Hi Ian:
Thanks for the answer. I followed exactly your procedure and I was very
surprised of having
a failing compilation. Than I starting tracing back the problem.
* All the thorns except one were compiling correctly.
* The failing thorn was CarpetIOHDF5 and of the 5 source files present only 3
failed
* The error was very strange because the only real problem was related to
a system include
“/opt/local/lib/gcc49/gcc/x86_64-apple-darwin14/4.9.2/include/mmintrin.h”
and was related to conversion using AVX intel intrinsic. The error were of
the type:
error: can’t convert between vector values of different size
return (__m64) __builtin_ia32_vec_init_v2si (__i, 0);
I was think about bad iteration between include files. Something like macro
expansion
of system file happening after incluse of application macro.
* I decide to give a try to just change the system include on the top of the
failing source
files to looks like the compiling one. Basicaly I just added
#include <cstdlib>
#include <cstring>
#include <list>
#include <sstream>
#include <string>
#include <vector>
#include <map>
#include <algorithm>
on the top of the 3 failing files
* with these limited changes to just 3 files I obtained a compiling executable
that
passed the whole testsuite.
==============================================================
Here is the results about the active hdf5 library in mac ports on my machine.
tycho:python_util depietri$ port installed "*hdf5*"
The following ports are currently installed:
hdf5 @1.8.15_0+cxx
hdf5 @1.8.15_0+cxx+fortran+gfortran (active)
On the sequence of installing ports the only difference was in the order, that
is
I installed subversion and python before the sequence in osx-macports.cfg
With my change I got
/opt/local/include/gcc49/c++/algorithm
include before
/Users/depietri/EinsteinToolkit/ET_dev/Cactus/arrangements/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
that the other way around.
This is my understanding. The thing that happens in the two files that
successfully compiled.
Here is failed include sequence:
COMPILING arrangements/Carpet/CarpetIOHDF5/src/Output.cc
In file included from
/opt/local/lib/gcc49/gcc/x86_64-apple-darwin14/4.9.2/include/x86intrin.h:29:0,
from
/opt/local/include/gcc49/c++/x86_64-apple-darwin14/bits/opt_random.h:33,
from /opt/local/include/gcc49/c++/random:50,
from /opt/local/include/gcc49/c++/bits/stl_algo.h:66,
from /opt/local/include/gcc49/c++/algorithm:62,
from
/Users/depietri/EinsteinToolkit/ET_dev/Cactus/arrangements/Carpet/CarpetLib/src/defs.hh:6,
from
/Users/depietri/EinsteinToolkit/ET_dev/Cactus/arrangements/Carpet/CarpetLib/src/bbox.hh:10,
from
/Users/depietri/EinsteinToolkit/ET_dev/Cactus/configs/sim/bindings/include/bbox.hh:4,
from
/Users/depietri/EinsteinToolkit/ET_dev/Cactus/arrangements/Carpet/Carpet/src/functions.hh:17,
from
/Users/depietri/EinsteinToolkit/ET_dev/Cactus/arrangements/Carpet/Carpet/src/carpet_public.hh:8,
from
/Users/depietri/EinsteinToolkit/ET_dev/Cactus/configs/sim/bindings/include/carpet.hh:4,
from
/Users/depietri/EinsteinToolkit/ET_dev/Cactus/arrangements/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh:11,
from
/Users/depietri/EinsteinToolkit/ET_dev/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:13:
Roberto
> On 22 May 2015, at 15:35, Ian Hinder <[email protected]> wrote:
>
>
> On 22 May 2015, at 12:44, Roberto De Pietri <[email protected]> wrote:
>
>> Dear Corner and Erik:
>>
>> After a while a decided to have the EinsteinToolkit compiled on my personal
>> laptop. I did all from scratch.
>>
>> * Latest versione of OSX (10.10.3)
>> * Latest (clean) version of macports (MacPorts 2.3.3)
>> sudo port install subversion
>> sudo port install python27
>> sudo port select --set python python27
>> sudo port install py-numpy py-scipy
>> sudo port install py-matplotlib
>> sudo port install py-ipython
>> sudo port select --set ipython ipython27
>> sudo port install pkgconfig gcc49 fftw-3 gsl jpeg zlib hdf5
>> +fortran +gfortran openmpi openssl
>> sudo port install py-h5py
>> sudo port install gcc5
>> * Latest version of the EinsteinToolkit (Hilbert and dev)
>> * I used the provided option list
>> simfactory/mdb/optionlists/osx-macports.cfg
>
>
> Hi Roberto,
>
> What we have tested carefully is to use exactly the list of ports in the
> osx-macports.cfg config file. I tested this by moving my usual /opt/local
> out of the way, and installing MacPorts from scratch using exactly the "port
> install" command listed in the optionlist.
>
> Unfortunately, having multiple versions of things like compilers and MPI in
> the places that Cactus searches for them (e.g. /opt/local) generically
> causes problems when compiling software from source. I notice that you have
> used exactly this command line (sudo port install pkgconfig gcc49 fftw-3 gsl
> jpeg zlib hdf5 +fortran +gfortran openmpi openssl), but you also have other
> ports installed, and it's possible that some of these might conflict during
> the autodetection stage, causing some undesirable mixtures. My main
> suspicion, looking at your compilation errors, is something to do with
> vectorisation and HDF5. You have installed py-h5py, which may well have has
> pulled in a different HDF5 library. You may now have more than one HDF5
> library installed, and it's possible that this is causing confusion. What is
> the output of
>
> port installed "*hdf5*"
>
> Am I correct in understanding that by adding those additional include files,
> you were able to compile CarpetIOHDF5? Maybe it's pulling in an hdf5.h from
> a different version of hdf5 than is expected?
>
>
>
------------------------------------------------------------------
Roberto De Pietri e-mail:[email protected]
Dipartimento di Fisica http://www.fis.unipr.it/~roberto.depietri
Universita' di Parma tel: +39 (0521) 905280
Via G.P.Usberti 7/A fax: +39 (0521) 905223
I-43100 PARMA --- ITALY
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