[CIG-SHORT] PyLith version 2.2.0 installation from source
Josimar Alves da Silva
jsilva.mit at gmail.com
Tue Jun 13 05:22:47 PDT 2017
Brad,
Just to let you know that, thanks to the help of my colleague Eshan
Haghighat <http://juanesgroup.mit.edu/ehsanh>, this problem was solved and
I was able to compile PyLith version 2.2.0.
In summary, some lessons learned:
1) wget "link_to_pylith_installer"
2) make sure the following structure of directories is available:
/home/josimar/pylith_install/src/pylith/pylith-installer-2.2.0-0
3)use mpich and python 2.7.3 for centos6
4) ./configure --with-python --prefix=DIR
thank you,
Josimar
On Fri, Jun 9, 2017 at 3:54 PM, Josimar Alves da Silva <jsilva.mit at gmail.com
> wrote:
> Brad,
>
> See below for the information you asked.
>
> Following up on on the suggestions that Matt gave, I went to "
> /home/josimar/build/pylith/python-build" and when I do "make" I get the
> error below.
>
> 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
>
> gcc: error: strict: No such file or directory
>
> gcc: error: unrecognized command line option ‘-fp-model’
> make: *** [Modules/python.o] Error 1
>
> Linux information here:
>
> LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.
> 0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-
> 4.0-amd64:printing-4.0-noarch
>
> Distributor ID: CentOS
>
> Description: CentOS release 6.8 (Final)
>
> Release: 6.8
>
> Codename: Final
>
> Linux 2.6.32-504.30.3.el6.x86_64 x86_64
>
>
> thanks
>
> Josimar
>
>
>
> On Fri, Jun 9, 2017 at 2:41 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
>
>> Josimar,
>>
>> What Linux distribution and version are you using?
>>
>> Brad
>>
>>
>>
>> On 6/9/17 11:12 AM, Josimar Alves da Silva wrote:
>>
>>> 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
>>> <mailto: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>
>>> <mailto: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>
>>> <mailto: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>
>>>
>>> <https://www.dropbox.com/sh/g48lkxf81nn3hio/AADASW4qBvEWs42v
>>> KN4blEfIa?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>>
>>> <mailto: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>>
>>> <mailto: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>>
>>>
>>>
>>> <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
>>> <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>>
>>> <mailto: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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