[cig-commits] r20179 - in seismo/3D/SPECFEM3D/trunk: . doc/USER_MANUAL

dkomati1 at geodynamics.org dkomati1 at geodynamics.org
Sat May 19 11:50:11 PDT 2012 

Author: dkomati1
Date: 2012-05-19 11:50:10 -0700 (Sat, 19 May 2012)
New Revision: 20179

Modified:
   seismo/3D/SPECFEM3D/trunk/configure.ac
   seismo/3D/SPECFEM3D/trunk/doc/USER_MANUAL/manual_SPECFEM3D.pdf
   seismo/3D/SPECFEM3D/trunk/doc/USER_MANUAL/manual_SPECFEM3D.tex
   seismo/3D/SPECFEM3D/trunk/flags.guess
   seismo/3D/SPECFEM3D/trunk/todo_list_please_dont_remove.txt
Log:
better IBM compiler options.
also updated the manual


Modified: seismo/3D/SPECFEM3D/trunk/configure.ac
===================================================================
--- seismo/3D/SPECFEM3D/trunk/configure.ac	2012-05-19 18:48:12 UTC (rev 20178)
+++ seismo/3D/SPECFEM3D/trunk/configure.ac	2012-05-19 18:50:10 UTC (rev 20179)
@@ -10,7 +10,7 @@
 
 
 AC_PREREQ(2.61)
-AC_INIT([Specfem 3D], [2.0.1], [jtromp AT princeton.edu], [Specfem3D])
+AC_INIT([Specfem 3D], [2], [jtromp AT princeton.edu], [Specfem3D])
 AC_CONFIG_SRCDIR([README])
 AC_CONFIG_HEADER([config.h])
 AC_CONFIG_MACRO_DIR([m4])
@@ -421,7 +421,7 @@
 # Checks for library functions.
 
 
-AC_CONFIG_FILES([Makefile in_data_files/Par_file in_data_files/CMTSOLUTION in_data_files/STATIONS src/meshfem3D/Makefile src/meshfem3D/constants.h src/meshfem3D/precision.h  src/decompose_mesh_SCOTCH/Makefile src/specfem3D/Makefile src/generate_databases/Makefile src/shared/constants.h src/shared/precision.h src/decompose_mesh_SCOTCH/scotch_5.1.11/src/Makefile.inc src/check_mesh_quality_CUBIT_Abaqus/Makefile])
+AC_CONFIG_FILES([Makefile src/meshfem3D/Makefile src/meshfem3D/constants.h src/meshfem3D/precision.h  src/decompose_mesh_SCOTCH/Makefile src/specfem3D/Makefile src/generate_databases/Makefile src/shared/constants.h src/shared/precision.h src/decompose_mesh_SCOTCH/scotch_5.1.11/src/Makefile.inc src/check_mesh_quality_CUBIT_Abaqus/Makefile])
 AC_OUTPUT
 
 

Modified: seismo/3D/SPECFEM3D/trunk/doc/USER_MANUAL/manual_SPECFEM3D.pdf
===================================================================
(Binary files differ)

Modified: seismo/3D/SPECFEM3D/trunk/doc/USER_MANUAL/manual_SPECFEM3D.tex
===================================================================
--- seismo/3D/SPECFEM3D/trunk/doc/USER_MANUAL/manual_SPECFEM3D.tex	2012-05-19 18:48:12 UTC (rev 20178)
+++ seismo/3D/SPECFEM3D/trunk/doc/USER_MANUAL/manual_SPECFEM3D.tex	2012-05-19 18:50:10 UTC (rev 20179)
@@ -317,7 +317,7 @@
 If you run very large meshes on a relatively small number
 of processors, the memory size needed on each processor might become
 greater than 2 gigabytes, which is the upper limit for 32-bit addressing.
-In this case, on some compilers you may need to add \texttt{``-mcmodel=medium}''
+In this case, on some compilers you may need to add \texttt{``-mcmodel=medium}'' or \texttt{``-mcmodel=medium -shared-intel}''
 to the compiler options of CFLAGS, FCFLAGS and LDFLAGS otherwise the compiler will display an error
 message (for instance \texttt{``relocation truncated to fit: R\_X86\_64\_PC32 against .bss''} or something similar);
 on an IBM machine with the \texttt{xlf} and \texttt{xlc} compilers, using \texttt{-q64} is usually sufficient.\\
@@ -408,6 +408,11 @@
 and in double precision on your system and compare the seismograms.
 If they are identical (and in most cases they will), you can select single precision for your future runs.\\
 
+\section{Visualizing the subroutine calling tree of the source code}
+
+Packages such as \texttt{doxywizard} can be used to visualize the subroutine calling tree of the source code.
+\texttt{Doxywizard} is a GUI front-end for configuring and running \texttt{doxygen}.
+
 \chapter{\label{cha:Mesh-Generation}Mesh Generation}
 
 The first step in running a spectral-element simulation consists of constructing a high-quality mesh for the region under consideration. We provide two possibilities to do so: (1) relying on the external, hexahedral mesher CUBIT, or (2) using the provided, internal mesher \texttt{xmeshfem3D}. In the following, we explain these two approaches.

Modified: seismo/3D/SPECFEM3D/trunk/flags.guess
===================================================================
--- seismo/3D/SPECFEM3D/trunk/flags.guess	2012-05-19 18:48:12 UTC (rev 20178)
+++ seismo/3D/SPECFEM3D/trunk/flags.guess	2012-05-19 18:50:10 UTC (rev 20179)
@@ -151,13 +151,16 @@
         #
         if test x"$FLAGS_NO_CHECK" = x; then
 # deleted -qxflag=dvz because it requires handler function __xl_dzx and thus linking will fail 
-            FLAGS_NO_CHECK="-O3 -qstrict -q64 -qtune=auto -qarch=auto -qcache=auto -qfree=f90 -qsuffix=f=f90 -qhalt=w -qlanglvl=90pure -qsuppress=1518-317 -qflttrap=overflow:zerodivide:invalid:enable -qfloat=nans -qinitauto=7FBFFFFF -Q -Q+rank,swap_all -Wl,-relax -qunroll=yes"
+            FLAGS_NO_CHECK="-O3 -qsave -qstrict -q64 -qtune=auto -qarch=auto -qcache=auto -qfree=f90 -qsuffix=f=f90 -qhalt=w -qlanglvl=90pure -qsuppress=1518-317 -Q -Q+rank,swap_all -Wl,-relax -qunroll=yes"
         # on MareNostrum at the Barcelona SuperComputing Center (Spain) one can use
-        # -qtune=ppc970 -qarch=ppc64v -qsave     instead of -qtune=auto -qarch=auto
+        # -qtune=ppc970 -qarch=ppc64v instead of -qtune=auto -qarch=auto
+        # on "Babel" IBM BlueGene at IDRIS (France) use:
+        # -qtune=auto -qarch=450d -qsave     instead of -qtune=auto -qarch=auto
         fi
         if test x"$FLAGS_CHECK" = x; then
         #
         # to debug with IBM xlf, one can add this: -g -O0 -C -qddim -qfullpath
+        # to debug, one can add these three flags: -qflttrap=overflow:zerodivide:invalid:enable -qfloat=nans -qinitauto=7FBFFFFF
         #
             FLAGS_CHECK="\$(FLAGS_NO_CHECK) -g -C -qddim -qfullpath"
         fi

Modified: seismo/3D/SPECFEM3D/trunk/todo_list_please_dont_remove.txt
===================================================================
--- seismo/3D/SPECFEM3D/trunk/todo_list_please_dont_remove.txt	2012-05-19 18:48:12 UTC (rev 20178)
+++ seismo/3D/SPECFEM3D/trunk/todo_list_please_dont_remove.txt	2012-05-19 18:50:10 UTC (rev 20179)
@@ -404,8 +404,12 @@
 
 Regarding the implicit time schemes that Zhinan has implemented in 2D, I agree that it would be great to put that in the official SVN version relatively soon to avoid losing the changes if we wait for too long. But I think we only need this in 2D for now, so let us not do it in 3D (at least for now in 2012). Let us just commit Zhinan's 2D version of the implicit routines to the official SVN code (making it off by default; the default should remain a purely explicit second-order Newmark scheme). 
 
+- suggestion 29:
+----------------
 
+Elliott Sales de Andrade will fix the configure.ac autoconf scripts in SPECFEM2D, SPECFEM3D and SPECFEM3D_GLOBE.
 
+
 Older to-do lists of SPECFEM2D, SPECFEM3D and SPECFEM3D_GLOBE (some items are probably still useful to implement):
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