[CIG-SHORT] hdf5 issue while compiling
Matthew Knepley
knepley at mcs.anl.gov
Thu Nov 6 14:53:22 PST 2014
On Thu, Nov 6, 2014 at 8:46 PM, Charles Williams <willic3 at gmail.com> wrote:
> Dear Romain,
>
> The FIAT people are already aware of the problem, and there is a branch of
> FIAT that does not use ScientificPython (I think you still need to check it
> out from the git repository). I am using this, and so far things seem to
> be working. PETSc still requires you to have ScientificPython, but I don’t
> think it’s used any longer.
>
PETSc does not require ScientificPython anymore.
Thanks,
Matt
> Cheers,
> Charles
>
>
>
> > On 7/11/2014, at 12:58 am, Romain Jolivet <rjolivet at caltech.edu> wrote:
> >
> > I managed to install everything manually and it works (finally :-)).
> >
> > Although there are a few things I had to modify myself:
> >
> > - In the proj4 tarball, one needs to modify the include org_proj_PJ.h
> into org_proj_Projections.h in jniproj.c (Proj-4.8.0/src/jniproj.c).
> >
> > - It is not possible to use the latest version of Numpy, as they removed
> oldnumeric, which is used by ScientificPython and FIAT. I found on a forum
> somewhere that the ScientificPython developer does not want to deal with
> this issue and he is going to leave it like that (i.e. ScientificPython
> cannot be used with versions of Numpy newer than 1.7). If I am correct,
> maybe it would be worth notifying the FIAT people so they get rid of
> ScientificPython in FIAT, or at least to the Derivative functions).
> >
> > - I don’t know why, but configure in spatialdata and in pylith are
> adding a -Wl,-framework,Python option to the libtool commands. This leads
> libtool to link to MacOSX native python wether you set up your
> DYLD_LIBRARY_PATH correctly or not. So, I hacked the configure script in
> both cases but it is pretty dirty, so if someone wants to check what I did,
> I can send the scripts.
> >
> > Cheers,
> > Romain
> >
> > On 6 Nov 2014, at 06:50, cig-short-request at geodynamics.org wrote:
> >
> >> Send CIG-SHORT mailing list submissions to
> >> cig-short at geodynamics.org
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >> or, via email, send a message with subject or body 'help' to
> >> cig-short-request at geodynamics.org
> >>
> >> You can reach the person managing the list at
> >> cig-short-owner at geodynamics.org
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of CIG-SHORT digest..."
> >>
> >>
> >> Today's Topics:
> >>
> >> 1. Re: hdf5 issue while compiling (Brad Aagaard)
> >> 2. Problem when compiling Pylith from source. (Laura Blanco Martin)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Wed, 5 Nov 2014 12:55:53 -0800
> >> From: Brad Aagaard <baagaard at usgs.gov>
> >> To: <cig-short at geodynamics.org>
> >> Subject: Re: [CIG-SHORT] hdf5 issue while compiling
> >> Message-ID: <545A8ED9.4030005 at usgs.gov>
> >> Content-Type: text/plain; charset="windows-1252"; format=flowed
> >>
> >> Romain,
> >>
> >> I just built PyLith using the installer on both a linux (ubuntu 14.04)
> >> and mac (Mavericks) without problems. I did change the setup.sh for the
> >> mac, replacing LD_LIBRARY_PATH with DYLD_LIBRARY_PATH. I will update the
> >> pylith installer so that it uses DYLD_LIBRARY_PATH automatically on
> >> darwin system.
> >>
> >> On the mac, I made use of the following tools which I installed by hand:
> >>
> >> gcc 4.7.3
> >> autoconf 2.69
> >> automake 1.12.6
> >> libtool 2.4
> >>
> >> To you configure arguments, I added
> >>
> >> --with-fetch=curl --enable-pcre --enable-swig
> >>
> >> As with all software builds, you need to be very careful about
> >> management of your paths and multiple instances of the same software.
> >> Linux package managers are very good and rarely install multiple
> >> instances of gcc etc, but this is often not the case under Darwin. I
> >> gave up on Macports because of this.
> >>
> >> You may want to consider using environment tools like virtualenv,
> >> modules (http://modules.sourceforge.net/), or lmod
> >> (https://www.tacc.utexas.edu/research-development/tacc-projects/lmod)
> if
> >> you find yourself wanting to change environment variables for various
> >> packages. These are the types of tools most supercomputer centers
> >> provide so that users can select the appropriate tools and have their
> >> environments setup correctly.
> >>
> >> Regards,
> >> Brad
> >>
> >>
> >> On 11/05/2014 07:51 AM, Romain Jolivet wrote:
> >>> Dear all,
> >>>
> >>> I managed to compile things by using the macport version of hdf5.
> >>> For that, I had to manually compile Numpy, ScientificPython, FIAT,
> cppunit, spatialdata, nemesis, petsc and finally pylith.
> >>> The libtests in pylith are now passed fine (no hdf5 problems anymore),
> but the python interpreter does not start.
> >>>
> >>> it says:
> >>>
> >>> Fatal Python error: PyThreadState_Get: no current thread
> >>>
> >>> This probably has to do with the fact that it links spatialdata with
> the System?s native python...
> >>>
> >>> pikaru 15:38:50 ~/MYBIN/PyLith/pylith-byhand/spatialdata-build > otool
> -L
> ../pylith-2.0.3/lib/python2.7/site-packages/spatialdata/spatialdb/_spatialdbmodule.so
> >>>
> ../pylith-2.0.3/lib/python2.7/site-packages/spatialdata/spatialdb/_spatialdbmodule.so:
> >>>
> /Users/rjolivet/MYBIN/PyLith/pylith-byhand/pylith-2.0.3/lib/libspatialdata.0.dylib
> (compatibility version 1.0.0, current version 1.0.0)
> >>> /opt/local/lib/libproj.0.dylib (compatibility version 8.0.0,
> current version 8.0.0)
> >>> /System/Library/Frameworks/Python.framework/Versions/2.7/Python
> (compatibility version 2.7.0, current version 2.7.5)
> >>> /opt/local/lib/libgcc/libstdc++.6.dylib (compatibility version
> 7.0.0, current version 7.20.0)
> >>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 1197.1.1)
> >>> /opt/local/lib/libgcc/libgcc_s.1.dylib (compatibility version
> 1.0.0, current version 1.0.0)
> >>>
> >>> I use the following to compile spatialdata (similar to what does the
> installer):
> >>>
> >>> ../spatialdata-master/configure
> --prefix=/Users/rjolivet/MYBIN/PyLith/pylith-byhand/pylith-2.0.3 CFLAGS="-g
> -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS="-g -O2"
> CPPFLAGS=-I/Users/rjolivet/MYBIN/PyLith/pylith-byhand/pylith-2.0.3/include
> LDFLAGS="-L/Users/rjolivet/MYBIN/PyLith/pylith-byhand/pylith-2.0.3/lib
> -L/opt/local/lib" CC=gcc CXX=g++ FC=gfortran --enable-testing --enable-swig
> PYTHON=python PYTHONPATH=$PYTHONPATH
> >>>
> >>> Do you know where the native python interpreter could jump into the
> compilation?
> >>>
> >>> Cheers,
> >>> R
> >>>
> >>>
> >>> On 5 Nov 2014, at 09:40, cig-short-request at geodynamics.org wrote:
> >>>
> >>>> Send CIG-SHORT mailing list submissions to
> >>>> cig-short at geodynamics.org
> >>>>
> >>>> To subscribe or unsubscribe via the World Wide Web, visit
> >>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >>>> or, via email, send a message with subject or body 'help' to
> >>>> cig-short-request at geodynamics.org
> >>>>
> >>>> You can reach the person managing the list at
> >>>> cig-short-owner at geodynamics.org
> >>>>
> >>>> When replying, please edit your Subject line so it is more specific
> >>>> than "Re: Contents of CIG-SHORT digest..."
> >>>>
> >>>>
> >>>> Today's Topics:
> >>>>
> >>>> 1. Re: hdf5 issue while compiling (Romain Jolivet)
> >>>>
> >>>>
> >>>> ----------------------------------------------------------------------
> >>>>
> >>>> Message: 1
> >>>> Date: Wed, 5 Nov 2014 09:40:50 +0000
> >>>> From: Romain Jolivet <rjolivet at caltech.edu>
> >>>> To: cig-short at geodynamics.org
> >>>> Subject: Re: [CIG-SHORT] hdf5 issue while compiling
> >>>> Message-ID: <671B974A-C95F-4453-9347-CE2FF5DF454C at caltech.edu>
> >>>> Content-Type: text/plain; charset="windows-1252"
> >>>>
> >>>> Please find the config.log file attached.
> >>>> Does not work with lines removed/correclty commented?
> >>>> R
> >>>>
> >>>> -------------- next part --------------
> >>>> A non-text attachment was scrubbed...
> >>>> Name: config.log
> >>>> Type: application/octet-stream
> >>>> Size: 38009 bytes
> >>>> Desc: not available
> >>>> URL: <
> http://lists.geodynamics.org/pipermail/cig-short/attachments/20141105/261846bc/attachment.obj
> >
> >>>> -------------- next part --------------
> >>>>
> >>>>
> >>>>
> >>>> On 4 Nov 2014, at 22:34, cig-short-request at geodynamics.org wrote:
> >>>>
> >>>>> Send CIG-SHORT mailing list submissions to
> >>>>> cig-short at geodynamics.org
> >>>>>
> >>>>> To subscribe or unsubscribe via the World Wide Web, visit
> >>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >>>>> or, via email, send a message with subject or body 'help' to
> >>>>> cig-short-request at geodynamics.org
> >>>>>
> >>>>> You can reach the person managing the list at
> >>>>> cig-short-owner at geodynamics.org
> >>>>>
> >>>>> When replying, please edit your Subject line so it is more specific
> >>>>> than "Re: Contents of CIG-SHORT digest..."
> >>>>>
> >>>>>
> >>>>> Today's Topics:
> >>>>>
> >>>>> 1. Re: hdf5 issue while compiling (Matthew Knepley)
> >>>>> 2. Re: CIG-SHORT Digest, Vol 98, Issue 3 (Romain Jolivet)
> >>>>> 3. Re: CIG-SHORT Digest, Vol 98, Issue 3 (Brad Aagaard)
> >>>>>
> >>>>>
> >>>>>
> ----------------------------------------------------------------------
> >>>>>
> >>>>> Message: 1
> >>>>> Date: Tue, 4 Nov 2014 21:41:15 +0000
> >>>>> From: Matthew Knepley <knepley at mcs.anl.gov>
> >>>>> To: "cig-short at geodynamics.org" <cig-short at geodynamics.org>
> >>>>> Subject: Re: [CIG-SHORT] hdf5 issue while compiling
> >>>>> Message-ID:
> >>>>> <
> CAMYG4GmDZAUYCAygb02++3Tr80pwWA7Cbr_AdQVEbnxJH8PfCw at mail.gmail.com>
> >>>>> Content-Type: text/plain; charset="utf-8"
> >>>>>
> >>>>> On Tue, Nov 4, 2014 at 2:45 PM, Romain Jolivet <rjolivet at caltech.edu>
> wrote:
> >>>>>
> >>>>>> Dear Brad et al.,
> >>>>>>
> >>>>>> I compiled pylith using the installer on an iMac (brand new),
> running Mac
> >>>>>> os X 10.9 (not Yosemite, Mavericks).
> >>>>>> As things were not going that smoothly, I decided to enable every
> options
> >>>>>> available with the installer, but not gcc (I have gcc4.9 from
> macports).
> >>>>>>
> >>>>>> When compiling hdf5, it stops, saying:
> >>>>>>
> >>>>>> ../../../hdf5-1.8.11/tools/lib/h5tools_dump.c:635:9: error: expected
> >>>>>> expression before '/' token
> >>>>>> //HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "Could not
> >>>>>> allocate buffer for ptdata?);
> >>>>>>
> >>>>>
> >>>>> It looks like they used a C99 comment, but your compiler does not
> like it.
> >>>>> Delete the line and try again is the
> >>>>> easiest option.
> >>>>>
> >>>>> Thanks,
> >>>>>
> >>>>> Matt
> >>>>>
> >>>>>
> >>>>>> The compiler used is mpicc (given what the Makefile says) that has
> been
> >>>>>> compiled using the pylith installer.
> >>>>>>
> >>>>>> Any idea?
> >>>>>> Cheers,
> >>>>>> Romain
> >>>>>>
> >>>>>>
> >>>>>> ?????????????????????????????????????
> >>>>>> ?????????????????????????????????????
> >>>>>> Romain Jolivet
> >>>>>> Postdoctoral Fellow
> >>>>>>
> >>>>>> University of Cambridge
> >>>>>> Department of Earth Sciences
> >>>>>> Bullard Labs
> >>>>>> Madingley Rise
> >>>>>> Madingley Road
> >>>>>> Cambridge CB3 0EZ
> >>>>>> United Kingdom
> >>>>>>
> >>>>>> email: rpj29 at cam.ac.uk
> >>>>>> Phone: +44 1223 748 938
> >>>>>> Mobile: +44 7596 703 148
> >>>>>>
> >>>>>> France: +33 6 52 91 76 39
> >>>>>> US: +1 (626) 560 6356
> >>>>>> ?????????????????????????????????????
> >>>>>> ?????????????????????????????????????
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> CIG-SHORT mailing list
> >>>>>> CIG-SHORT at geodynamics.org
> >>>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> What most experimenters take for granted before they begin their
> >>>>> experiments is infinitely more interesting than any results to which
> their
> >>>>> experiments lead.
> >>>>> -- Norbert Wiener
> >>>>> -------------- next part --------------
> >>>>> An HTML attachment was scrubbed...
> >>>>> URL: <
> http://lists.geodynamics.org/pipermail/cig-short/attachments/20141104/8490d979/attachment-0001.html
> >
> >>>>>
> >>>>> ------------------------------
> >>>>>
> >>>>> Message: 2
> >>>>> Date: Tue, 4 Nov 2014 22:32:00 +0000
> >>>>> From: Romain Jolivet <rjolivet at caltech.edu>
> >>>>> To: cig-short at geodynamics.org
> >>>>> Subject: Re: [CIG-SHORT] CIG-SHORT Digest, Vol 98, Issue 3
> >>>>> Message-ID: <55DDBBFB-7A56-4FF9-908D-C5612D1BB659 at caltech.edu>
> >>>>> Content-Type: text/plain; charset="us-ascii"
> >>>>>
> >>>>> Using gcc4.7 does not change anything, although it does accept the
> // way of commenting (must be a change in standards between 4.8 and 4.9).
> >>>>> I am using the git version of pylith (main branch, nothing fancy).
> >>>>> I will send you the config.log file tomorrow, but I did not specify
> anything more than enabling all options for configure.
> >>>>> Also, I can try with the tarballs tomorrow morning.
> >>>>>
> >>>>> Cheers,
> >>>>> R
> >>>>>
> >>>>> ----------------------------------------------------------------
> >>>>> !!!!!! ADDRESS CHANGED!!!!!!
> >>>>> ----------------------------------------------------------------
> >>>>> Romain Jolivet
> >>>>> Postdoctoral Fellow
> >>>>>
> >>>>> University of Cambridge
> >>>>> Department of Earth Sciences
> >>>>> Bullard Laboratories
> >>>>> Madingley Road,
> >>>>> Cambridge, CB3 0EZ,
> >>>>> United Kingdom
> >>>>>
> >>>>> email: rpj29 at cam.ac.uk
> >>>>> Phone: +44 7 596 703 148
> >>>>> Phone (Fr): +33 7 52 91 76 39
> >>>>> ----------------------------------------------------------------
> >>>>> ----------------------------------------------------------------
> >>>>>
> >>>>> On Nov 4, 2014, at 20: 00, cig-short-request at geodynamics.org wrote:
> >>>>>
> >>>>>> Send CIG-SHORT mailing list submissions to
> >>>>>> cig-short at geodynamics.org
> >>>>>>
> >>>>>> To subscribe or unsubscribe via the World Wide Web, visit
> >>>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >>>>>> or, via email, send a message with subject or body 'help' to
> >>>>>> cig-short-request at geodynamics.org
> >>>>>>
> >>>>>> You can reach the person managing the list at
> >>>>>> cig-short-owner at geodynamics.org
> >>>>>>
> >>>>>> When replying, please edit your Subject line so it is more specific
> >>>>>> than "Re: Contents of CIG-SHORT digest..."
> >>>>>>
> >>>>>>
> >>>>>> Today's Topics:
> >>>>>>
> >>>>>> 1. Re: Follow up on hdf5 issue while compiling (Brad Aagaard)
> >>>>>>
> >>>>>>
> >>>>>>
> ----------------------------------------------------------------------
> >>>>>>
> >>>>>> Message: 1
> >>>>>> Date: Tue, 4 Nov 2014 08:17:05 -0800
> >>>>>> From: Brad Aagaard <baagaard at usgs.gov>
> >>>>>> To: <cig-short at geodynamics.org>
> >>>>>> Subject: Re: [CIG-SHORT] Follow up on hdf5 issue while compiling
> >>>>>> Message-ID: <5458FC01.2080108 at usgs.gov>
> >>>>>> Content-Type: text/plain; charset="windows-1252"; format=flowed
> >>>>>>
> >>>>>> On 11/04/2014 07:52 AM, Romain Jolivet wrote:
> >>>>>>> Dear Brad et al.,
> >>>>>>>
> >>>>>>> Following my previous email:
> >>>>>>> I compiled pylith using the installer on an iMac (brand new),
> running Mac os X
> >>>>>>> 10.9 (not Yosemite, Mavericks).
> >>>>>>> As things were not going that smoothly, I decided to enable every
> options
> >>>>>>> available with the installer, but not gcc (I have gcc4.9 from
> macports).
> >>>>>>>
> >>>>>>> When compiling hdf5, it stops, saying:
> >>>>>>>
> >>>>>>> ../../../hdf5-1.8.11/tools/lib/h5tools_dump.c:635:9: error:
> expected expression
> >>>>>>> before '/' token
> >>>>>>> //HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "Could
> not allocate
> >>>>>>> buffer for ptdata?);
> >>>>>>>
> >>>>>>> The compiler used is mpicc (given what the Makefile says) that has
> been compiled
> >>>>>>> using the pylith installer.
> >>>>>>>
> >>>>>>> I went inside the hdf5 code and modified the way comment were
> implemented at a
> >>>>>>> few places, replacing // by the classic /* */.
> >>>>>>> It compiled, but this small issue must hide something bigger
> because the tests
> >>>>>>> fail in pylith due to some hdf5 opening problem in pets (see
> testmeshio.log file
> >>>>>>> attached).
> >>>>>>
> >>>>>>
> >>>>>> This is a clear HDF5 bug. C files should use C style comments /*
> */, not
> >>>>>> C++ style comments //. Your fix is correct. I am not sure why gcc
> 4.8.2
> >>>>>> let this pass when I built HDF5.
> >>>>>>
> >>>>>>> The tests that fail are in unittests/libtests/meshio
> >>>>>>> It also fails when running the 2d subduction examples and any
> other example that
> >>>>>>> writes hdf5 outputs.
> >>>>>>>
> >>>>>>> Any idea? In the mean time, I will try with the 4.7 version of gcc
> from MacPorts
> >>>>>>> (faster to install than the one from the installer),
> >>>>>>
> >>>>>> What are the config arguments to the PyLith installer? I want to
> know if
> >>>>>> you are using the tarballs or repositories for PETSc and PyLith. If
> >>>>>> using the repositories, what branches are you using?
> >>>>>>
> >>>>>> Brad
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> ------------------------------
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> CIG-SHORT mailing list
> >>>>>> CIG-SHORT at geodynamics.org
> >>>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >>>>>>
> >>>>>> End of CIG-SHORT Digest, Vol 98, Issue 3
> >>>>>> ****************************************
> >>>>>
> >>>>> -------------- next part --------------
> >>>>> An HTML attachment was scrubbed...
> >>>>> URL: <
> http://lists.geodynamics.org/pipermail/cig-short/attachments/20141104/d877409b/attachment-0001.html
> >
> >>>>>
> >>>>> ------------------------------
> >>>>>
> >>>>> Message: 3
> >>>>> Date: Tue, 4 Nov 2014 14:34:35 -0800
> >>>>> From: Brad Aagaard <baagaard at usgs.gov>
> >>>>> To: <cig-short at geodynamics.org>
> >>>>> Subject: Re: [CIG-SHORT] CIG-SHORT Digest, Vol 98, Issue 3
> >>>>> Message-ID: <5459547B.5010705 at usgs.gov>
> >>>>> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
> >>>>>
> >>>>> Romain,
> >>>>>
> >>>>> Yes, please send your complete configure arguments, so I can try to
> >>>>> replicate the error.
> >>>>>
> >>>>> Brad
> >>>>>
> >>>>>
> >>>>> On 11/4/14, 2:32 PM, Romain Jolivet wrote:
> >>>>>> Using gcc4.7 does not change anything, although it does accept the
> //
> >>>>>> way of commenting (must be a change in standards between 4.8 and
> 4.9).
> >>>>>> I am using the git version of pylith (main branch, nothing fancy).
> >>>>>> I will send you the config.log file tomorrow, but I did not specify
> >>>>>> anything more than enabling all options for configure.
> >>>>>> Also, I can try with the tarballs tomorrow morning.
> >>>>>>
> >>>>>> Cheers,
> >>>>>> R
> >>>>>>
> >>>>>> ----------------------------------------------------------------
> >>>>>> !!!!!! ADDRESS CHANGED!!!!!!
> >>>>>> ----------------------------------------------------------------
> >>>>>> Romain Jolivet
> >>>>>> Postdoctoral Fellow
> >>>>>>
> >>>>>> University of Cambridge
> >>>>>> Department of Earth Sciences
> >>>>>> Bullard Laboratories
> >>>>>> Madingley Road,
> >>>>>> Cambridge, CB3 0EZ,
> >>>>>> United Kingdom
> >>>>>>
> >>>>>> email: rpj29 at cam.ac.uk <mailto:rpj29 at cam.ac.uk>
> >>>>>> Phone: +44 7 596 703 148
> >>>>>> Phone (Fr): +33 7 52 91 76 39
> >>>>>> ----------------------------------------------------------------
> >>>>>> ----------------------------------------------------------------
> >>>>>>
> >>>>>> On Nov 4, 2014, at 20: 00, cig-short-request at geodynamics.org
> >>>>>> <mailto:cig-short-request at geodynamics.org> wrote:
> >>>>>>
> >>>>>>> Send CIG-SHORT mailing list submissions to
> >>>>>>> cig-short at geodynamics.org <mailto:cig-short at geodynamics.org>
> >>>>>>>
> >>>>>>> To subscribe or unsubscribe via the World Wide Web, visit
> >>>>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >>>>>>> or, via email, send a message with subject or body 'help' to
> >>>>>>> cig-short-request at geodynamics.org
> >>>>>>>
> >>>>>>> You can reach the person managing the list at
> >>>>>>> cig-short-owner at geodynamics.org
> >>>>>>>
> >>>>>>> When replying, please edit your Subject line so it is more specific
> >>>>>>> than "Re: Contents of CIG-SHORT digest..."
> >>>>>>>
> >>>>>>>
> >>>>>>> Today's Topics:
> >>>>>>>
> >>>>>>> 1. Re: Follow up on hdf5 issue while compiling (Brad Aagaard)
> >>>>>>>
> >>>>>>>
> >>>>>>>
> ----------------------------------------------------------------------
> >>>>>>>
> >>>>>>> Message: 1
> >>>>>>> Date: Tue, 4 Nov 2014 08:17:05 -0800
> >>>>>>> From: Brad Aagaard <baagaard at usgs.gov>
> >>>>>>> To: <cig-short at geodynamics.org>
> >>>>>>> Subject: Re: [CIG-SHORT] Follow up on hdf5 issue while compiling
> >>>>>>> Message-ID: <5458FC01.2080108 at usgs.gov>
> >>>>>>> Content-Type: text/plain; charset="windows-1252"; format=flowed
> >>>>>>>
> >>>>>>> On 11/04/2014 07:52 AM, Romain Jolivet wrote:
> >>>>>>>> Dear Brad et al.,
> >>>>>>>>
> >>>>>>>> Following my previous email:
> >>>>>>>> I compiled pylith using the installer on an iMac (brand new),
> running
> >>>>>>>> Mac os X
> >>>>>>>> 10.9 (not Yosemite, Mavericks).
> >>>>>>>> As things were not going that smoothly, I decided to enable every
> options
> >>>>>>>> available with the installer, but not gcc (I have gcc4.9 from
> macports).
> >>>>>>>>
> >>>>>>>> When compiling hdf5, it stops, saying:
> >>>>>>>>
> >>>>>>>> ../../../hdf5-1.8.11/tools/lib/h5tools_dump.c:635:9: error:
> expected
> >>>>>>>> expression
> >>>>>>>> before '/' token
> >>>>>>>> //HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "Could
> >>>>>>>> not allocate
> >>>>>>>> buffer for ptdata?);
> >>>>>>>>
> >>>>>>>> The compiler used is mpicc (given what the Makefile says) that has
> >>>>>>>> been compiled
> >>>>>>>> using the pylith installer.
> >>>>>>>>
> >>>>>>>> I went inside the hdf5 code and modified the way comment were
> >>>>>>>> implemented at a
> >>>>>>>> few places, replacing // by the classic /* */.
> >>>>>>>> It compiled, but this small issue must hide something bigger
> because
> >>>>>>>> the tests
> >>>>>>>> fail in pylith due to some hdf5 opening problem in pets (see
> >>>>>>>> testmeshio.log file
> >>>>>>>> attached).
> >>>>>>>
> >>>>>>>
> >>>>>>> This is a clear HDF5 bug. C files should use C style comments /*
> */, not
> >>>>>>> C++ style comments //. Your fix is correct. I am not sure why gcc
> 4.8.2
> >>>>>>> let this pass when I built HDF5.
> >>>>>>>
> >>>>>>>> The tests that fail are in unittests/libtests/meshio
> >>>>>>>> It also fails when running the 2d subduction examples and any
> other
> >>>>>>>> example that
> >>>>>>>> writes hdf5 outputs.
> >>>>>>>>
> >>>>>>>> Any idea? In the mean time, I will try with the 4.7 version of gcc
> >>>>>>>> from MacPorts
> >>>>>>>> (faster to install than the one from the installer),
> >>>>>>>
> >>>>>>> What are the config arguments to the PyLith installer? I want to
> know if
> >>>>>>> you are using the tarballs or repositories for PETSc and PyLith. If
> >>>>>>> using the repositories, what branches are you using?
> >>>>>>>
> >>>>>>> Brad
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> ------------------------------
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> CIG-SHORT mailing list
> >>>>>>> CIG-SHORT at geodynamics.org
> >>>>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
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> >>
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> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Wed, 5 Nov 2014 22:49:47 -0800
> >> From: Laura Blanco Martin <lblancomartin at lbl.gov>
> >> To: cig-short at geodynamics.org
> >> Subject: [CIG-SHORT] Problem when compiling Pylith from source.
> >> Message-ID:
> >> <
> CAD7ShqttfbyHnH4FQ4abEeshBhUdvQV6rj-Kcip2aFuEGW3RAw at mail.gmail.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> Hello,
> >>
> >> I am trying to compile Pylith and I get errors logged in test-suite.log
> >> (see attached file). It seems that there is a problem with hdf5 and mpi.
> >> Do you know how to fix this?
> >>
> >> Thanks,
> >>
> >> Laura
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> >>
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>
> Charles A. Williams
> Scientist
> GNS Science
> 1 Fairway Drive, Avalon
> PO Box 30368
> Lower Hutt 5040
> New Zealand
> ph (office): 0064-4570-4566
> fax (office): 0064-4570-4600
> C.Williams at gns.cri.nz
>
> _______________________________________________
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>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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