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Collection of utilities, solvers and other components.

Home Page: http://www.opm-project.org

License: GNU General Public License v3.0

CMake 1.06% C 15.20% C++ 83.66% Shell 0.08%

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opm-core's Issues

cannot read /etc/lsb-release

when I modified my cdash cronjob to include OPM-core, i got the following error for the "release/2013.03" branch:

http://opm-project.org/CDash/viewConfigure.php?buildid=1424

this machine runs on openSUSE 12.2...

--with-{blas,lapack} options to configure complains very softly about invalid paths

If I configure with the command:

./configure --with-blas=/usr/lib/blumfrub --with-lapack=/usr/lib/snafu

i.e. points the build process to libraries that does not exist, then the configure script reverts to auto-magically locating libraries on my system and uses those. No hard error (i.e. aborting the build) is issued.

To realize that this went wrong, you'll have to look for the

checking for sgemm_ in /usr/lib/blumfrub... no

followed by

checking for sgemm_ in -lblas... yes

messages in the middle of the configure output, or check the output from grep ^BLAS_LIBS Makefile.

In my opinion this is a potential gotcha, but then maybe I don't check my build logs carefully enough :-)

undefined reference to 'call_UMFPACK'

With the newest commits of opm-core (branch release 2013/.03), I was faced with the following building error:

[ 93%] Building CXX object CMakeFiles/test_geom2d.dir/tests/test_geom2d.cpp.o
lib/libopmcore.a(TransportSolverTwophaseImplicit.cpp.o): In function 'void Opm::ImplicitTransportLinAlgSupport::CSRMatrixUmfpackSolver::solve<std::vector<double, std::allocator > >(CSRMatrix const&, std::vector<double, std::allocator > const&, std::vector<double, std::allocator >&)':
/private/laods/opm/RH5/realization_cmake/pure_cmake/src/opm-core/opm /core/transport/implicit/CSRMatrixUmfpackSolver.hpp:61: undefined reference to `call_UMFPACK'

Can this error have been introduced in PR #203? At least opm-core@e59db97128 builds fine.

tensor grid manager

Hi,
I'm trying to write an input file of SPE9 for testing opm-autodiff/sim_fibo_ad. I find that the tensor grid just support constant vector for the keyword "TOPS", but which in SPE9 is not constant yet, it's a nonuniform vector. So is there any other method to create a SPE9 grid or could the "TOPS" be enhanced to support nonuniform vector?
Thanks.

Howto build the documentation.

Can somebody tell me what the recommend way to build the doxygen documentation is?

Include directory for package is not added to test program compile line

It seems that the probed directory for include files which is added to CMAKE_REQUIRED_INCLUDES is not actually added to the command-line. This may be because of a difference between CMake versions.

configure without umfpack succeeds but compilation fails

If umfpack is not found, configure just issues a warning but succeeeds. Later compilation of some programs fails.

Either configure should fail without usable umfpack or the compilation of programs requiring umfpack should be deactivated.

Logs can be found at https://gist.github.com/3851627

Infer information about the source tree from DUNE-CMake's config mode files

OPM cannot include DUNE-CMake in config mode because it also needs information about which definitions that should be added to config.h, so that the DUNE headers is preprocessed identical in all libraries.

The current version simply uses the same probe routines as for the Autotools version, with some additional hints to guess the source directory from the location of the binary files.

An improvement to this would be to include the config mode files ourselves to first gather more information about where the source tree is located. The PkgConfig files cannot be used, as they point to the intended install location of the library instead of the build tree.

LinearSolverReport should have a default constructor

The documentation for Opm::LinearSolverInterface::LinearSolverReport (in opm/core/linalg/LinearSolverInterface.hpp) states that the only field that is mandatory to set is converged, and this option is exercised in e.g. Opm::LinearSolverUmfpack::solve (opm/core/linalg/LinearSolverUmfpack.cpp).

However, this results in returning undefined data from that method and the compiler sometimes [*] generates a warning about this.

[] It appearently thinks it sufficies to just notify me now and then so I won't forget, but it won't nag *every time, as that would be a bit rude.

Document WellReport::push()

The data will contain for each well the triple (BHP, total rate, WC).

Cache problems in FindERT

I just installed ERT and reran cmake. I experienced serveral problems:

First the headers were found but the libraries not. I had to use

-DCMAKE_LIBRARY_ARCHITECTURE=x86_64-linux-gnu
to fix this as on my Debian system the ERT libraries got install under lib/x86_64-linux-gnu

Now CMake always complained that HAVE_ERT is false. I think the cause for this that line 114 this value is put into the cache:

# write unsuccessful result to the cache, as the check_c_source_compiles
# would do if it failed

set (HAVE_ERT)
set (HAVE_ERT "${HAVE_ERT}" CACHE INTERNAL "Did an ERT sample program compile?")

I would like to understand why this is needed as in my case this seems the root of the bug.
BTW I could resolve this issue with manually unsetting HAVE_ERT in the cash:


unset(HAVE_ERT CACHE)

right before check_c_source_compiles. But this does not seem to be viable solution, as then the test will always be run

Commit #ae52de0 breaks build in examples/refine_wells on Ubuntu 12.04

Commit #ae52de0 breaks the build when compiling examples/refine_wells with the linker error: /usr/lib/liblapack.so.3gf: undefined reference to `ATL_xxx', where xxx is a BLAS function. /usr/lib/liblapack.so.3gf comes from the libatlas3gf-base package, version 3.8.4. The preceeding commit #d7998 builds.

The link command is:

g++ -g -O2 -o .libs/refine_wells refine_wells.o ../lib/.libs/libopmcore.so -L/usr/lib -lsuperlu -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lgfortran -lquadmath -lblas -lumfpack -lcholmod -lccolamd -lcolamd -lcamd -lamd -lm -ldunecommon

I suspect this is due to the above mentioned commit adding $(BLAS) to examples/Makefile.am, since if I remove -lblas from the line above, it compiles. Unfortunately, I don't have time to test further today.

Output noise from transport solver

When running steadystate_test_implicit I get a hole lot of noise, that is tons of lines

Warning: initIteration() - s was clamped in some cells.

This message is printed by initIteration(...) in 'opm/core/transport/implicit/SinglePointUpwindTwoPhase.hpp' whenever the saturation in a cell is outside its limits. I understand that this warning has a purpose, but printing thousands of them is annoying for the user. There is also no reference to which cell this applies. Maybe a better solution is to print this message only once when calling initIteration(...)?

make check should run unit tests

In the cmake branch, they are currently only compiled not run.

linking with boost-filesystem fails since commit e79dba271452721cc807b4d891ddbead1ed1ac78

Since the merge of pull request #43, building opm-core fails on my system:

--- going to build opm-core  ---
WARNING: commandline parameters will overwrite setting in opts file "/home/mblatt/src/dune/opts/agmg.opts"
--- calling make for opm-core ---
make  "V=1" "all"
make  all-recursive
make[1]: Entering directory `/home/mblatt/src/dune/2.2/opm-core'
Making all in .
make[2]: Entering directory `/home/mblatt/src/dune/2.2/opm-core'
make[2]: Leaving directory `/home/mblatt/src/dune/2.2/opm-core'
Making all in tests
make[2]: Entering directory `/home/mblatt/src/dune/2.2/opm-core/tests'
make[2]: Für das Ziel »all« ist nichts zu tun.
make[2]: Leaving directory `/home/mblatt/src/dune/2.2/opm-core/tests'
Making all in examples
make[2]: Entering directory `/home/mblatt/src/dune/2.2/opm-core/examples'
/bin/bash ../libtool  --tag=CXX   --mode=link g++  -DNDEBUG -O4 -Wall -I/home/mblatt/src/dune/2.2/dune-common-2.2.0 -I/home/mblatt/src/dune/2.2/dune-istl-2.2.0  -L/home/mblatt/src/dune/2.2/dune-common-2.2.0/lib/.libs -o sim_2p_comp_reorder sim_2p_comp_reorder.o ../lib/libopmcore.la -lumfpack -lcholmod -lccolamd -lcolamd -lcamd -lamd -lm -ldunecommon 
libtool: link: g++ -DNDEBUG -O4 -Wall -I/home/mblatt/src/dune/2.2/dune-common-2.2.0 -I/home/mblatt/src/dune/2.2/dune-istl-2.2.0 -o .libs/sim_2p_comp_reorder sim_2p_comp_reorder.o  -L/home/mblatt/src/dune/2.2/dune-common-2.2.0/lib/.libs ../lib/.libs/libopmcore.so -lumfpack -lcholmod -lccolamd -lcolamd -lcamd -lamd -lm /home/mblatt/src/dune/2.2/dune-common-2.2.0/lib/.libs/libdunecommon.a -llapack
/usr/bin/ld: sim_2p_comp_reorder.o: undefined reference to symbol '_ZN5boost11filesystem36detail18create_directoriesERKNS0_4pathEPNS_6system10error_codeE'
/usr/bin/ld: note: '_ZN5boost11filesystem36detail18create_directoriesERKNS0_4pathEPNS_6system10error_codeE' is defined in DSO /usr/lib/libboost_filesystem.so.1.49.0 so try adding it to the linker command line
/usr/lib/libboost_filesystem.so.1.49.0: could not read symbols: Invalid operation
collect2: error: ld returned 1 exit status
make[2]: *** [sim_2p_comp_reorder] Fehler 1
make[2]: Leaving directory `/home/mblatt/src/dune/2.2/opm-core/examples'
make[1]: *** [all-recursive] Fehler 1
make[1]: Leaving directory `/home/mblatt/src/dune/2.2/opm-core'
make: *** [all] Fehler 2
--- Failed to build opm-core ---
Terminating dunecontrol due to previous errors!
´´´´

[Cmake release][out-of-source]: OPMPackage should first try find_package in config-mode

Currently, the dune core modules with cmake support are not found correctly (see OPM/opm-grid#15 ).

I would propose to insert a find_packe call using Config mode before trying with pkg-config or find_xxx directives. By this way dune modules built out of source would be detected correctly.

CMakeError: CHOLMOD

Hi,

I have started the work of testing the branch release/2013.03 on Statoils workstations (rhel 5). Since I want to use cmake and version 2.2 of DUNE, I have used the repos https://svn.dune-project.org/svn/dune-{common,geometry,grid,istl}/branches/release-cmake-2.2. According to @blattms this will soon be stable, but for now I have used revision 1876 of dune-istl due to a bug in earlier revisions. All DUNE modules builds fine with dunecontrol:

dune-common/bin/dunecontrol --use-cmake --opts=config.opts all

My config file simply contains paths to boost and superlu libraries:

CMAKE_FLAGS="-DCMAKE_PREFIX_PATH=\"/project/res/x86_64_RH_5/share/opm/boost;/project/res/x86_64_RH_5/share/opm/SuperLU_4.0\" "

However, when building opm-core, I get the following error message:

CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
CHOLMOD_LIBRARY
linked by target "cmTryCompileExec" in directory /private/laods/opm/RH5/realization_cmake/dune2.2/opm-core/build-cmake/CMakeFiles/CMakeTmp

The hole log file can be viewed here: https://gist.github.com/laods/5141706.

Does opm-core require cholmod (if so this has passed me by)? I also observe that other tests fail, e.g. SUPERLU_MIN_VERSION_4_3 and HAVE_TINYXML, and that ERT and AGMG are not found. Are these serious warnings?

Can we remove the m4 directory?

We seem to still have an m4 directory full of autotools-related macros. Can this be safely deleted?

m4/opm_superlu.m4 confuses other modules and deactivates SuperLU

the new test, which makes SuperLU available in opm-core, confuses the rest of the OPM modules.
For them the SuperLU test of DUNE is run first and everything is setup correctly. Later on the test from opm-core is run in addition and does not find SuperLU. Ergo it unsets the SUPERLU flags in the makefiles (the entries in config.h are kept as they are). One can test this by checking SUPERLU_CPPFLAGS in the Makefile (grep ^SUPERLU_CPPFLAGS Makefile), which is empty on my system for OPM modules other than opm-core.

This means that SuperLU is not available for the other OPM modules.

Merge CMake branch with master

Best place to put binary packages

We need to provide tarballs for download. It would also be beneficiary for the project to have ready-made packages for most distributions. Question is: Should we put those up on the respective open repositories (EPEL for RHEL, LaunchPad for Debian/Ubuntu, OpenSuSE repositories), or should we put up packages (and a mirror of dependencies) on our own web host?

Change the source term in tutorial2?

tutorials/tutorial2.cpp declares a grid of 40x40x1 blocks using the GridManager constructor where dx, dy is implicitly set to 1. Thus the area of each side is 1m^2.

It then proceeds to set a source term on the first and last block, which in the Cartesian grid are two corners. The active surface of those two blocks are thus 2m^2 each.

Now, from examples/sim_2p_incomp.cpp and computePorevolume in opm/core/utility/miscUtilities.cpp we see evidence that the source term is actually a volumetric flux in volume units (meters) per second, meaning that tutorial2 has a source term of 100m^3/s, yielding a velocity of 50m/s (and a Reynolds number on the order 10^7).

Isn't this a tad... unrealistic?

To-do list for release 2013.02

This is an attempt to collect various things that must be done/fixed before we can do a release. Alternatively, we may post each separate thing as an issue, please state your opinion!

Before branching: merging any code that should be in the release, renaming any classes or functions that are ill-named, restructuring the directory hierarchy if necessary.
Branch the release (need to find a useful branch name, it will live forever). I would like to do this January 23rd (Wednesday), if possible.
Ensure that the library builds with cmake on all relevant platforms.
Build debian packages (issue #112).

cmake build system fails in FindSuiteSparse

During enablement of CDash, I tried out the new cmake build system (using the 'cmake' branch) on openSUSE Tumbleweed.

It failed and produced the following logfiles:

http://poware.org/opm-core/CMakeError.log
http://poware.org/opm-core/CMakeOutput.log

(BTW: does anybody know if there is a more convenient way to attach files to the github bugtracker than gists?) The output on the terminal was the following:

lauser@jabba:/temp/lauser/build/opm-core > cmake ~/src/opm-core/
-- The C compiler identification is GNU 4.7.1
-- The CXX compiler identification is GNU 4.7.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Build type: Debug
-- Performing Test HAVE_C99
-- Performing Test HAVE_C99 - Success
-- Found C99: -std=c99
-- Checking to see if CXX compiler accepts flag -std=c++11
-- Checking to see if CXX compiler accepts flag -std=c++11 - yes
-- Performing Test HAVE_NULLPTR
-- Performing Test HAVE_NULLPTR - Success
-- Performing Test HAVE_ARRAY
-- Performing Test HAVE_ARRAY - Success
-- Performing Test HAVE_INTEGRAL_CONSTANT
-- Performing Test HAVE_INTEGRAL_CONSTANT - Success
-- Performing Test HAVE_ATTRIBUTE_ALWAYS_INLINE
-- Performing Test HAVE_ATTRIBUTE_ALWAYS_INLINE - Success
-- Performing Test HAS_ATTRIBUTE_UNUSED
-- Performing Test HAS_ATTRIBUTE_UNUSED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED
-- Performing Test HAS_ATTRIBUTE_DEPRECATED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG - Success
-- Performing Test HAVE_STATIC_ASSERT
-- Performing Test HAVE_STATIC_ASSERT - Success
-- Performing Test HAVE_VARIADIC_TEMPLATES
-- Performing Test HAVE_VARIADIC_TEMPLATES - Success
-- Performing Test HAVE_VARIADIC_CONSTRUCTOR_SFINAE
-- Performing Test HAVE_VARIADIC_CONSTRUCTOR_SFINAE - Success
-- Performing Test HAVE_RVALUE_REFERENCES
-- Performing Test HAVE_RVALUE_REFERENCES - Success
-- Looking for C++ include tuple
-- Looking for C++ include tuple - found
-- Looking for C++ include tr1/tuple
-- Looking for C++ include tr1/tuple - found
-- Looking for C++ include type_traits
-- Looking for C++ include type_traits - found
-- Looking for C++ include tr1/type_traits
-- Looking for C++ include tr1/type_traits - found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- A library with BLAS API found.
-- A library with BLAS API found.
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
CMake Error at cmake/Modules/FindSuiteSparse.cmake:153 (list):
list sub-command REMOVE_DUPLICATES requires list to be present.
Call Stack (most recent call first):
cmake/Modules/OpmFind.cmake:69 (find_package)
cmake/Modules/OpmFind.cmake:98 (find_and_append_package_to)
cmake/Modules/OpmFind.cmake:104 (find_and_append_package_list_to)
CMakeLists.txt:53 (find_and_append_package_list)

CMake Error at cmake/Modules/FindSuiteSparse.cmake:154 (list):
list sub-command REVERSE requires list to be present.
Call Stack (most recent call first):
cmake/Modules/OpmFind.cmake:69 (find_package)
cmake/Modules/OpmFind.cmake:98 (find_and_append_package_to)
cmake/Modules/OpmFind.cmake:104 (find_and_append_package_list_to)
CMakeLists.txt:53 (find_and_append_package_list)

CMake Error at cmake/Modules/FindSuiteSparse.cmake:155 (list):
list sub-command REMOVE_DUPLICATES requires list to be present.
Call Stack (most recent call first):
cmake/Modules/OpmFind.cmake:69 (find_package)
cmake/Modules/OpmFind.cmake:98 (find_and_append_package_to)
cmake/Modules/OpmFind.cmake:104 (find_and_append_package_list_to)
CMakeLists.txt:53 (find_and_append_package_list)

CMake Error at cmake/Modules/FindSuiteSparse.cmake:156 (list):
list sub-command REVERSE requires list to be present.
Call Stack (most recent call first):
cmake/Modules/OpmFind.cmake:69 (find_package)
cmake/Modules/OpmFind.cmake:98 (find_and_append_package_to)
cmake/Modules/OpmFind.cmake:104 (find_and_append_package_list_to)
CMakeLists.txt:53 (find_and_append_package_list)

-- Could NOT find SuiteSparse (missing: SuiteSparse_LIBRARIES SuiteSparse_INCLUDE_DIRS)
-- Performing Test HAVE_MEM_USAGE_T_EXPANSIONS
-- Performing Test HAVE_MEM_USAGE_T_EXPANSIONS - Failed
-- Performing Test SUPERLU_MIN_VERSION_4_3
-- Performing Test SUPERLU_MIN_VERSION_4_3 - Failed
-- Performing Test SUPERLU_POST_2005_VERSION
-- Performing Test SUPERLU_POST_2005_VERSION - Failed
-- Could NOT find SuperLU (missing: SUPERLU_INCLUDE_DIR SUPERLU_LIBRARY)
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.8")
-- Boost version: 1.49.0
-- Found the following Boost libraries:
-- date_time
-- filesystem
-- system
-- unit_test_framework
-- A library with BLAS API found.
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.25")
-- Performing Test HAVE_DUNE_COMMON
-- Performing Test HAVE_DUNE_COMMON - Failed
CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:97 (message):
Could NOT find dune-common (missing: _req_vars)
Call Stack (most recent call first):
/usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:291 (_FPHSA_FAILURE_MESSAGE)
cmake/Modules/OpmPackage.cmake:164 (find_package_handle_standard_args)
cmake/Modules/Finddune-common.cmake:14 (find_opm_package)
cmake/Modules/OpmPackage.cmake:69 (find_package)
cmake/Modules/Finddune-istl.cmake:14 (find_opm_package)
cmake/Modules/OpmFind.cmake:69 (find_package)
cmake/Modules/OpmFind.cmake:98 (find_and_append_package_to)
cmake/Modules/OpmFind.cmake:104 (find_and_append_package_list_to)
CMakeLists.txt:53 (find_and_append_package_list)

-- Configuring incomplete, errors occurred!

problems with linking dune-cornerpoint to opm-core

@rolk

I have struggled for a while with installing dune-cornerpoint. I get lots of undefined references looking like this for instance:

readEclipseFormat.cpp:(.text+0x3906): undefined reference to `Opm::EclipseGridInspector::gridSize() const'

I saw your newest commit 2c1df0b and hoped it would fix the problem, but it didn't. I have install opm-core with cmake and used dunecontrol to build dune-cornerpoint.

How to specify the path of boost and libtool

Hi,

Does anyone help me to specify the path of boost and libtool?
When I build the opm-core using cd path/to/build and cmake ../opm-core DCMAKE_BUILD_TYPE=Release, there are two errors:

-- Finding package Boost using module mode
CMake Error at /usr/local/cmake-2.8.6/share/cmake-2.8/Modules/FindBoost.cmake:1197 (message):
Unable to find the requested Boost libraries.

Boost version: 1.33.1

Boost include path: /usr/include

Detected version of Boost is too old. Requested version was 1.39 (or
newer).

The following Boost libraries could not be found:
```
    boost_date_time
    boost_filesystem
    boost_system
    boost_unit_test_framework
```
No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to the
directory containing Boost libraries or BOOST_ROOT to the location of
Boost.
Call Stack (most recent call first):
cmake/Modules/OpmFind.cmake:138 (find_package)
cmake/Modules/OpmFind.cmake:188 (find_and_append_package_to)
CMakeLists.txt:117 (find_and_append_package_list_to)
-- Found Doxygen: /usr/bin/doxygen
-- Libtool not found!
-- Configuring incomplete, errors occurred!

Actually, I found my Boost is under /usr/local, and there are 4 different version of Boost. If I want to use /usr/local/boost-1.50.1, how do I set the path?
And for libtool, it is under /usr/share/libtool. It seems that it did not find libtool.

How should I specify the path for boost and libtool?
Please help me.

FIND_OPM_PACKAGE (OpmPackage.cmake) does not honour build type

It appears that FIND_OPM_PACKAGE (from OpmPackage.cmake) does not honour build-type specific compiler flags (e.g., CMAKE_CXX_FLAGS_DEBUG) during configuration. I noticed this when trying to set up a debug configuration of the dune-cornerpoint.

The direct cause of the configuration failure, summarised in Gist https://gist.github.com/bska/5411208, is that I built (and installed) the Dune core modules (common, geometry, istl, and grid) using the debug and sanity/correctness-checking mode of libstdc++ (http://gcc.gnu.org/onlinedocs/libstdc++/manual/debug_mode.html). As a result, functions compiled into libdunegrid.a which otherwise accept or return a std::vector will accept/return a __gnu_debug::vector instead. This leads to (potential) linker errors during configuration unless the compile/link tests define the macros _GLIBCXX_DEBUG and _GLIBCXX_DEBUG_PEDANTIC.

As far as I can tell, appending something like CMAKE_CXX_FLAGS_${CMAKE_BUILD_TYPE} to CMAKE_REQUIRED_DEFINITIONS at or around line 249 of OpmPackage.cmake (as of commit e8e3960) should be sufficient, but I haven't figured how to do that. The downside to using CMAKE_BUILD_TYPE is, of course, that the technique will be limited to Make-based generators.

Built files change if I redo cmake configuration

If I build an executable and store it, then remake that file without reconfiguration, the files compare identical. However, if I reconfigure and rebuild they differ.

Why does this happen? Is some timestamp being embedded? I think this is unfortunate behaviour, but do not know what to do about it.

Does generate_doc_figures.py belong in the project root?

This script references the directory ../Documentation, which does not exist, and looks for data files in the project root. I guess it is meant to perhaps be located in the tutorials directory? (And where is user xavierr, BTW?)

Possible bug in csrmatrix_new_elms_pushback (in opm/core/linalg/sparse_sys.c)

I believe I've ecountered a bug in the csrmatrix_new_elms_pushback helper function for constructing a CSRMatrix. At least according to the description given here: http://web.eecs.utk.edu/~dongarra/etemplates/node373.html

The final element in the ia array should be nnz + 1 (or just nnz when indexing starts at zero I assume). It appears to me that the constructed ia array is right-shifted, having an extra zero at the begining and missing the nnz at the end.

Commit that I think should be correct:
https://github.com/Ivarun/opm-core/commit/2d3ab36e047ec92144e6a0865192cbe70b9b78f1

I'm asking first though since I'm not sure if there are different approaches to the csr datastructure, or maybe I'm just plain mistaken.

opm-core does not build

Using dunectrol and dune ppa packages on ubuntu 12.04. Git commit 643d54e fails to build opm-core. Compiling fails for refine_wells with the following output:

CXXLD refine_wells
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zptgemm' /usr/lib/liblapack.so.3gf: undefined reference toATL_scopy'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_stpsv' /usr/lib/liblapack.so.3gf: undefined reference toATL_saxpy'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_srotg' /usr/lib/liblapack.so.3gf: undefined reference toATL_ztrsv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zhpr' /usr/lib/liblapack.so.3gf: undefined reference toATL_cswap'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_drot' /usr/lib/liblapack.so.3gf: undefined reference toATL_zgeru'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_stbsv' /usr/lib/liblapack.so.3gf: undefined reference toATL_dsyr'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zher2' /usr/lib/liblapack.so.3gf: undefined reference toATL_cptgemm'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_cset' /usr/lib/liblapack.so.3gf: undefined reference toATL_zdrot'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_ssyreflect' /usr/lib/liblapack.so.3gf: undefined reference toATL_scnrm2'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_stbmv' /usr/lib/liblapack.so.3gf: undefined reference toATL_zpther2k'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_cpthemm' /usr/lib/liblapack.so.3gf: undefined reference toATL_cpttrsm'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_ztbsv' /usr/lib/liblapack.so.3gf: undefined reference toATL_sspr'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_csyreflect' /usr/lib/liblapack.so.3gf: undefined reference toATL_dpttrmm'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dscal' /usr/lib/liblapack.so.3gf: undefined reference toATL_dsyr2'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zGetNB' /usr/lib/liblapack.so.3gf: undefined reference toATL_ddot'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zaxpy' /usr/lib/liblapack.so.3gf: undefined reference toATL_cgeru'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_ssymv' /usr/lib/liblapack.so.3gf: undefined reference toATL_dzasum'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_sptsyrk' /usr/lib/liblapack.so.3gf: undefined reference toATL_ztbmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_snrm2' /usr/lib/liblapack.so.3gf: undefined reference toATL_cptherk'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zhpmv' /usr/lib/liblapack.so.3gf: undefined reference toATL_cptsyr2k'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zgbmv' /usr/lib/liblapack.so.3gf: undefined reference toATL_dptgemm'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_ccopy' /usr/lib/liblapack.so.3gf: undefined reference toATL_dset'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_cptsymm' /usr/lib/liblapack.so.3gf: undefined reference toATL_sger'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_cher2' /usr/lib/liblapack.so.3gf: undefined reference toATL_dGetNB'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_crotg' /usr/lib/liblapack.so.3gf: undefined reference toATL_zswap'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dtbsv' /usr/lib/liblapack.so.3gf: undefined reference toATL_zdotc_sub'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zptherk' /usr/lib/liblapack.so.3gf: undefined reference toATL_ctpmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zpttrsm' /usr/lib/liblapack.so.3gf: undefined reference toATL_ctrsv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dptsyrk' /usr/lib/liblapack.so.3gf: undefined reference toATL_zsyreflect'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dspr' /usr/lib/liblapack.so.3gf: undefined reference toATL_dtrsv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_sptgemm' /usr/lib/liblapack.so.3gf: undefined reference toATL_zgemv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_cher' /usr/lib/liblapack.so.3gf: undefined reference toATL_ssbmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_caxpy' /usr/lib/liblapack.so.3gf: undefined reference toATL_sptsymm'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_cgerc' /usr/lib/liblapack.so.3gf: undefined reference toATL_dnrm2'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dsyreflect' /usr/lib/liblapack.so.3gf: undefined reference toATL_sdsdot'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_spttrmm' /usr/lib/liblapack.so.3gf: undefined reference toATL_cscal'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_stpmv' /usr/lib/liblapack.so.3gf: undefined reference toATL_sspmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_cdotu_sub' /usr/lib/liblapack.so.3gf: undefined reference toATL_ctbmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_icamax' /usr/lib/liblapack.so.3gf: undefined reference toATL_sscal'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_sptsyr2k' /usr/lib/liblapack.so.3gf: undefined reference toATL_ssyr'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_ctbsv' /usr/lib/liblapack.so.3gf: undefined reference toATL_drotmg'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_spttrsm' /usr/lib/liblapack.so.3gf: undefined reference toATL_zhpr2'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_ctpsv' /usr/lib/liblapack.so.3gf: undefined reference toATL_zpthemm'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dpttrsm' /usr/lib/liblapack.so.3gf: undefined reference toATL_strmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zcopy' /usr/lib/liblapack.so.3gf: undefined reference toATL_idamax'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zscal' /usr/lib/liblapack.so.3gf: undefined reference toATL_cdotc_sub'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dtbmv' /usr/lib/liblapack.so.3gf: undefined reference toATL_sspr2'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_cpther2k' /usr/lib/liblapack.so.3gf: undefined reference toATL_ztrmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zcopyConj' /usr/lib/liblapack.so.3gf: undefined reference toATL_zmoveConj'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zptsyrk' /usr/lib/liblapack.so.3gf: undefined reference toATL_cgemv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zcplxinvert' /usr/lib/liblapack.so.3gf: undefined reference toATL_cscalConj'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_sasum' /usr/lib/liblapack.so.3gf: undefined reference toATL_zscalConj'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dcopy' /usr/lib/liblapack.so.3gf: undefined reference toATL_zaxpby'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_cmoveConj' /usr/lib/liblapack.so.3gf: undefined reference toATL_scasum'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_srotmg' /usr/lib/liblapack.so.3gf: undefined reference toATL_dtpsv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_sdot' /usr/lib/liblapack.so.3gf: undefined reference toATL_chpr2'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zhemv' /usr/lib/liblapack.so.3gf: undefined reference toATL_zdotu_sub'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zptsyr2k' /usr/lib/liblapack.so.3gf: undefined reference toATL_chbmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_sswap' /usr/lib/liblapack.so.3gf: undefined reference toATL_ccplxinvert'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zptsymm' /usr/lib/liblapack.so.3gf: undefined reference toATL_izamax'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_drotg' /usr/lib/liblapack.so.3gf: undefined reference toATL_dtrmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_ztpmv' /usr/lib/liblapack.so.3gf: undefined reference toATL_zher'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_srot' /usr/lib/liblapack.so.3gf: undefined reference toATL_dsdot'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_ztpsv' /usr/lib/liblapack.so.3gf: undefined reference toATL_srotm'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_daxpby' /usr/lib/liblapack.so.3gf: undefined reference toATL_sset'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zpttrmm' /usr/lib/liblapack.so.3gf: undefined reference toATL_daxpy'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dgemv' /usr/lib/liblapack.so.3gf: undefined reference toATL_cpttrmm'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_ctrmv' /usr/lib/liblapack.so.3gf: undefined reference toATL_ccopyConj'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zgerc' /usr/lib/liblapack.so.3gf: undefined reference toATL_dgbmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dspr2' /usr/lib/liblapack.so.3gf: undefined reference toATL_sgbmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dptsyr2k' /usr/lib/liblapack.so.3gf: undefined reference toATL_dsymv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_sgemv' /usr/lib/liblapack.so.3gf: undefined reference toATL_dsbmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dasum' /usr/lib/liblapack.so.3gf: undefined reference toATL_saxpby'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dswap' /usr/lib/liblapack.so.3gf: undefined reference toATL_chpmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_isamax' /usr/lib/liblapack.so.3gf: undefined reference toATL_caxpby'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dtpmv' /usr/lib/liblapack.so.3gf: undefined reference toATL_dptsymm'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_chpr' /usr/lib/liblapack.so.3gf: undefined reference toATL_dznrm2'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_ssyr2' /usr/lib/liblapack.so.3gf: undefined reference toATL_sGetNB'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_zset' /usr/lib/liblapack.so.3gf: undefined reference toATL_zhbmv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dger' /usr/lib/liblapack.so.3gf: undefined reference toATL_chemv'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_cGetNB' /usr/lib/liblapack.so.3gf: undefined reference toATL_csrot'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_dspmv' /usr/lib/liblapack.so.3gf: undefined reference toATL_xerbla'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_drotm' /usr/lib/liblapack.so.3gf: undefined reference toATL_cptsyrk'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_cgbmv' /usr/lib/liblapack.so.3gf: undefined reference toATL_zrotg'
/usr/lib/liblapack.so.3gf: undefined reference to ATL_strsv' collect2: ld returned 1 exit status make[2]: *** [refine_wells] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: Leaving directory/home/andreas/Opm/opm-core/examples'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/andreas/Opm/opm-core'
make: *** [all] Error 2
--- Failed to build opm-core ---
Terminating dunecontrol due to previous errors!

Grid file is written as formatted data by writeECLdata()

Commit 1281d17 made writeECLdata() write restart files unformatted by default. However, the produced grid file (.FEGRID) is still written as formatted by default. Should this also be changed? It would also be nice if a .INIT file is written by writeECLdata(), so that the static variables can be accessed.

linking breakes at compute_tof

uname -a
Linux ***** 3.4.28-2.20-desktop #1 SMP PREEMPT Tue Jan 29 16:51:37 UTC 2013 (143156b) x86_64 x86_64 x86_64 GNU/Linux

built command

sudo dunecontrol all

breaks at line
....
make
[ 79%] Built target opmcore
Linking CXX executable bin/compute_tof

Linker error message:

_ZThn16_N5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian16bad_day_of_monthEEEED1Ev' referenced in section.rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section .gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian16bad_day_of_monthEEEED5Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin) _ZThn16_N5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian16bad_day_of_monthEEEED0Ev' referenced in section .rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section.gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian16bad_day_of_monthEEEED0Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin)
_ZThn56_N5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian16bad_day_of_monthEEEED1Ev' referenced in section.rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section .gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian16bad_day_of_monthEEEED5Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin) _ZThn56_N5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian16bad_day_of_monthEEEED0Ev' referenced in section .rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section.gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian16bad_day_of_monthEEEED0Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin)
_ZThn16_N5boost16exception_detail10clone_implINS0_19error_info_injectorISt12out_of_rangeEEED1Ev' referenced in section.rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section .gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorISt12out_of_rangeEEED5Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin) _ZThn16_N5boost16exception_detail10clone_implINS0_19error_info_injectorISt12out_of_rangeEEED0Ev' referenced in section .rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section.gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorISt12out_of_rangeEEED0Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin)
_ZThn56_N5boost16exception_detail10clone_implINS0_19error_info_injectorISt12out_of_rangeEEED1Ev' referenced in section.rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section .gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorISt12out_of_rangeEEED5Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin) _ZThn56_N5boost16exception_detail10clone_implINS0_19error_info_injectorISt12out_of_rangeEEED0Ev' referenced in section .rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section.gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorISt12out_of_rangeEEED0Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin)
_ZThn16_N5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian11bad_weekdayEEEED1Ev' referenced in section.rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section .gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian11bad_weekdayEEEED5Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin) _ZThn16_N5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian11bad_weekdayEEEED0Ev' referenced in section .rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section.gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian11bad_weekdayEEEED0Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin)
_ZThn56_N5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian11bad_weekdayEEEED1Ev' referenced in section.rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section .gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian11bad_weekdayEEEED5Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin) _ZThn56_N5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian11bad_weekdayEEEED0Ev' referenced in section .rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section.gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian11bad_weekdayEEEED0Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin)
_ZThn16_N5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian8bad_yearEEEED1Ev' referenced in section.rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section .gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian8bad_yearEEEED5Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin) _ZThn16_N5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian8bad_yearEEEED0Ev' referenced in section .rodata' of /tmp/cckUwee2.ltrans5.ltrans.o: defined in discarded section.gnu.linkonce.t._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_9gregorian8bad_yearEEEED0Ev' of CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o (symbol from plugin)
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/usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: bin/compute_tof: hidden symbol `.LTHUNK4.16436' isn't defined
/usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
make[2]: *** [bin/compute_tof] Error 1
make[1]: *** [CMakeFiles/compute_tof.dir/all] Error 2
make: *** [all] Error 2
--- Failed to build opm-core ---
Terminating dunecontrol due to previous errors!

Who can help?
Thanks, Oliver Kastner

Feature request: Make DUNE_ISTL_VERSION, etc. available from config.h

I intend to make available some of the recent ISTL improvements. As they will only be available in the trunk or the inofficial 2.2.1 release with CMake support, I need to detect the version during preprocessing.

What it be possible to make the following defines available from config.h:
DUNE_ISTL_VERSION
DUNE_ISTL_VERSION_MAJOR
DUNE_ISTL_VERSION_MINOR
DUNE_ISTL_VERSION_REVISION

(ISTL would suffice for this particular case, but making this consistently for other DUNE module would be cool!)
These can be extracted from the dune.module files of the DUNE modules.

Cannot compile opm-core with C++0x compiler

make CXXFLAGS='-std=c++0x -DHAVE_NULLPTR' opm/core/wells/WellsGroup.lo fails (commit e6df79)

SuperLU breaks the build

currently, I get the following if I try to compile opm-porsol

lauser@unni:~/src/opm-porsol|master > make
Makefile:467: *** target pattern contains no `%'. Stop.

investigating the Makefile, one finds the following at lin 467:

SUPERLU_CPPFLAGS = -I./configure: eval: line 41318: syntax error near unexpected token (' ./configure: eval: line 41318:cd yes (version 4.3 or newer)'/include/superlu -DENABLE_SUPERLU

I guess this means that something went wrong in the SuperLU M4 test.

BTW: how can I attach files on the github bugtracker? I would like to provide config.log...

Remove unportable code from opm/core/io/eclipse/EclipseGridInspector.hpp

The header uses std::tr1::array as the return type in several methods. This might break for some compilers as the use std::array instead.

As opm is supposed to work without DUNE, I propose to use boost::array instead. If this is an accepted solution I am willing to provide a patch.

[CMake branch] Does not configure on Ubuntu 10.04 LTS

This is on the CMake branch, currently being evaluated for inclusion into mainline OPM-Core (cf. issue #119). I am unable to perform even basic configuration on my current work station which runs Ubuntu 10.04 LTS (x86_64).

The FindBLAS.cmake macro that comes with CMake 2.8.0 (package version on Ubuntu 10.04) requires Fortran. I had to enable_languages (Fortran) in the CMakeLists.txt file.
The FindSUPERLU.cmake implementation in uses the cmake_push_check_state() macro (on line 69 as of commit 1a94211). As far as I can tell, the cmake_push_check_state() macro was not introduced until CMake 2.8.6. What is the minimum version of CMake required to configure the project?

[Cmake release][out-of-source] configure calls cmake always in root source directory

I was curious whether I can build out of source and tried this:

cd opm-core; mkdir build-cmake; cd build-cmake;
../configure
make
make: *** No targets specified and no makefile found.  Stop.

Apparently, cmake is called in the root source directory as CMakeCache.txt is created there. This will probably break dune-control (of the official 2.2.1 release) as it assumes the make files to be in the other directory.

I am not tagging this as a bug, as I am unsure whether out-of-source builds are supported.

CompressibleTpfa::computeWellDynamicData: Properties for injectors

Comparison with eclipse 100 seems to indicate that injectors should be treated similar to producers, thus simply be assigned the properties of the perforation grid cells ...

make clean does nothing

I normally assume that "make clean" removes all libraries and programs. Unfortunately, for all OPM modules that I tested (building out of source) it does exactly nothing. This seems to be an issue of OPM as in other projects make clean works as exspected.

cmake build system fails in FindSuiteSparse

During enablement of CDash, I tried out the new cmake build system (using the 'cmake' branch) on openSUSE Tumbleweed.

It failed and produced the following logfiles:

http://poware.org/opm-core/CMakeError.log
http://poware.org/opm-core/CMakeOutput.log

(BTW: does anybody know if there is a more convenient way to attach files to the github bugtracker than gists?) The output on the terminal was the following:

-- Checking to see if CXX compiler accepts flag -std=c++11
-- Checking to see if CXX compiler accepts flag -std=c++11 - yes
-- Performing Test HAVE_NULLPTR
-- Performing Test HAVE_NULLPTR - Success
-- Performing Test HAVE_ARRAY
-- Performing Test HAVE_ARRAY - Success
-- Performing Test HAVE_INTEGRAL_CONSTANT
-- Performing Test HAVE_INTEGRAL_CONSTANT - Success
-- Performing Test HAVE_ATTRIBUTE_ALWAYS_INLINE
-- Performing Test HAVE_ATTRIBUTE_ALWAYS_INLINE - Success
-- Performing Test HAS_ATTRIBUTE_UNUSED
-- Performing Test HAS_ATTRIBUTE_UNUSED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED
-- Performing Test HAS_ATTRIBUTE_DEPRECATED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG - Success
-- Performing Test HAVE_STATIC_ASSERT
-- Performing Test HAVE_STATIC_ASSERT - Success
-- Performing Test HAVE_VARIADIC_TEMPLATES
-- Performing Test HAVE_VARIADIC_TEMPLATES - Success
-- Performing Test HAVE_VARIADIC_CONSTRUCTOR_SFINAE
-- Performing Test HAVE_VARIADIC_CONSTRUCTOR_SFINAE - Success
-- Performing Test HAVE_RVALUE_REFERENCES
-- Performing Test HAVE_RVALUE_REFERENCES - Success
-- Looking for C++ include tuple
-- Looking for C++ include tuple - found
-- Looking for C++ include tr1/tuple
-- Looking for C++ include tr1/tuple - found
-- Looking for C++ include type_traits
-- Looking for C++ include type_traits - found
-- Looking for C++ include tr1/type_traits
-- Looking for C++ include tr1/type_traits - found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE

-- A library with BLAS API found.
-- A library with BLAS API found.
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
CMake Error at cmake/Modules/FindSuiteSparse.cmake:153 (list):
list sub-command REMOVE_DUPLICATES requires list to be present.
Call Stack (most recent call first):
cmake/Modules/OpmFind.cmake:69 (find_package)
cmake/Modules/OpmFind.cmake:98 (find_and_append_package_to)
cmake/Modules/OpmFind.cmake:104 (find_and_append_package_list_to)
CMakeLists.txt:53 (find_and_append_package_list)

-- Configuring incomplete, errors occurred!

[Release] Linker problems with AGMG

When I configure opm-core with AGMG, the library builds fine but I get the following linker problems:

[ 80%] Building CXX object CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o
Linking CXX executable bin/compute_tof
/usr/bin/cmake -E cmake_link_script CMakeFiles/compute_tof.dir/link.txt --verbose=1
/usr/bin/c++   -pipe -Wall -Wno-unknown-pragmas -std=c++11 -ggdb3 -g -O0 -DDEBUG  -Wl,--as-needed   CMakeFiles/compute_tof.dir/examples/compute_tof.cpp.o  -o bin/compute_tof -rdynamic lib/libopmcore.a -lboost_date_time-mt -lboost_filesystem-mt -lboost_system-mt -lumfpack -lamd -llapack -lm -lsuperlu /usr/lib/libf77blas.so.3gf /usr/lib/libatlas.so.3gf -lgfortran -lquadmath 
lib/libopmcore.a(dagmg.f90.o): In function `__dagmg_allroutines_MOD_dagmg_mumpsseq':
/home/mblatt/src/3rdParty/AGMG_3.1.2/SRC/dagmg.f90:4480: undefined reference to `dagmg_mumps_'
/home/mblatt/src/3rdParty/AGMG_3.1.2/SRC/dagmg.f90:4488: undefined reference to `dagmg_mumps_'
/home/mblatt/src/3rdParty/AGMG_3.1.2/SRC/dagmg.f90:4519: undefined reference to `dagmg_mumps_'
/home/mblatt/src/3rdParty/AGMG_3.1.2/SRC/dagmg.f90:4540: undefined reference to `dagmg_mumps_'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/compute_tof] Fehler 1
make[1]: *** [CMakeFiles/compute_tof.dir/all] Fehler 2
make: *** [all] Fehler 2

The weired thing is, that the symbol seems to be in libopmcore.a:

strings lib/libopmcore.a | grep mumps
__dagmg_allroutines_MOD_dagmg_mumpsseq
mumps_par
mumps_par
dmumps_root_struc
dmumps_struc
__dagmg_allroutines_MOD_dagmg_mumpsseq
dagmg_mumpsseq
mumps_par.3062
__dagmg_allroutines_MOD_dagmg_mumpsseq
dagmg_mumps_

Build tutorials using CMake

Build breaks for dune-cornerpoint

One of the four commits from yesterday broke building of dune-cornerpoint over here. I have added Atgeirr, Bård and Roland to the mail notifications, and Bangalore tells me it should go through this time around.

Installing opm-core on Suse 12.1, problems with UMFPACK?

./configure gir blant annet følgende beskjed:

........
checking suitesparse/umfpack.h usability... yes
checking suitesparse/umfpack.h presence... yes
checking for suitesparse/umfpack.h... yes
.......
checking for library containing cholmod_l_start... no
checking for library containing umfpack_dl_solve... no
configure: Found no working installation of UMFPACK.
UMFPACK support is disabled.
........

Hva er galt?

Tor Harald Sandve

Linker problem when building with MPI

As I am trying to build OPM with MPI enabled, I have met some obstacles. When building on RHEL5 everything builds fine when setting USE_MPI=ON. But on RHEL6 we don't have the MPI library in a standard location, and thus I have to specify be path explicitly. I am doing this with _MPI_PREFIX_PATH (I think @rolk told me so some time ago). My call to cmake is:

cmake -DDUNE_ROOT="/project/res/x86_64_RH_6/share/opm/dune" \
-DSUPERLU_ROOT="/project/res/x86_64_RH_6/share/opm/SuperLU_4.0" \
-DUSE_MPI=ON -D_MPI_PREFIX_PATH="/prog/sdpsoft/openmpi-1.6.3" ../

However, now the configuration process can't find dune-common or dune-istl anymore (even though the reported DUNE_COMMON_ROOT is correct):

-- Finding package MPI using module mode
-- Found MPI_C: /prog/sdpsoft/openmpi-1.6.3/lib/libmpi.so  
-- Found MPI_CXX: /prog/sdpsoft/openmpi-1.6.3/lib/libmpi.so;/prog/sdpsoft/openmpi-1.6.3/lib/libmpi_cxx.so  
-- Performing Test HAVE_DUNE_COMMON
-- Performing Test HAVE_DUNE_COMMON - Failed
DUNE_COMMON_ROOT = /project/res/x86_64_RH_6/share/opm/dune/dune-common
-- Could NOT find dune-common (missing:  HAVE_DUNE_COMMON)

I find this error message a bit strange as dune-common and istl is found if _MPI_PREFIX_PATH is not set.

tests/not-unit/ header files pointing wrong

I tried to compile some tests under /tests/not-unit/, but there are some wrong. Then I found these mistakes are about the eclipse header file which in the file ./opm-core/tests/not-unit/relperm_test.cpp, test_ert.cpp test_readpolymer.cpp bo_resprop_test.cpp and pvt_test.cpp . It should be #include<opm/core/io/eclipse/EclipseGridParser.hpp> and <opm/core/io/eclipse/EclipseGridInspector.hpp>, but they missed "io". Then I corrected them and tried to compile pvt_test.cpp, it said failed, do they depend something else or not?

ask for the commit "25dd2fadaa....&&70eebfdad8..." to be reverted

Dear all.
Forgive my mistake, when I do the test and after compiled the source code, I made push to the master. Following Joakim Hove's instruction, I tried to make a pull request to fix this problem, but it failed. So, if any one of you can fix this problem, I will appreciated. Sorry again for my mistake.
Best Regards.
Liu Ming

Use system TinyXML installation

Currently, a copy of tinyxml is stored in opm/core/utility/parameters/tinyxml; this should be replaced with a link to the system installed tinyxml package.

(I am working on a CMake module for this)