[CIG-SHORT] PyLith version 2.2.0 installation from source
Brad Aagaard
baagaard at usgs.gov
Thu Jun 8 08:05:07 PDT 2017
Josimar,
The problem is that you asked the installer to install gcc but not MPI,
so it is using the system MPI that was built with the system gcc. I will
add a test to the installer configure script to catch this incompatibility.
CURRENT SETTINGS
PyLith dependencies to be installed:
gcc: yes, languages: c,c++,fortran
Python: yes
mpi: no <----------------- THIS IS INCOMPATIBLE WITH GCC==yes
autotools: no
setuptools: yes
cppunit: yes
proj4: yes
hdf5: yes
h5py: yes
netcdf: yes
netCDF4 (python): yes
pcre: no
swig: no
nemesis: yes
numpy: yes w/own blas/lapack: no
fiat: yes
spatialdata: yes
cmake: yes
petsc: yes, options: --download-chaco=1 --download-ml=1
--download-f2cblaslapack=1
pyre/pythia: yes
pylith-parameters GUI: yes
On a cluster, we recommend using the compilers and MPI installed by the
system administrator as this should ensure that the MPI has the correct
settings for the cluster hardware.
RECOMMENDED SETTINGS
gcc: no <---- WAS YES
Python: yes
mpi: no
autotools: no
setuptools: yes
cppunit: yes
proj4: yes
hdf5: yes
h5py: yes
netcdf: yes
netCDF4 (python): yes
pcre: no
swig: no
nemesis: yes
numpy: yes w/own blas/lapack: no
fiat: yes
spatialdata: yes
cmake: yes
petsc: yes, options: --download-chaco=1 --download-ml=1
--download-f2cblaslapack=1
pyre/pythia: yes
pylith-parameters GUI: yes
Brad
On 06/08/2017 05:58 AM, Josimar Alves da Silva wrote:
> Brad,
>
> Thank you so much for the help. The MPI version seems compatible with
> what is asked on the installation file:
>
> "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
>
> 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
>
>
>
> _______________________________________________
> 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
>
More information about the CIG-SHORT
mailing list