[CIG-SHORT] PyLith version 2.2.0 installation from source
Josimar Alves da Silva
jsilva.mit at gmail.com
Thu Jun 8 16:54:36 PDT 2017
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> 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> 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
>>>
>>> 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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