Différences

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

--- pelicans [2014/11/29 18:28] – [serveur judith] gerard
+++ pelicans [2015/01/30 10:30] – [Test parallèle (tutorial)] gerard
@@ Ligne 11: / Ligne 11: @@
 [henry@judith ~]$ isis_run -h
 </code>
-  * FIXME: ajouter MPI, METIS, et java pour l'interface graphique
+  * 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
+<code>
+[devel1@judith ~/metis-4.0.3]$ make | & tee MAKE.LOG
+</code>
+==== pelicans sans metis ====
+<code>
+[devel1@judith ~/isis-4.1.0]$ diff PELICANS/etc/extra-Linux.mak-ori PELICANS/etc/extra-Linux.mak
+c10
+< WITH_MPI      = 0
+---
+> WITH_MPI      = 1
+c148
+< MPIRUN = /home/semar/pelican/ExternalPackages/Linux/openmpi/bin/mpirun
+---
+> MPIRUN = /usr/lib64/openmpi/bin/mpirun
+,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
+</code>
+<code>
+[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'
+</code>
+on passe les tests MPI
+<code>
+[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
+</code>
+==== pelicans avec metis ====
+<code>
+[devel1@judith ~/isis-4.1.0]$ diff PELICANS/etc/extra-Linux.mak-ori PELICANS/etc/extra-Linux.mak
+c10
+< WITH_MPI      = 0
+---
+> WITH_MPI      = 1
+c24
+< WITH_METIS    = 0
+---
+> WITH_METIS    = 1
+c148
+< MPIRUN = /home/semar/pelican/ExternalPackages/Linux/openmpi/bin/mpirun
+---
+> MPIRUN = /usr/lib64/openmpi/bin/mpirun
+,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
+c236
+< METISPATH = $(EXTRA_LIBS_DIR)/metis
+---
+> METISPATH = /local/apps/metis-4.0.3
+</code>
+et on lance la compilation
+<code>
+[devel1@judith ~/isis-4.1.0]$ 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'
+</code>
+==== Test parallèle (tutorial) ====
+on modifie le data.pel, comme indiqué dans le tutorial (p72):
+<code>
+[ghenry@holopherne RoomFire]$ grep parallel *.pel
+data.pel:execution_mode="parallel"
+[ghenry@holopherne RoomFire]$ grep splitt *.pel
+data.pel:splitting_strategy="METIS"
+</code>
+et on lance le calcul, sur une machine qui a 30 slots (CentOS 7, openmpi openmpi-1.6.4-3):
+<code>
+[ghenry@holopherne RoomFire]$ which mpirun
+/usr/lib64/openmpi/bin/mpirun
+</code>
+<code>
+[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).
+--------------------------------------------------------------------------
+</code>
 ====== pelicans ======