[CIG-SHORT] PyLith version 2.2.0 installation from source
Brad Aagaard
baagaard at usgs.gov
Thu Jun 8 13:29:41 PDT 2017
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/AACLybuo8ckIvk9tZwOl6IrVa?dl=0
> <https://www.dropbox.com/sh/xjr5dn23ptxivv3/AACLybuo8ckIvk9tZwOl6IrVa?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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