[CIG-SHORT] Problem when building Pylith from source.

Fri Jul 10 16:43:07 PDT 2015

Brad,

Thank you very much for your quick action. I have tried again, and
encountered the same type of problem with files (in package hdf5-1.8.11p1)
"tools/lib/h5tools_str.c", and also "tools/h5dump/h5dump_ddl.c".
After changing the comments identified with "//", the package was installed
correctly.
Then, I had trouble with pythia-0.8.1.16, because even after disabling the
firewall, I couldn't get script "setuptools-0.6c11-py2.7.egg". Luckily I
had made a copy of all files before removing the Virtual Machine from my
old PC. Maybe I did not disable the firewall correctly, or maybe the script
is no longer accessible from
https://pypi.python.org/packages/2.7/s/setuptools/

I have been able to build Pylith and I have run one of the examples
successfully.

Thank you very much again!
Have a nice weekend,

Laura

Laura Blanco Martin
Earth Sciences Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd, MS74R 316C
Berkeley, CA 94720

On Fri, Jul 10, 2015 at 2:46 PM, Brad Aagaard <baagaard at usgs.gov> wrote:

> I have patched the HDF5 tarball on the CIG webserver and posted a new
> PyLith installer release (2.1.0-2) that uses this tarball.
>
> Regards,
> Brad
>
>
> On 07/10/2015 12:38 PM, Brad Aagaard wrote:
>
>> Laura,
>>
>> This error is a compilation error associated with a bad comment line
>> within HDF5. Some compilers are more lenient than others when they
>> encounter C++ style comments in C code.
>>
>> ../../../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");
>>
>>
>>
>> Change line 635 of hdf5-1.8.11/tools/lib/h5tools_dump.c from
>>
>> //HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "Could not allocate
>> buffer for ptdata");
>>
>> to
>>
>> /* HGOTO_ERROR(dimension_break, H5E_tools_min_id_g, "Could not allocate
>> buffer for ptdata"); */
>>
>>
>>
>> I will create a patched version of the HDF5 tarball on the CIG website
>> to fix this.
>>
>> Thanks for reporting this.
>>
>> Brad
>>
>>
>>
>> On 07/10/2015 12:11 PM, Laura Blanco Martin wrote:
>>
>>> Matt,
>>>
>>> Sorry for that. I attach the three files again.
>>>
>>> Laura
>>>
>>> Laura Blanco Martin
>>> Earth Sciences Division
>>> Lawrence Berkeley National Laboratory
>>> 1 Cyclotron Rd, MS74R 316C
>>> Berkeley, CA 94720
>>>
>>> On Fri, Jul 10, 2015 at 11:24 AM, Laura Blanco Martin
>>> <lblancomartin at lbl.gov
>>>
>>>> wrote:
>>>>
>>>
>>>  Brad, Matt,
>>>>
>>>> Thanks for your quick replies! I attach the 2 files config.log, plus
>>>> log.txt containing all the output from make. Let me know if you need any
>>>> other file.
>>>>
>>>> Thanks so much,
>>>>
>>>> Laura
>>>>
>>>> Laura Blanco Martin
>>>> Earth Sciences Division
>>>> Lawrence Berkeley National Laboratory
>>>> 1 Cyclotron Rd, MS74R 316C
>>>> Berkeley, CA 94720
>>>>
>>>> On Fri, Jul 10, 2015 at 10:41 AM, Laura Blanco Martin <
>>>> lblancomartin at lbl.gov> wrote:
>>>>
>>>>  Hi,
>>>>>
>>>>> I am trying to build Pylith from source in Ubuntu 15.04 and I get an
>>>>> error when building HDF5:
>>>>>
>>>>> make[6]: *** [h5tools_dump.lo] Error 1
>>>>> make[6]: Leaving directory
>>>>> `/home/laura/build/pylith/hdf5-build/tools/lib'
>>>>> make[5]: *** [all-recursive] Error 1
>>>>> make[5]: Leaving directory `/home/laura/build/pylith/hdf5-build/tools'
>>>>> make[4]: *** [all-recursive] Error 1
>>>>> make[4]: Leaving directory `/home/laura/build/pylith/hdf5-build'
>>>>> make[3]: *** [hdf5] Error 2
>>>>> make[3]: Leaving directory `/home/laura/build/pylith'
>>>>> make[2]: *** [installed_hdf5] Error 2
>>>>> make[2]: Leaving directory `/home/laura/build/pylith'
>>>>> make[1]: *** [installed_netcdf] Error 2
>>>>> make[1]: Leaving directory `/home/laura/build/pylith'
>>>>> make: *** [installed_pylith] Error 2
>>>>>
>>>>> I have tried to build other versions of the package available in
>>>>> http://geoweb.cse.ucdavis.edu/~buildbot/deps/
>>>>>
>>>>> but I always get the same error. Following suggestions in the install
>>>>> file, I have also tried to change the features/packages selected
>>>>> when doing
>>>>> configure, but the error is always the same.
>>>>> I have built Pylith from source before, on a Virtual Machine. Now I am
>>>>> using a Liinux PC. Could the problem be related to incompatibilities
>>>>> between make and autoreconf, etc ? At the beginning I was using make
>>>>> v4,
>>>>> and it seems that it has some backwards incompatibilities. I have
>>>>> installed
>>>>> v3.81, but I get the same error. When using make v4, before line
>>>>> "make[6]:
>>>>> *** [h5tools_dump.lo] Error 1" above, I used to get a line
>>>>> "Makefile.553 :
>>>>> recipe for target 'h5tools_dump.lo' failed".
>>>>>
>>>>> Any help will be appreciated.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Laura
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>
>>>
>>
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