• /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

installé par centos → 1.6.4 (3.el7)

• 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

[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

[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'

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).
--------------------------------------------------------------------------

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

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<std::InputIterator, std::T, std::Size>(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;”

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

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<std::InputIterator, std::T, std::Size>(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<std::InputIterator, std::T, std::Size>(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<std::InputIterator, std::T, std::Size>(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<std::InputIterator, std::T, std::Size>(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

- 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?

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

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"!