[CIG-SHORT] PyLith version 2.2.0 installation from source
Josimar Alves da Silva
jsilva.mit at gmail.com
Fri Jun 9 11:12:12 PDT 2017
Brad,
Thanks for the reply. I did try --enable-gcc --enable-mpi=openmpi
--enable-python and still find the same issue. I will try to follow up on
the suggestion that Matt mentioned, which is to try to build python
manually.
Let me know if you have any other suggestions.
Thank you in advance,
Josimar
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’
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....
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
On Thu, Jun 8, 2017 at 11:35 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
> 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/AADASW4qBvEWs42vK
>> N4blEfIa?dl=0
>> <https://www.dropbox.com/sh/g48lkxf81nn3hio/AADASW4qBvEWs42v
>> KN4blEfIa?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/AACLybuo8ckIvk9tZ
>> wOl6IrVa?dl=0
>> <https://www.dropbox.com/sh/xjr5dn23ptxivv3/AACLybuo8ckIvk9t
>> ZwOl6IrVa?dl=0>
>>
>> <https://www.dropbox.com/sh/xjr5dn23ptxivv3/AACLybuo8ckIvk9t
>> ZwOl6IrVa?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>
>> <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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