-mrs.fr/~henry/reseau/calcul/pelicanssvn.diff|PelicansSVN.diff]] à propos du comportment du compilateur CC: * [[http://forums.sun.com/thread.jspa?messageID=10567417]] * http://developers.sun.com/solaris/articles/cmp_stlport_libCstd.html * http://docs.sun.com/source/820-4155/c++_faq.html ====== 8 jan 09 utilisation de Apache C++ stdlib ====== __modifications__ nemo-henry% diff /tmp/SunOS-CC.mak local_arch_64/SunOS-CC.mak 24c24 < CXXFLAGS += $(OPT) -KPIC --- > CXXFLAGS += $(OPT) -KPIC -I/local/apps/lib/amd64/APACHE-4.2.1/include 29c29,30 < LDFLAGS += $(OPT) -KPIC --- > LDFLAGS += $(OPT) -KPIC -R/local/apps/lib/amd64/APACHE-4.2.1/lib/ -L/local/apps/lib/amd64/APACHE-4.2.1/lib/ > 35c36 < LDLIBSSO = -lCstd -lCrun --- > LDLIBSSO = -library=%none -lstd15D#-lCstd -lCrun __erreur à la compilation__ "/local/henry/PelicansSVN/PDEsolver/src/PDE_BasisFunctionCell.cc", line 205: Error: Could not find a match for std::count(PDE_BasisFunctionCell**, PDE_BasisFunctionCell**, PDE_BasisFunctionCell*) needed in PDE_BasisFunctionCell::set_child_parent_relationship(PDE_BasisFunctionCell*, double, bool). "/local/henry/PelicansSVN/PDEsolver/src/PDE_BasisFunctionCell.cc", line 207: Error: Could not find a match for std::count(PDE_BasisFunctionCell**, PDE_BasisFunctionCell**, PDE_BasisFunctionCell*) needed in PDE_BasisFunctionCell::set_child_parent_relationship(PDE_BasisFunctionCell*, double, bool). "/local/henry/PelicansSVN/PDEsolver/src/PDE_BasisFunctionCell.cc", line 480: Error: Could not find a match for std::count(PDE_BasisFunctionCell**, PDE_BasisFunctionCell**, PDE_BasisFunctionCell*) needed in PDE_BasisFunctionCell::set_ascendant_relationship(PDE_BasisFunctionCell*). "/local/henry/PelicansSVN/PDEsolver/src/PDE_BasisFunctionCell.cc", line 482: Error: Could not find a match for std::count(PDE_BasisFunctionCell**, PDE_BasisFunctionCell**, PDE_BasisFunctionCell*) needed in PDE_BasisFunctionCell::set_ascendant_relationship(PDE_BasisFunctionCell*). 4 Error(s) detected. make[1]: *** [/local/henry/PelicansSVN/lib/SunOS-CC/opt2/PDE_BasisFunctionCell.o] Error 4 ====== 7 avril 05 ====== ====== 2 mai 05 qq remarques: ====== - l. chailan me parle d'opengl, mais c'est a 0 dans extra-sunos.mak?! - ca compile avec le flag EXTENDED_MATH mais ca ne linke jamais avec la perflib de sun? ====== 19 avril 05 creation d'un compte pelicans ====== accessible par les gens de l'irsn sur nemo, mon repertoire PELICANS est recopie dans /local/pelicans/PELICANS il y a des erreurs pendant la copie: nemo-root% cp -rp ~henry/PELICANS /local/pelicans/ cp: cannot access /local/henry/PELICANS/07_04_2005/doc/Site/APPLICATION_Documentations/Tutorial/tests/fem/doc/save.gene cp: cannot access /local/henry/PELICANS/07_04_2005/doc/Site/APPLICATION_Documentations/Tutorial/tests/fem/doc/visu cp: cannot access /local/henry/PELICANS/07_04_2005/doc/Site/APPLICATION_Documentations/Tutorial/tests/fvm/doc/save.gene cp: cannot access /local/henry/PELICANS/07_04_2005/doc/Site/APPLICATION_Documentations/Tutorial/tests/fvm/doc/visu cp: cannot access /local/henry/PELICANS/07_04_2005/doc/Site/APPLICATION_Documentations/Helmholtz_Galerkin/tests/sincos/doc/save.gene c'est parce que: nemo-root% ll /local/henry/PELICANS/07_04_2005/doc/Site/APPLICATION_Documentations/NavierStokes_StaggeredGrid/tests/Poiseuille3D/doc/visu 2 lrwxrwxrwx 1 henry sysadmin 99 Apr 13 08:26 /local/henry/PELICANS/07_04_2005/doc/Site/APPLICATION_Documentations/NavierStokes_StaggeredGrid/tests/Poiseuille3D/doc/visu -> /home/semar/pelican/CURRENT/StandardApplications/NavierStokes_StaggeredGrid/tests/Poiseuille3D/visu la doc pointe sur un rep qui n'existe pas ====== 13 avril 05: installation de pelicans ====== plateforme: amd64 OS: SunOS compilateur: cc - utiliser gmake au lieu de make - creer un fichier SunOS-CC.mak et extra-SunOS.mak dans $PELARCHDIR - ajouter les variables d'environnment: CCC=CC PELARCHDIR=... - gmake -e environment - pel arch -v CC - gmake -e all >& MAKE-CC.LOG - gmake -e check >& CHEK-CC.LOG Le fichier CHEK-CC.LOG contient 23 "FATAL ERROR"!