[CIG-SHORT] PyLith version 2.2.0 installation from source
Matthew Knepley
knepley at gmail.com
Thu Jun 8 13:57:17 PDT 2017
Brad, as I said in the last message, I think it comes from Python since it
is building a module. I would try manually building Python.
Thanks
Matt
On Jun 8, 2017 4:30 PM, "Brad Aagaard" <baagaard at usgs.gov> wrote:
> Josimar,
>
> I am stumped as to where the -fp-model strict is coming from. It looks
> like it is coming from the MPI installation or a compiler that is detected.
>
> Did you clean out /home/josimar/pylith before reconfiguring and
> rebuilding? You should do this before configuring the PyLith installer,
> whenever you change any of the PyLith installer configure options.
>
> Also make sure "which gcc" points to the gcc used to build MPI AFTER you
> do "source setup.sh" and before "make" for the installer.
>
> Also, is there a reason why you are building Python. It looks like you
> have python 2.7.10 in your path already at /cm/shared/engaging/python/2.7.10/bin.
> If it was built with the same version of gcc as the MPI, then you should be
> able to use it (run "python" to see the compiler). If you then you can drop
> the --enable-python configure argument.
>
> Brad
>
>
> On 06/08/2017 09:44 AM, Josimar Alves da Silva wrote:
>
>> Dear Brad and Matt,
>>
>> Following up on your suggestions: I used the recommended settings that
>> you mentioned on the previous e-mail but unfortunately the error persist.
>>
>> gcc: no <---- WAS YES
>> Python: yes
>> mpi: no
>> [...]
>>
>> See all the log files below on the dropbox link.
>>
>> https://www.dropbox.com/sh/g48lkxf81nn3hio/AADASW4qBvEWs42vKN4blEfIa?dl=0
>>
>> Perhaps I should try again using "--enable-gcc", " --enable-mpi" and
>> "--enable-python" ?
>>
>> thank you
>> Josimar
>>
>>
>> On Thu, Jun 8, 2017 at 10:57 AM, Matthew Knepley <knepley at rice.edu
>> <mailto:knepley at rice.edu>> wrote:
>>
>> On Thu, Jun 8, 2017 at 7:58 AM, Josimar Alves da Silva
>> <jsilva.mit at gmail.com <mailto:jsilva.mit at gmail.com>> wrote:
>>
>> Brad,
>>
>> Thank you so much for the help. The MPI version seems compatible
>> with what is asked on the installation file:
>>
>>
>> The question is where -fp-model is coming from. I think it might be
>> from the Python installation, since this is compiling
>> a module. This would lead me to build my own Python, since the
>> Python you have must have been built with
>> something else (clang?).
>>
>> Thanks,
>>
>> Matt
>>
>> "mpicc -show" results in:
>>
>> gcc -I/cm/shared/engaging/openmpi/1.8.8/include -pthread
>> -Wl,-rpath -Wl,/cm/shared/engaging/openmpi/1.8.8/lib
>> -Wl,--enable-new-dtags -L/cm/shared/engaging/openmpi/1.8.8/lib
>> -lmpi
>>
>>
>> However, the gcc version is older than what is asked on the
>> installation file:
>>
>>
>> cm/shared/apps/gcc/4.8.4/bin/gcc
>>
>>
>>
>> In order to update the gcc version, I attempted to build PyLith
>> again using the following configuration:
>>
>> ./configure --with-make-threads=2 --prefix=$HOME/pylith
>> --enable-python --enable-force-install --enable-gcc
>>
>>
>> However I still got the error message that I sent on the
>> previous e-mail. Note that I did load the "setup.sh" file before
>> "make".
>>
>> You can find all the log files that you asked on the previous
>> e-mail, along with a shell script that I am using to build
>> pylith, on the dropbox link below:
>>
>> https://www.dropbox.com/sh/xjr5dn23ptxivv3/AACLybuo8ckIvk9tZ
>> wOl6IrVa?dl=0
>> <https://www.dropbox.com/sh/xjr5dn23ptxivv3/AACLybuo8ckIvk9t
>> ZwOl6IrVa?dl=0>
>>
>> Let me know if you have any further suggestions.
>>
>> thank you in advance for the help,
>>
>> Josimar
>>
>>
>>
>>
>> On Wed, Jun 7, 2017 at 6:10 PM, Brad Aagaard <baagaard at usgs.gov
>> <mailto:baagaard at usgs.gov>> wrote:
>>
>> Josimar,
>>
>> The error you are getting seems to suggest that the compiler
>> does not recognize the -fp-model strict command line
>> argument. This could be the case if a different compiler is
>> being used than the one it thinks it should be using.
>>
>> Check to make sure the gcc and MPI in your path are
>> consistent. Usually "mpicc -show" will show you which
>> compiler is being used. Also make sure the shell environment
>> when you build matches the one used during the configure
>> (and loads the setup.sh generated in the configure process).
>>
>> If you still get stuck, send the config.log for the
>> top-level installer configure, and the config.log and
>> make.log (capture all of the make output) for the package
>> that fails to build.
>>
>> Regards,
>> Brad
>>
>>
>>
>>
>>
>>
>> On 06/07/2017 01:39 PM, Josimar Alves da Silva wrote:
>>
>> Dear Brad,
>>
>> I am building PyLith version 2.2.0 from source on a
>> linux machine. I am getting the error below.
>>
>> See computer information below along with the error
>> message at the end of the e-mail. The config.log file is
>> also attached.
>>
>> Please let me know if you have seen this error before
>> and how to correct it.
>>
>> thank you in advance,
>> Josimar
>>
>>
>>
>> ############# BASIC COMPUTER INFORMATION HERE
>>
>> Linux eofe4 2.6.32-504.30.3.el6.x86_64 #1 SMP Wed Jul 15
>> 10:13:09 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>>
>>
>> ########################
>>
>> Architecture: x86_64
>>
>> CPU op-mode(s): 32-bit, 64-bit
>>
>> Byte Order: Little Endian
>>
>> CPU(s): 16
>>
>> On-line CPU(s) list: 0-15
>>
>> Thread(s) per core: 1
>>
>> Core(s) per socket: 8
>>
>> Socket(s): 2
>>
>> NUMA node(s): 2
>>
>> Vendor ID: GenuineIntel
>>
>> CPU family: 6
>>
>> Model: 45
>>
>> Model name: Intel(R) Xeon(R) CPU E5-2650 0 @
>> 2.00GHz
>>
>> Stepping: 7
>>
>> CPU MHz: 1999.998
>>
>> BogoMIPS: 3999.47
>>
>> Virtualization: VT-x
>>
>> L1d cache: 32K
>>
>> L1i cache: 32K
>>
>> L2 cache: 256K
>>
>> L3 cache: 20480K
>>
>> NUMA node0 CPU(s): 0,2,4,6,8,10,12,14
>>
>> NUMA node1 CPU(s): 1,3,5,7,9,11,13,15
>>
>>
>>
>>
>>
>> ############# ERRO MESSAGE FROM PYLITH INSTALLATION HERE
>> #############
>>
>> make[4]: Entering directory
>> `/home/josimar/build/pylith/python-build'
>>
>> mpicc -c -fno-strict-aliasing -fp-model strict -g -O2
>> -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I.
>> -IInclude -I../Python-2.7.13/Include
>> -I/home/josimar/pylith/include -fPIC -DPy_BUILD_CORE -o
>> Modules/python.o ../Python-2.7.13/Modules/python.c
>>
>> mpicc -c -fno-strict-aliasing -fp-model strict -g -O2
>> -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I.
>> -IInclude -I../Python-2.7.13/Include
>> -I/home/josimar/pylith/include -fPIC -DPy_BUILD_CORE -o
>> Parser/acceler.o ../Python-2.7.13/Parser/acceler.c
>>
>> gcc: error: strict: No such file or directory
>>
>> gcc: error: unrecognized command line option ‘-fp-model’
>>
>> make[4]: *** [Modules/python.o] Error 1
>>
>> make[4]: *** Waiting for unfinished jobs....
>>
>> gcc: error: strict: No such file or directory
>>
>> gcc: error: unrecognized command line option ‘-fp-model’
>>
>> make[4]: *** [Parser/acceler.o] Error 1
>>
>> make[4]: Leaving directory
>> `/home/josimar/build/pylith/python-build'
>>
>> make[3]: *** [python] Error 2
>>
>> make[3]: Leaving directory `/home/josimar/build/pylith'
>>
>> make[2]: *** [installed_python] Error 2
>>
>> make[2]: Leaving directory `/home/josimar/build/pylith'
>>
>> make[1]: *** [installed_swig] Error 2
>>
>> make[1]: Leaving directory `/home/josimar/build/pylith'
>>
>> make: *** [installed_pylith] Error 2
>>
>>
>>
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