On 28 May 2015, at 01:03, Erik Schnetter <[email protected]> wrote:
> Instead of changing the order, can we add "#undef __attribute__" after > #inluding <hdf5.h>, with a respective comment? This would undo more of the > damage. So the definition of __attribute__ in hdf5 is overriding the built-in symbol with a macro, which allows us to then undefine the macro afterwards, which allows the built-in symbol to be visible again? I was confused because I was thinking that undefining __attribute__ was the cause of the original problem. > > -erik > > On Wed, May 27, 2015 at 10:48 AM, Ian Hinder <[email protected]> wrote: > > On 27 May 2015, at 16:30, Roberto De Pietri <[email protected]> wrote: > >> Dear Comer: >> >> I would like to confirm you that Ian and Eric were able to correctly find >> out the problem that originated the build >> problem on build using macports >> * The HDF5 MacPorts port was updated from 1.8.14 to 1.8.15 on 16-May-2015 >> (https://trac.macports.org/log/trunk/dports/science/hdf5/Portfile), 2 days >> before the ET release >> * HDF5 is undefining __attribute__, and this is creating site effect >> (caused by including hdf5.h) >> that have standard c++ include to fail. This is true for gcc4.8 and gcc5.1 >> * A simple solution is to change the order of includes in the include file: >> arrangements/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh. you can replace this >> include with the >> one attached to the present mail. > > This seems like a viable workaround until the problem is fixed in HDF5, so I > propose that it be implemented in CarpetIOHDF5 and backported to the release > branch. > > >> * to have a fast start you may also copy the attached file: osx-macports.run >> in >> simfactory/mdb/runscript. >> * then set your local machine with the command >> >>> simfactory/bin/sim setup >> >> * edit the local machine file you created (using the previous command) in >> simfactory/mdb/machine >> to have: >> >> >> *** ASSUMING MACPORT IS INSTALLED (subversion is needed cause the version >> that comes with XCOde >> *** will not work [new XCODE 6.3.2 and MacPorts 2.3.3] >> >> >> sudo port install subversion >> sudo port install pkgconfig gcc49 fftw-3 gsl jpeg zlib hdf5 +fortran >> +gfortran openmpi openssl >> >> ### [FROM a MAIN DIRECTORY for the Cactus tree] >> >> curl -kLO >> https://raw.githubusercontent.com/gridaphobe/CRL/ET_2015_05/GetComponents >> chmod a+x GetComponents >> ./GetComponents --parallel >> https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2015_05/einsteintoolkit.th >> >> ### [the enter in the cactus directory] >> >> cd Cactus >> >> cp [where_you_save_it]/CarpetIOHDF5.hh >> arrangements/Carpet/CarpetIOHDF5/src/ >> cp [where_you_save_it]/osx-macports.run simfactory/mdb/runscript >> simfactory/bin/sim setup >> >> ### [DO the local editing. In my case was the file named] >> ### the following line should be present >> ### >> ### optionlist = osx-macports.cfg >> ### runscript = osx-macports.run >> ### ppn = 4 >> ### max-num-threads = 4 >> ### num-threads = 1 >> ### nodes = 1 >> ### >> ### NOT: my machine is “iMac (27-inch, Late 2009)” >> ### OS X Yosemite 10.10.3 >> ### >> ### Processor Name: Intel Core i5 >> ### Processor Speed: 2,66 GHz >> ### Number of Processors: 1 >> ### Total Number of Cores: 4 >> ### L2 Cache (per Core): 256 KB >> ### L3 Cache: 8 MB >> ### Memory: 8 GB >> >> >> simfactory/bin/sim build --thornlist thornlists/einsteintoolkit.th >> simfactory/bin/sim create-run static_tov --parfile=par/static_tov.par >> --proc=4 --num-threads=2 >> >> ### Now the test TOV simulations should be running code is running on two >> process using two cores each. >> >> >> ## 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-h5py >> ## sudo port install py-ipython >> ## sudo port select —set ipython ipython27 >> ## >> ## >> ## TO SEE THE RESULTS: >> >>> ipython —-pylab >> In [..]: >> FILE='/Users/depietri/simulations/static_tov/output-0000/static_tov/hydrobase-rho.maximum.asc' >> In [..]: d=loadtxt(FILE) >> In [..]: plot(d[:,1],d[:,2]*1e3,'k-') >> In [..]: ylim(1.25,1.30) >> In [..]: xlabel(r’time [CU c=1, G=1, $M_\odot$=1]') >> In [..]: ylabel(r'max($\rho \cdot 10^3$) [CU c=1, G=1, $M_\odot$=1]') >> In [..]: >> >> >> >> <CarpetIOHDF5.hh><osx-macports.run> >> ------------------------------------------------------------------ >> 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 >> >> >> >> >> > > -- > Ian Hinder > http://members.aei.mpg.de/ianhin > > > > > -- > Erik Schnetter <[email protected]> > http://www.perimeterinstitute.ca/personal/eschnetter/ -- Ian Hinder http://members.aei.mpg.de/ianhin
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