[CIG-SHORT] hdf5 issue while compiling
Romain Jolivet
rjolivet at caltech.edu
Wed Nov 5 07:51:08 PST 2014
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
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>
> 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
>>> ****************************************
>>
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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
> ****************************************
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