[CIG-SHORT] PyLith version 2.2.0 installation from source
Brad Aagaard
baagaard at usgs.gov
Thu Jun 8 20:35:30 PDT 2017
Josimar,
PyLith should build with any recent version of gcc. I believe gcc 4.x
and later should all work. There could be issues related to older
versions and the newer HDF5 and NetCDF versions.
You can try --enable-gcc --enable-mpi=openmpi --enable-python to see if
that will build. You may need to adjust the MPI configure requirements
to be consistent with your hardware (e.g., infiniband).
Brad
On 6/8/17 4:54 PM, Josimar Alves da Silva wrote:
> Brad,
>
> I clean the /home/josimar/pylith as indicated in the installation
> instructions whenever any changes are made on the PyLith configurations.
>
> After running the ./configure and after "source setup.sh", but before
> "make", the output of "which gcc" is: /cm/shared/apps/gcc/4.8.4/bin/gcc
>
> My understanding is that gcc does not point to a version that is
> compatible with the PyLith installation requirements (it requires
> version 5.4.0 according to the instructions), and that's is why I was
> using "--enable-gcc". Is this correct ?
>
> thanks,
> Josimar
>
>
> On Thu, Jun 8, 2017 at 4:57 PM, Matthew Knepley <knepley at gmail.com
> <mailto:knepley at gmail.com>> wrote:
>
> 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
> <mailto: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
> <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>
> <mailto: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>
> <mailto: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>
>
> <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>
> <mailto: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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