syou83syou83 commented 6 years ago

Hi,

When I ran sh f2py.sh in my Ubuntu 16.04 LTS in Canopy, I found the following info. I am a beginner of python and know little about fortran. Could you tell me what happened here? Because ImportError: No module named py_gmm, I assume it must not be installed successfully. When I was trying to run it on Binder before installation, it also showed an error: Unable to locate package libopenblas-base.

All I want to calculate is the extinction cross section of a doublet aggregate, with each particle size about 90 micron. Thank you so much for your help.

Reading fortran codes... Reading file 'gmm_f2py_module.f90' (format:free) rmbadname1: Replacing "short" with "short_bn". rmbadname1: Replacing "long" with "long_bn". Post-processing... Block: gmm_py Block: local_kinds In: :gmm_py:gmm_f2py_module.f90:local_kinds get_parameters: got "unexpected EOF while parsing (, line 1)" on '0.0d0' Block: gmm_f2py_module In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module get_useparameters: no module vec_trans info used by gmm_f2py_moduImportError: /home/sichen/.local/share/canopy/edm/envs/User/bin/../lib/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by ../py_gmm/gmm_py.so)le In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module get_useparameters: no module linear_solver info used by gmm_f2py_module In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module get_useparameters: no module shared_data info used by gmm_f2py_module In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module get_useparameters: no module operators info used by gmm_f2py_module In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module get_useparameters: no module sing_part info used by gmm_f2py_module In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module get_useparameters: no module gmmsubs info used by gmm_f2py_module In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module get_useparameters: no module datatypes info used by gmm_f2py_module In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module get_useparameters: no module local_field info used by gmm_f2py_module In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module get_useparameters: no module basicsubs info used by gmm_f2py_module Block: emn In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:emn get_useparameters: no module vec_trans info used by emn In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:emn get_useparameters: no module linear_solver info used by emn In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:emn get_useparameters: no module shared_data info used by emn In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:emn get_useparameters: no module operators info used by emn In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:emn get_useparameters: no module sing_part info used by emn In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:emn get_useparameters: no module gmmsubs info used by emn In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:emn get_useparameters: no module datatypes info used by emn In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:emn get_useparameters: no module local_field info used by emn In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:emn get_useparameters: no module basicsubs info used by emn Block: expansion_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:expansion_coefficients get_useparameters: no module vec_trans info used by expansion_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:expansion_coefficients get_useparameters: no module linear_solver info used by expansion_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:expansion_coefficients get_useparameters: no module shared_data info used by expansion_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:expansion_coefficients get_useparameters: no module operators info used by expansion_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:expansion_coefficients get_useparameters: no module sing_part info used by expansion_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:expansion_coefficients get_useparameters: no module gmmsubs info used by expansion_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:expansion_coefficients get_useparameters: no module datatypes info used by expansion_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:expansion_coefficients get_useparameters: no module local_field info used by expansion_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:expansion_coefficients get_useparameters: no module basicsubs info used by expansion_coefficients Block: exyz In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:exyz get_useparameters: no module vec_trans info used by exyz In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:exyz get_useparameters: no module linear_solver info used by exyz In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:exyz get_useparameters: no module shared_data info used by exyz In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:exyz get_useparameters: no module operators info used by exyz In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:exyz get_useparameters: no module sing_part info used by exyz In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:exyz get_useparameters: no module gmmsubs info used by exyz In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:exyz get_useparameters: no module datatypes info used by exyz In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:exyz get_useparameters: no module local_field info used by exyz In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:exyz get_useparameters: no module basicsubs info used by exyz Block: efar In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar get_useparameters: no module vec_trans info used by efar In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar get_useparameters: no module linear_solver info used by efar In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar get_useparameters: no module shared_data info used by efar In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar get_useparameters: no module operators info used by efar In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar get_useparameters: no module sing_part info used by efar In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar get_useparameters: no module gmmsubs info used by efar In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar get_useparameters: no module datatypes info used by efar In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar get_useparameters: no module local_field info used by efar In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar get_useparameters: no module basicsubs info used by efar Block: efar_poynting In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar_poynting get_useparameters: no module vec_trans info used by efar_poynting In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar_poynting get_useparameters: no module linear_solver info used by efar_poynting In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar_poynting get_useparameters: no module shared_data info used by efar_poynting In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar_poynting get_useparameters: no module operators info used by efar_poynting In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar_poynting get_useparameters: no module sing_part info used by efar_poynting In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar_poynting get_useparameters: no module gmmsubs info used by efar_poynting In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar_poynting get_useparameters: no module datatypes info used by efar_poynting In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar_poynting get_useparameters: no module local_field info used by efar_poynting In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:efar_poynting get_useparameters: no module basicsubs info used by efar_poynting Block: dip_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:dip_coefficients get_useparameters: no module vec_trans info used by dip_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:dip_coefficients get_useparameters: no module linear_solver info used by dip_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:dip_coefficients get_useparameters: no module shared_data info used by dip_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:dip_coefficients get_useparameters: no module operators info used by dip_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:dip_coefficients get_useparameters: no module sing_part info used by dip_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:dip_coefficients get_useparameters: no module gmmsubs info used by dip_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:dip_coefficients get_useparameters: no module datatypes info used by dip_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:dip_coefficients get_useparameters: no module local_field info used by dip_coefficients In: :gmm_py:gmm_f2py_module.f90:gmm_f2py_module:dip_coefficients get_useparameters: no module basicsubs info used by dip_coefficients Post-processing (stage 2)... Block: gmm_py Block: unknown_interface Block: local_kinds Block: gmm_f2py_module Block: emn Block: expansion_coefficients Block: exyz Block: efar Block: efar_poynting Block: dip_coefficients Saving signatures to file "./gmm_py.pyf" running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "gmm_py" sources f2py options: [] f2py: gmm_py.pyf Reading fortran codes... Reading file 'gmm_py.pyf' (format:free) Post-processing... Block: gmm_py Block: local_kinds Block: gmm_f2py_module In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module get_useparameters: no module vec_trans info used by gmm_f2py_module In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module get_useparameters: no module linear_solver info used by gmm_f2py_module In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module get_useparameters: no module shared_data info used by gmm_f2py_module In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module get_useparameters: no module operators info used by gmm_f2py_module In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module get_useparameters: no module sing_part info used by gmm_f2py_module In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module get_useparameters: no module gmmsubs info used by gmm_f2py_module In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module get_useparameters: no module datatypes info used by gmm_f2py_module In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module get_useparameters: no module local_field info used by gmm_f2py_module In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module get_useparameters: no module basicsubs info used by gmm_f2py_module Block: emn In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:emn get_useparameters: no module vec_trans info used by emn In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:emn get_useparameters: no module linear_solver info used by emn In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:emn get_useparameters: no module shared_data info used by emn In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:emn get_useparameters: no module operators info used by emn In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:emn get_useparameters: no module sing_part info used by emn In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:emn get_useparameters: no module gmmsubs info used by emn In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:emn get_useparameters: no module datatypes info used by emn In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:emn get_useparameters: no module local_field info used by emn In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:emn get_useparameters: no module basicsubs info used by emn Block: expansion_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:expansion_coefficients get_useparameters: no module vec_trans info used by expansion_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:expansion_coefficients get_useparameters: no module linear_solver info used by expansion_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:expansion_coefficients get_useparameters: no module shared_data info used by expansion_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:expansion_coefficients get_useparameters: no module operators info used by expansion_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:expansion_coefficients get_useparameters: no module sing_part info used by expansion_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:expansion_coefficients get_useparameters: no module gmmsubs info used by expansion_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:expansion_coefficients get_useparameters: no module datatypes info used by expansion_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:expansion_coefficients get_useparameters: no module local_field info used by expansion_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:expansion_coefficients get_useparameters: no module basicsubs info used by expansion_coefficients Block: exyz In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:exyz get_useparameters: no module vec_trans info used by exyz In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:exyz get_useparameters: no module linear_solver info used by exyz In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:exyz get_useparameters: no module shared_data info used by exyz In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:exyz get_useparameters: no module operators info used by exyz In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:exyz get_useparameters: no module sing_part info used by exyz In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:exyz get_useparameters: no module gmmsubs info used by exyz In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:exyz get_useparameters: no module datatypes info used by exyz In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:exyz get_useparameters: no module local_field info used by exyz In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:exyz get_useparameters: no module basicsubs info used by exyz Block: efar In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar get_useparameters: no module vec_trans info used by efar In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar get_useparameters: no module linear_solver info used by efar In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar get_useparameters: no module shared_data info used by efar In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar get_useparameters: no module operators info used by efar In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar get_useparameters: no module sing_part info used by efar In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar get_useparameters: no module gmmsubs info used by efar In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar get_useparameters: no module datatypes info used by efar In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar get_useparameters: no module local_field info used by efar In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar get_useparameters: no module basicsubs info used by efar Block: efar_poynting In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar_poynting get_useparameters: no module vec_trans info used by efar_poynting In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar_poynting get_useparameters: no module linear_solver info used by efar_poynting In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar_poynting get_useparameters: no module shared_data info used by efar_poynting In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar_poynting get_useparameters: no module operators info used by efar_poynting In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar_poynting get_useparameters: no module sing_part info used by efar_poynting In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar_poynting get_useparameters: no module gmmsubs info used by efar_poynting In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar_poynting get_useparameters: no module datatypes info used by efar_poynting In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar_poynting get_useparameters: no module local_field info used by efar_poynting In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:efar_poynting get_useparameters: no module basicsubs info used by efar_poynting Block: dip_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:dip_coefficients get_useparameters: no module vec_trans info used by dip_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:dip_coefficients get_useparameters: no module linear_solver info used by dip_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:dip_coefficients get_useparameters: no module shared_data info used by dip_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:dip_coefficients get_useparameters: no module operators info used by dip_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:dip_coefficients get_useparameters: no module sing_part info used by dip_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:dip_coefficients get_useparameters: no module gmmsubs info used by dip_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:dip_coefficients get_useparameters: no module datatypes info used by dip_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:dip_coefficients get_useparameters: no module local_field info used by dip_coefficients In: gmm_py.pyf:gmm_py:unknown_interface:gmm_f2py_module:dip_coefficients get_useparameters: no module basicsubs info used by dip_coefficients Post-processing (stage 2)... Block: gmm_py Block: unknown_interface Block: local_kinds Block: gmm_f2py_module Block: emn Block: expansion_coefficients Block: exyz Block: efar Block: efar_poynting Block: dip_coefficients Building modules... Building module "gmm_py"... Constructing F90 module support for "local_kinds"... Variables: twopi dbl short_bn pio2_d sqrt2_d sgl zerodbl e0 me c e lo vshort twopi_d length sqrt2 pio2 pi pi_d long_bn euler euler_d undo_rmbadname1: Replacing "short_bn" with "short". undo_rmbadname1: Replacing "long_bn" with "long". undo_rmbadname1: Replacing "short_bn" with "short". undo_rmbadname1: Replacing "long_bn" with "long". undo_rmbadname1: Replacing "short_bn" with "short". undo_rmbadname1: Replacing "long_bn" with "long". undo_rmbadname1: Replacing "short_bn" with "short". undo_rmbadname1: Replacing "long_bn" with "long". Constructing F90 module support for "gmm_f2py_module"... Constructing wrapper function "gmm_f2py_module.emn"... v_emn,error = emn(nstop) Constructing wrapper function "gmm_f2py_module.expansion_coefficients"... m_coeff,v_cext,v_csca,v_cabs = expansion_coefficients(m_xyz_inp,v_r_inp,m_eps_inp,fint,ref_index,lambda_inp,alpha0,beta0,gamma0,nstop,quasi_static_flag,[ns]) Constructing wrapper function "gmm_f2py_module.exyz"... ex,ey,ez,eabs,error = exyz(flaginc,nstop,ratio,lambda_inp,alpha0,beta0,gamma0,x,y,z,v_amnbmn,v_dmncmn,v_emn,m_xyz_inp,m_eps_inp,v_r_inp,ref_index,quasi_static_flag,[ns]) Constructing wrapper function "gmm_f2py_module.efar"... m_sc,scatot,error = efar(k,nstop,phimin,phimax,phistep,thetastep,betap,v_amnbmn,m_xyz_inp,[ns]) Constructing wrapper function "gmm_f2py_module.efar_poynting"... m_sc,scatot,error = efar_poynting(k,nstop,phimin,phimax,phistep,thetastep,betap,v_amnbmn,m_xyz_inp,[ns]) Constructing wrapper function "gmm_f2py_module.dip_coefficients"... m_coeff,v_w = dip_coefficients(ndip,m_xyz_inp,v_r_inp,m_eps_inp,fint,q0,ref_index,lambda_inp,alpha0,beta0,gamma0,nstop,quasi_static_flag,[ns]) Wrote C/API module "gmm_py" to file "tmp/src.linux-x86_64-2.7/gmm_pymodule.c" Fortran 90 wrappers are saved to "tmp/src.linux-x86_64-2.7/gmm_py-f2pywrappers2.f90" adding './tmp/src.linux-x86_64-2.7/tmp/src.linux-x86_64-2.7/fortranobject.c' to sources. adding './tmp/src.linux-x86_64-2.7/tmp/src.linux-x86_64-2.7' to include_dirs. adding 'tmp/src.linux-x86_64-2.7/gmm_py-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize Gnu95FCompiler Found executable /usr/bin/gfortran Found executable /usr/bin/gfortran customize Gnu95FCompiler using build_ext building 'gmm_py' extension compiling C sources C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -fPIC

compile options: '-I./tmp/src.linux-x86_64-2.7/tmp/src.linux-x86_64-2.7 -I/home/sichen/.local/share/canopy/edm/envs/User/lib/python2.7/site-packages/numpy/core/include -I/home/sichen/.local/share/canopy/edm/envs/User/include/python2.7 -c' gcc: tmp/src.linux-x86_64-2.7/gmm_pymodule.c In file included from /home/sichen/.local/share/canopy/edm/envs/User/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0, from /home/sichen/.local/share/canopy/edm/envs/User/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /home/sichen/.local/share/canopy/edm/envs/User/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from ./tmp/src.linux-x86_64-2.7/tmp/src.linux-x86_64-2.7/fortranobject.h:13, from tmp/src.linux-x86_64-2.7/gmm_pymodule.c:19: /home/sichen/.local/share/canopy/edm/envs/User/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

warning "Using deprecated NumPy API, disable it by " \

^ compiling Fortran 90 module sources Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -O3 -fpic -m64 -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -O3 -fpic -m64 -fPIC -O3 -funroll-loops compile options: '-I./tmp/src.linux-x86_64-2.7/tmp/src.linux-x86_64-2.7 -I/home/sichen/.local/share/canopy/edm/envs/User/lib/python2.7/site-packages/numpy/core/include -I/home/sichen/.local/share/canopy/edm/envs/User/include/python2.7 -c' extra options: '-J./tmp/ -I./tmp/' gfortran:f90: kinds.f90 gfortran:f90: datatypes.f90 gfortran:f90: operators.f90 gfortran:f90: shared_data.f90 gfortran:f90: basicsubs.f90 gfortran:f90: gmmsubs.f90 gfortran:f90: sing_part.f90 gfortran:f90: vec_trans.f90 gfortran:f90: local_field.f90 gfortran:f90: linear_solver.f90 gfortran:f90: gmm_f2py_module.f90 compiling Fortran sources Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -O3 -fpic -m64 -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -O3 -fpic -m64 -fPIC -O3 -funroll-loops compile options: '-I./tmp/src.linux-x86_64-2.7/tmp/src.linux-x86_64-2.7 -I/home/sichen/.local/share/canopy/edm/envs/User/lib/python2.7/site-packages/numpy/core/include -I/home/sichen/.local/share/canopy/edm/envs/User/include/python2.7 -c' extra options: '-J./tmp/ -I./tmp/' gfortran:f90: tmp/src.linux-x86_64-2.7/gmm_py-f2pywrappers2.f90 /usr/bin/gfortran -Wall -g -Wall -g -shared ./tmp/tmp/src.linux-x86_64-2.7/gmm_pymodule.o ./tmp/tmp/src.linux-x86_64-2.7/tmp/src.linux-x86_64-2.7/fortranobject.o ./tmp/kinds.o ./tmp/datatypes.o ./tmp/operators.o ./tmp/shared_data.o ./tmp/basicsubs.o ./tmp/gmmsubs.o ./tmp/sing_part.o ./tmp/vec_trans.o ./tmp/local_field.o ./tmp/linear_solver.o ./tmp/gmm_f2py_module.o ./tmp/tmp/src.linux-x86_64-2.7/gmm_py-f2pywrappers2.o -L/home/sichen/.local/share/canopy/edm/envs/User/lib -lopenblas -lpython2.7 -lgfortran -o ./gmm_py.so

gevero commented 6 years ago

Hi! Did you use anaconda? If yes try conda install openblas. Otherwise run apt-cache search openblas and install the relevant openblas packages.

syou83syou83 commented 6 years ago

Hi Gevero, I am using Enthought Canopy. And I did the following. But this seems doesn't work either for Binder or for my installation.

(User)sichen@sichen:~$ apt-cache search openblas libblas-test - Basic Linear Algebra Subroutines 3, testing programs libopenblas-base - Optimized BLAS (linear algebra) library (shared library) libopenblas-dev - Optimized BLAS (linear algebra) library (development files) (User)sichen@sichen:~$ sudo apt-get install libopenblas-dev [sudo] password for sichen: Reading package lists... Done Building dependency tree
Reading state information... Done libopenblas-dev is already the newest version (0.2.18-1ubuntu1). The following packages were automatically installed and are no longer required: linux-headers-4.10.0-28 linux-headers-4.10.0-28-generic linux-headers-4.13.0-26 linux-headers-4.13.0-26-generic linux-image-4.10.0-28-generic linux-image-4.13.0-26-generic linux-image-extra-4.10.0-28-generic linux-image-extra-4.13.0-26-generic linux-oem-tools-4.13.0-1012 linux-oem-tools-4.13.0-1015 linux-oem-tools-4.13.0-1017 linux-tools-4.13.0-1012-oem linux-tools-4.13.0-1015-oem linux-tools-4.13.0-1017-oem Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded. (User)sichen@sichen:~$ sudo apt-get install libopenblas-base Reading package lists... Done Building dependency tree
Reading state information... Done libopenblas-base is already the newest version (0.2.18-1ubuntu1). libopenblas-base set to manually installed. The following packages were automatically installed and are no longer required: linux-headers-4.10.0-28 linux-headers-4.10.0-28-generic linux-headers-4.13.0-26 linux-headers-4.13.0-26-generic linux-image-4.10.0-28-generic linux-image-4.13.0-26-generic linux-image-extra-4.10.0-28-generic linux-image-extra-4.13.0-26-generic linux-oem-tools-4.13.0-1012 linux-oem-tools-4.13.0-1015 linux-oem-tools-4.13.0-1017 linux-tools-4.13.0-1012-oem linux-tools-4.13.0-1015-oem linux-tools-4.13.0-1017-oem Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.

After running Au_dimer_scattering.ipynb, I got : ImportError: /home/sichen/.local/share/canopy/edm/envs/User/bin/../lib/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by ../py_gmm/gmm_py.so)

gevero commented 6 years ago

Well, this looks like a canopy issue.

gevero commented 6 years ago

PS... binder platform is always changing. It used to work, but now probably i need to update the dockerfile

syou83syou83 commented 6 years ago

Thanks gevero. I will work on it and let you know if I can solve it.

gevero commented 6 years ago

My advice is to use conda. It has work on many for many different users on many different platforms. Give it a try!

gevero commented 4 years ago

Hi

This should work

Install docker on your machine (do this, and the following, as root if using linux)
in the py_gmm base folder, run docker build --tag pygmm:1.0 .
run sudo docker run --publish 8888:8888 --detach --name pygmm pygmm:1.0 to build the container and open the 8888 port for the jupyter server that is already running inside the container
run docker exec -it pygmm jupyter notebook list to get the token to access the server

Best

Giovanni

gevero / py_gmm

installation issue #16

warning "Using deprecated NumPy API, disable it by " \