a list of compatible FEniCS packages

Asked by Charl on 2013-03-26

Hello,

I am installing on a 16-core Xeon machine which I don't have root access to. I am compiling all dependencies (beyond Ubuntu 12.04 base install) from source.

My request is to have a list of recent FEniCS packages that will work together. This is most likely based on Dolfin's 1.1 branch, but maybe something even more recent (that is not /too/ experimental). The version numbers of compatible external dependencies would also be appreciated.

Thank you!

Question information

Language:
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Status:
Solved
For:
DOLFIN Edit question
Assignee:
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Solved by:
Charl
Solved:
2013-03-28
Last query:
2013-03-28
Last reply:
2013-03-27
Johannes Ring (johannr) said : #2

Here is the list of the latest stable FEniCS packages:

DOLFIN 1.2.0
FFC 1.2.0
FIAT 1.1
Instant 1.2.0
UFC 2.2.0
UFL 1.2.0

See for instance the package files in Dorsal for compatible external dependencies.

Hi,

Compiling with VTK support yields the following error message. I have tried with VTK5.8 (viz. Dorsal) and also the latest 5.10.

Much obliged.

[ 76%] Building CXX object dolfin/CMakeFiles/dolfin.dir/io/HDF5File.cpp.o
In file included from /home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5File.h:38:0,
                 from /home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5File.cpp:51:
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5Interface.h: In static member function ‘static void dolfin::HDF5Interface::write_dataset(hid_t, std::string, const std::vector<T>&, std::pair<long unsigned int, long unsigned int>, std::vector<long unsigned int>, bool, bool)’:
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5Interface.h:265:63: error: there are no arguments to ‘H5Pset_dxpl_mpio’ that depend on a template parameter, so a declaration of ‘H5Pset_dxpl_mpio’ must be available [-fpermissive]
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5Interface.h:265:63: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5Interface.h: In static member function ‘static void dolfin::HDF5Interface::write_dataset(hid_t, std::string, const std::vector<T>&, std::pair<long unsigned int, long unsigned int>, std::vector<long unsigned int>, bool, bool) [with T = double, hid_t = int, std::string = std::basic_string<char>]’:
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5File.cpp:106:74: instantiated from here
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5Interface.h:265:7: error: ‘H5Pset_dxpl_mpio’ was not declared in this scope
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5Interface.h: In static member function ‘static void dolfin::HDF5Interface::write_dataset(hid_t, std::string, const std::vector<T>&, std::pair<long unsigned int, long unsigned int>, std::vector<long unsigned int>, bool, bool) [with T = long unsigned int, hid_t = int, std::string = std::basic_string<char>]’:
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5File.h:186:5: instantiated from ‘void dolfin::HDF5File::write_data(std::string, const std::vector<T>&, std::vector<long unsigned int>) [with T = long unsigned int, std::string = std::basic_string<char>]’
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5File.cpp:206:63: instantiated from here
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5Interface.h:265:7: error: ‘H5Pset_dxpl_mpio’ was not declared in this scope
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5Interface.h: In static member function ‘static void dolfin::HDF5Interface::write_dataset(hid_t, std::string, const std::vector<T>&, std::pair<long unsigned int, long unsigned int>, std::vector<long unsigned int>, bool, bool) [with T = int, hid_t = int, std::string = std::basic_string<char>]’:
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5File.h:186:5: instantiated from ‘void dolfin::HDF5File::write_data(std::string, const std::vector<T>&, std::vector<long unsigned int>) [with T = int, std::string = std::basic_string<char>]’
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5File.cpp:503:3: instantiated from ‘void dolfin::HDF5File::write_mesh_function(const dolfin::MeshFunction<T>&, std::string) [with T = int, std::string = std::basic_string<char>]’
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5File.cpp:226:41: instantiated from here
/home/charl/FEniCS/src/dolfin/dolfin-1.2.0/dolfin/io/HDF5Interface.h:265:7: error: ‘H5Pset_dxpl_mpio’ was not declared in this scope
make[2]: *** [dolfin/CMakeFiles/dolfin.dir/io/HDF5File.cpp.o] Error 1
make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2
make: *** [all] Error 2

Chris Richardson (chris-bpi) said : #4

Looks like your version of HDF5 is not compatible - this should be picked up in the CMake build tests, really...
What version of hdf5 do you have installed?

dpkg -l *hdf5*

Hi Chris,

Looks like v1.8.4-p1. I just finished compiling v1.8.10-p1 from source, was trying to figure out how to tell CMake to look for the static library in my home directory...

Cheers

$ dpkg -l *hdf5*
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name Version Description
+++-=======================================-=======================================-==============================================================================================
ii hdf5-tools 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - Runtime tools
un libhdf5-1.8 <none> (no description available)
un libhdf5-1.8.3 <none> (no description available)
un libhdf5-1.8.4 <none> (no description available)
un libhdf5-dev <none> (no description available)
un libhdf5-doc <none> (no description available)
ii libhdf5-mpi-dev 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - development files - MPICH version
ii libhdf5-openmpi-1.8.4 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - runtime files - OpenMPI version
ii libhdf5-openmpi-dev 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - development files - OpenMPI version
rc libhdf5-serial-1.8.4 1.8.4-patch1-3ubuntu2 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
un libhdf5-serial-dev <none> (no description available)
ii libjhdf5-java 2.6.1-2build1 Java HDF5 Object Package
ii libjhdf5-jni 2.6.1-2build1 Java HDF5 Object Package (Java JNI library)