[CIG-SHORT] hdf5 issue while compiling
Charles Williams
willic3 at gmail.com
Wed Nov 5 12:11:40 PST 2014
Hi Romain,
I haven’t been following this thread closely, but I’ve been able to build successfully on both Mavericks and Yosemite by using packages from macports:
python27
gcc48
openmpi-gcc48 +gfortran
openmpi-default +gcc48
hdf5 +cxx+gcc48+openmpi+szip
hwloc
netcdf +dap+gcc48+netcdf4+openmpi
netcdf-cxx +gcc48+openmpi
netcdf-cxx4 +gcc48+openmpi
proj
py27-numpy
It is definitely critical to have your paths correct.
Cheers,
Charles
> On 6/11/2014, at 4:51 am, Romain Jolivet <rjolivet at caltech.edu> 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 <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: 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
>>
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>>
>>
>> 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
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>>>
>>> ------------------------------
>>>
>>> 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 --------------
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>>>
>>> ------------------------------
>>>
>>> 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
>>>>>
>>>>> End of CIG-SHORT Digest, Vol 98, Issue 3
>>>>> ****************************************
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> CIG-SHORT mailing list
>>>> CIG-SHORT at geodynamics.org
>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> _______________________________________________
>>> 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 4
>>> ****************************************
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> 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 5
>> ****************************************
>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
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 <mailto:C.Williams at gns.cri.nz>
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