[doc] add reference to KAMG paper

fix #1

See merge request !24
(cherry picked from commit 4477d811)

Signed-off-by: Steffen Müthing <muething@dune-project.org>

Don't end configure if BLAS is not found. Only the SuperLU
test should fail, which will be the case anyway.

(cherry picked from commit 4e461be4)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

Fix Wshadow warnings

As always, please add your wishes for alternative renaming of variable names.

See merge request !16
(cherry picked from commit 6b890e74)

Signed-off-by: Steffen Müthing <muething@dune-project.org>

The BCRSMatrix code clearly shows that you have to call endrowsizes before calling
addindex.  Therefore the third way to build a BCRSMatrix in the 'random' way is wrong
and should be removed from the test.

(cherry picked from commit 55d6576e)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

Feature/smaller cleanups

as the title suggests, these are a couple of smaller fixes, which are not directly related and aren't important enough to manage them in separate branches.

See merge request !13
(cherry picked from commit 7fb6aa4d)

Signed-off-by: Steffen Müthing <muething@dune-project.org>

(cherry picked from commit 1299ddb1)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

Some exceptions were caught and did not fail the test.

(cherry picked from commit f28b81c9)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

needed for webpage.

(cherry picked from commit e41e47f4)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

Feature/fs1659 matlab output of dynamic matrix

fixed flyspray/FS#1659

See merge request !3
(cherry picked from commit 52617735)

Signed-off-by: Steffen Müthing <muething@dune-project.org>

This partially fixes FS#1724.

(cherry picked from commit 74ed27a8)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

Similar to commit e8d16384 which
added the same for UMFPack.
This avoids strange bugs when using the setSubMatrix method: that method
automatically removes rows and columns from the matrix, and expects
_the user_ to do the same for the x and b vectors.

(cherry picked from commit 1a2f4d0f)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

(cherry picked from commit 23d94ffb)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

This avoids strange bugs when using the setSubMatrix method: that method
automatically removes rows and columns from the matrix, and expects _the user_
to do the same for the x and b vectors.

(cherry picked from commit e8d16384)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

different versions of ParMetis.

(cherry picked from commit b14c2447)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

Parmetis has the option of using non-standard integral types
for the indices. In this case compilation failed. This is
fixed by using the type even for the graph representation
fed to metis/parmetis.

(cherry picked from commit 0ca78d5f)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

(cherry picked from commit c0679f6e)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

(cherry picked from commit 691ac90c)
Signed-off-by: Steffen Müthing <muething@dune-project.org>

This enables users to have several build directories like
build-clang, build-gcc5, build-debug, and still get all
of them ignored.
(cherry picked from commit a1b1f072)

We need this commit for 2.4 otherwise dune-istl test
will not compile with cmake.

(cherry picked from commit a0415709)

In commit 3e405a0b a parameter 'eps'
was introduced for testAggregate(). However this parameter is not
supplied in the call (breaking the test) and it is never used
in the method.

(cherry picked from commit 491ca46b)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

(cherry picked from commit 3e405a0b)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

(cherry picked from commit 80534570)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

These are either masterline bugfixes or have been cherry-picked via a
merge-commit.

[release] Merge fix for handling 64 bit IDXTYPEWIDTH in parmetis>3

(cherry picked from commit 698352e0)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

(cherry picked from commit fd1d87c2)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

This lists all commits marked tagged as bugfix or release
that where explicitly not cherry-picked. Possible reasons for this:

* commits from a branch that was also merged to the release
* commits from a branch where the merge was cherry-picked
* bugfixes for code new to master
* commits that where picked but are not recognized as such

modification of member data. This is needed in OPM.

namespace.

This namespace was probably meant to mark implementation details.  However it
led to violations of the ODR (one definition rule), and to warnings about
defined-but-unused functions (see below).

To illustrate the problem consider the function template
Dune::readMatrixMarket:

  template<typename T, typename A, int brows, int bcols>
  void readMatrixMarket(Dune::BCRSMatrix<Dune::FieldMatrix<T,brows,bcols>,A>& matrix,
                        std::istream& istr)
  {
    // ...
    readSparseEntries(matrix, istr, entries, header, NumericWrapper<T>());
  }

The ODR states (§3.2/5):

  There can be more than one definition of a [...] non-static function
  template (14.5.6) [...] in a program provided that each definition appears
  in a different translation unit, and provided the definitions satisfy the
  following requirements.  Given such an entity named D defined in more than
  one translation unit, then

  - each definition of D shall consist of the same sequence of tokens; and

  - in each definition of D, corresponding names, looked up according to 3.4,
    shall refer to an entity defined within the definition of D, or shall
    refer to the same entity, after overload resolution (13.3) and after
    matching of partial template specialization (14.8.3), except that a name
    can refer to a const object with internal or no linkage if the object has
    the same literal type in all definitions of D, and the object is
    initialized with a constant expression (5.19), and the value (but not the
    address) of the object is used, and the object has the same value in all
    definitions of D; and

  [...]

This is violated by e.g. both readSparseEntries, which is defined in the
anonymous namespace.  Since it is not defined within readMatrixMarket, it must
refer to the same entity in all translation units.  However, its name is
effectively Dune::<unique>::readSparseEntries, where <unique> is unique to
each translation unit, and thus it effectively refers to a different entity in
each translation unit, and the program is ill-formed as soon as move than one
translation unit does #include <dune/istl/matrixmarket.hh>.

The warnings by g++-4.9 looked like this:
======================================================================
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../../..  -pthread -I/home/joe/Projekte/pdelab-2.4/dune-common -I/home/joe/Projekte/pdelab-2.4/dune-common -I../../.. -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -pthread -DMPIPP_H -DENABLE_MPI=1   -g -O3 -Wall -MT matrixmarkettest-matrixmarkettest.o -MD -MP -MF .deps/matrixmarkettest-matrixmarkettest.Tpo -c -o matrixmarkettest-matrixmarkettest.o `test -f 'matrixmarkettest.cc' || echo './'`matrixmarkettest.cc
[...]
In file included from matrixmarkettest.cc:11:0:
../../../dune/istl/matrixmarket.hh:501:10: warning: ‘void Dune::{anonymous}::readNextLine(std::istream&, std::ostringstream&, Dune::{anonymous}::LineType&)’ defined but not used [-Wunused-function]
     void readNextLine(std::istream& file, std::ostringstream&, LineType& type)
          ^
In file included from matrixmarkettest.cc:11:0:
../../../dune/istl/matrixmarket.hh:601:19: warning: ‘std::istream& Dune::{anonymous}::operator>>(std::istream&, Dune::{anonymous}::NumericWrapper<Dune::{anonymous}::PatternDummy>&)’ defined but not used [-Wunused-function]
     std::istream& operator>>(std::istream& is, NumericWrapper<PatternDummy>& num)
                   ^
======================================================================

(cherry picked from commit 1a19f1c1)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

The function is in an anonymous namespace, and it is used nowhere inside
dune-istl.

(cherry picked from commit c2a41b1c)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

(cherry picked from commit 2ee97f2a)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

The standard states (8.3.6/4) that adding default arguments in later
function declarations are only valid for non-template functions.
In matrixmarket.hh, the function template loadMatrixMarket is declared
and a default argument for the last parameter is provided. In
owneroverlapcopy.hh, OwnerOverlapCopyCommunication contains a friend
declaration of loadMatrixMarket without the default parameter. If now
owneroverlapcopy.hh is included before matrixmarket.hh, the friend
declaration is the first declaration and the default parameter in
matrixmarket.hh is invalid.
By including matrixmarket.hh in owneroverlapcopy.hh, we make sure that
the declaration which provides the default argument is always the first
one.

(cherry picked from commit 925dbac3)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

Previously, we assumed that if a_{ij} is stored in the sparse matrix
then a_{ji} must be stored also and used mat[i][j] to access. If the entry
was not stored then an exception somewhere in basearray.hh was thrown.
Unfortunately knowing the cause for this exception is insider knowledge,
seldomly leaked ;). In addition there is now reason to throw an expection here.

With this commit we the find method on the row to search for the entry a_{ji}.
If it is not present we simply treat it as being zero.

(cherry picked from commit 05c0a63a)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

Fixes FS#FS#1649.

(cherry picked from commit eadefdb9)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

(cherry picked from commit 184a1afe)
Signed-off-by: Carsten Gräser <graeser@dune-project.org>

This brings releases/2.4 on par with "master" at 287b0ae9.
We can't do a fast forward because another merge commit was
cherry-picked in between.