From 9184eadaef5518db7941d9999b4ce54dda088c73 Mon Sep 17 00:00:00 2001
From: Don Pellegrino <don@drexel.edu>
Date: Mon, 25 Jan 2010 18:55:47 +0000
Subject: Modified to build using the copy of PETSc already installed on Cobalt.

---
diff --git a/.gitignore b/.gitignore
index 8c55145..7b53edd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,6 @@
-*~
 *.o
+*~
+.deps
 COPYING
 INSTALL
 Makefile
diff --git a/autogen.sh b/autogen.sh
index c7c8611..967c298 100755
--- a/autogen.sh
+++ b/autogen.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
 automake --add-missing
-autoreconf
+autoreconf --force --install --symlink
diff --git a/configure.ac b/configure.ac
index f1ecdf9..aa1d3df 100644
--- a/configure.ac
+++ b/configure.ac
@@ -57,6 +57,11 @@ AC_SEARCH_LIBS([H5TBmake_table],[hdf5_hl],[],
 # MODULE: PETSc #
 #################
 
+AC_SEARCH_LIBS([pthread_atfork],[pthread])
+
+AC_SEARCH_LIBS([PetscInitialize],[petsc],[],
+[AC_MSG_ERROR("The Portable Extensible Toolkit for Scientific Computation (PETSc) is needed to build the system.")])
+
 # The AC_SEARCH_LIBS other-libraries list is not particularly useful.
 # Autoconf determines if the other-libraries are necessary however in
 # the cases where they are indeed necessary they are not actually
@@ -65,11 +70,10 @@ AC_SEARCH_LIBS([H5TBmake_table],[hdf5_hl],[],
 # These are the dependencies.  Random functions are selected from
 # these libraries from the list of otherwise undefined references at
 # link time.
-AC_SEARCH_LIBS([PetscInitialize],[petsc])
 AC_SEARCH_LIBS([VecNorm],[petscvec])
 
 # MatCreateSeqAIJ is acutally used in the code for this project.
 AC_SEARCH_LIBS([MatCreateSeqAIJ],[petscmat],[],
-[AC_MSG_ERROR("The Portable Extensible Tookit for Scientific Computation PETSc is needed to build the system.")])
+[AC_MSG_ERROR("The Portable Extensible Toolkit for Scientific Computation (PETSc) is needed to build the system.")])
 
 AC_OUTPUT
diff --git a/doc/build-cobalt.txt b/doc/build-cobalt.txt
deleted file mode 100644
index 76612a4..0000000
--- a/doc/build-cobalt.txt
+++ b/dev/null
@@ -1,42 +0,0 @@
-Building on NCSA Cobalt.
-
--- Soft
-.soft
-
-@remove +hdf4
-@remove +hdf4-4.2.1
-@remove +hdf5
-@remove +hdf5-1.6.5
-
-@remove +intel-compilers
-@remove +intel-compilers10.0
-@remove +intel-compilers10.1
-@remove +intel-c-10.1.017-f-10.1.017
-@remove +intel-c-11.1.064-f-11.1.064
-
-...defaults...
-
-+phdf5-1.8.4
-
--- Configure
-export PETSC_DIR=/u/ac/dpellegr/apps/Installers/petsc-3.0.0-p10
-
-export CPPFLAGS="\
--I$HDF5_HOME/include \
--I$NCBI_DIR/include \
--I$PETSC_DIR/include \
--I$PETSC_DIR/linux-gnu-c-debug/include"
-
-export LDFLAGS="\
--L$HDF5_HOME/lib \
--L/usr/apps/hdf/szip/lib \
--L/usr/local/intel/10.1.017/lib \
--L$NCBI_DIR/lib \
--L$PETSC_DIR/linux-gnu-c-debug/lib"
-
-export LD_LIBRARY_PATH=\
-$LD_LIBRARY_PATH:\
-/usr/apps/hdf/szip/lib:\
-$PETSC_DIR/linux-gnu-c-debug/lib
-
-
diff --git a/doc/env-cobalt.sh b/doc/env-cobalt.sh
new file mode 100644
index 0000000..5a7a6c3
--- a/dev/null
+++ b/doc/env-cobalt.sh
@@ -0,0 +1,56 @@
+#!/bin/bash
+
+# This script sets environment variables for building and running the
+# project on NCSA Cobalt.  Note that this script should be executed
+# with source env-cobalt.sh rather than ./env-cobalt.sh so that the
+# exports affect the current shell.
+
+# Building on NCSA Cobalt.
+
+# .soft
+#
+# @remove +hdf4
+# @remove +hdf4-4.2.1
+# @remove +hdf5
+# @remove +hdf5-1.6.5
+#
+# @remove +intel-compilers
+# @remove +intel-compilers10.0
+# @remove +intel-compilers10.1
+# @remove +intel-c-10.1.017-f-10.1.017
+# @remove +intel-c-11.1.064-f-11.1.064
+#
+# ...defaults...
+#
+# +phdf5-1.8.4
+
+# Configure
+
+echo "Setting CPPFLAGS."
+
+export CPPFLAGS="\
+-I$HDF5_HOME/include \
+-I$NCBI_DIR/include \
+-I$PETSC_DIR/$PETSC_ARCH/include"
+
+echo CPPFLAGS=$CPPFLAGS
+
+echo "Setting LDFLAGS."
+
+export LDFLAGS="\
+-L$HDF5_HOME/lib \
+-L/usr/apps/hdf/szip/lib \
+-L/usr/local/intel/10.1.017/lib \
+-L$NCBI_DIR/lib \
+-L$PETSC_DIR/$PETSC_ARCH/lib"
+
+echo LDFLAGS=$LDFLAGS
+
+echo "Setting LD_LIBRARY_PATH."
+
+export LD_LIBRARY_PATH=\
+$LD_LIBRARY_PATH:\
+/usr/apps/hdf/szip/lib:\
+$PETSC_DIR/$PETSC_ARCH/lib
+
+echo LD_LIBRARY_PATH=$LD_LIBRARY_PATH
--
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