[CIG-SHORT] PyLith version 2.2.0 installation from source
Josimar Alves da Silva
jsilva.mit at gmail.com
Fri Jun 9 12:54:58 PDT 2017
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
>>
>>
>>
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>>>
>>
>>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>
>>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>>
>>
>>
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>>>
>>
>>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>
>>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>>
>>
>>
>>
>> ______________________________
>> _________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>
>>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>>>
>>
>>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>
>>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>>
>>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>
>>
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>>
>>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>
>>
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>
>> <mailto:CIG-SHORT at geodynamics.org
>> <mailto:CIG-SHORT at geodynamics.org>>
>>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> >>
>>
>>
>>
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>> <http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short>
>>
>>
>>
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>>
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20170609/429b1cfa/attachment-0001.html>
More information about the CIG-SHORT
mailing list