Makefile does not see Python

[damirqa]

I entered make DOWNLOAD_CODES=1 I get /bin/sh: 1: python2.6: not found Makefile:35: *** the code is not configured, please run configure first. Stop. but valeriya@valeriya-VirtualBox:~/amuse/amuse-11.0$ python -V Python 2.7.12

What have I done wrong? Where it is necessary to correct, that he did not search for version 2.6, and used the latest version of the python? PS: Please, update the documentation and installation instructions. Surplus is difficult to understand, especially for people who are not very good at Linux

[ipelupessy]

you need to run configure first:

./configure

[ipelupessy]

(this will set the correct python etc to use)

[damirqa]

In fact of the matter. I ran the configure first. Issued warnings. I did not take them into consideration.

valeriya@valeriya-VirtualBox:~/amuse/amuse-11.0$ ./configure
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking whether the Fortran 90 compiler (gfortran -g -O2 ) works... yes
checking if the fortran compiler supports iso c binding... 
checking for python... /usr/bin/python
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for python-config... /usr/bin/python-config
checking for cython... no
checking Python.h usability... yes
checking Python.h presence... yes
checking for Python.h... yes
checking if possible to embed python... embedded python
yes
checking for java... no
checking for javac... no
checking for jar... no
checking whether Java compiler works... no
checking whether Java interpreter works... no
configure: WARNING: Java not found, Java codes disabled
checking for mpiexec... /usr/bin/mpiexec
checking for mpicxx... mpicxx
checking checking MPI C++ flags... flags found
checking for MPI_Init... yes
checking for mpi.h... yes
checking for mpicc... mpicc
checking checking MPI C flags... flags found
checking for mpi.h... yes
checking for mpif90... mpif90
checking checking MPI Fortran flags... flags found
checking for mpif.h... yes
checking for OpenMP flag of C compiler... -fopenmp
checking for OpenMP flag of Fortran compiler... -fopenmp
checking if gfortran accepts -dumpversion option... yes
checking gfortran version... 5.4.0
checking for a sed that does not truncate output... /bin/sed
checking whether we are using the Microsoft C compiler... no
checking CL/cl.h usability... no
checking CL/cl.h presence... no
checking for CL/cl.h... no
checking OpenCL/cl.h usability... no
checking OpenCL/cl.h presence... no
checking for OpenCL/cl.h... no
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking for OpenCL library... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking fftw3.h usability... yes
checking fftw3.h presence... yes
checking for fftw3.h... yes
checking for fftw_plan_dft_r2c in -lfftw3... yes
checking gmp.h usability... yes
checking gmp.h presence... yes
checking for gmp.h... yes
checking for __gmpz_init in -lgmp... yes
checking mpfr.h usability... yes
checking mpfr.h presence... yes
checking for mpfr.h... yes
checking for mpfr_init in -lmpfr... yes
checking how to run the C++ preprocessor... g++ -E
checking mpreal.h usability... no
checking mpreal.h presence... no
checking for mpreal.h... no
configure: WARNING: Cannot find header (mpreal.h) of the library MPFR with MPFR_FLAGS -I/home/valeriya/amuse/prerequisites/include.
checking hdf5.h usability... no
checking hdf5.h presence... no
checking for hdf5.h... no
configure: WARNING: Cannot find headers (hdf5.h) of the library HDF5 in /home/valeriya/amuse/prerequisites/include.
checking for H5_init_library in -lhdf5... no
configure: WARNING: libhdf5 : library missing. (Cannot find symbol H5_init_library) in /home/valeriya/amuse/prerequisites. Check if libhdf53 is installed and if the version is correct
checking for hdf5.h... (cached) no
configure: WARNING: Cannot find headers (hdf5.h) of the library HDF5 in /home/valeriya/amuse/prerequisites/include.
checking for H5_init_library in -lhdf5... (cached) no
configure: WARNING: libhdf5 : library missing. (Cannot find symbol H5_init_library). Check if libhdf5 is installed and if the version is correct
checking netcdf.h usability... no
checking netcdf.h presence... no
checking for netcdf.h... no
configure: WARNING: Cannot find headers (netcdf.h) of the library NETCDF in /home/valeriya/amuse/prerequisites/include.
checking Fortran netcdf presence... configure: WARNING: Cannot compile or link against library Fortran NETCDF in /home/valeriya/amuse/prerequisites
checking for nc_inq_libvers in -lnetcdf... no
configure: WARNING: libnetcdf : library missing. (Cannot find symbol nc_inq_libvers) in /home/valeriya/amuse/prerequisites. Check if libnetcdf3 is installed and if the version is correct
checking for netcdf.h... (cached) no
configure: WARNING: Cannot find headers (netcdf.h) of the library NETCDF in /home/valeriya/amuse/prerequisites/include.
checking for nc_inq_libvers in -lnetcdf... (cached) no
configure: WARNING: libnetcdf : library missing. (Cannot find symbol nc_inq_libvers). Check if libnetcdf is installed and if the version is correct
checking Fortran netcdf presence... configure: WARNING: Cannot compile or link against library Fortran NETCDF in /home/valeriya/amuse/prerequisites/
checking for gcc option to produce PIC... -fPIC
checking for GSL... yes
checking for python module numpy... found (1.11.0)
checking for python module mpi4py... found (3.0.0)
checking for python module h5py... found (2.6.0)
checking for python module nose... found (1.3.7)
checking for python module docutils... found (0.12)
checking for python module zlib... found (1.0)
checking for python module matplotlib... not found
configure: creating ./config.status
config.status: creating src/amuse/config.py
config.status: creating support/config.py
config.status: error: cannot find input file: `support3/configpy.in'
valeriya@valeriya-VirtualBox:~/amuse/amuse-11.0$ make DOWNLOAD_CODES=1
/bin/sh: 1: python2.6: not found
Makefile:35: *** the code is not configured, please run configure first.  Stop.
valeriya@valeriya-VirtualBox:~/amuse/amuse-11.0$ 

[ipelupessy]

are you using the source package? I see there could be an error in the src package, the support3 directory is missing... since you are using python 2.7 you can copy support to support3 (it will be ignored further):

cp -r support support3

and try again

I will make an issue for this, thanks!

[ipelupessy]

for the warnings, the ones about HDF5 are not relevant for the present problem, but may cause issues later (I would check the presence/ installation of HDF5)

[damirqa]

I downloaded the package from the AmuseCode.org page where the release date is 05.10.17. I use OpenMPI. Thanks for support3, that helped.

If I use OpenMPI I must use mpd &?

[ipelupessy]

ok, it turns out that the src release tar on the website and on the github were not the same (I think the github one is fixed)..

no, when using openmpi you should start the a script with mpiexec (there is no mpd)

[ipelupessy]

the release has been updated...

[ipelupessy]

..which however does not yet fix the issue...

[arjenve]

hmm, seems my testing went OK but maybe I was in the wrong directory, sorry for that, updating as we speak

[ipelupessy]

fixed now, thanks!