search

dfm / python-fsps

Python bindings to Charlie Conroy's Flexible Stellar Population Synthesis (FSPS) Fortran code
https://python-fsps.readthedocs.io
MIT License
65 stars 38 forks source link

installation issue #30

Closed bdr244 closed 9 years ago

bdr244 commented 9 years ago

Having a bit of trouble with installing this correctly - it seems like it's not finding the fortran FSPS code correctly somehow. I've verified that $SPS_HOME exists and is in the right spot and the necessary files exist (as far as I can tell) but when I go to install python-fsps, it doesn't work.

I've been in communication with Dan about it and the "obvious" fixes aren't working at least, so posting it here to see if anyone else has some suggestions.

Here's the output of the "python setup.py install" command for reference, even though it is a bit of a wall of text.

running install running bdist_egg running egg_info writing fsps.egg-info/PKG-INFO writing top-level names to fsps.egg-info/top_level.txt writing dependency_links to fsps.egg-info/dependency_links.txt reading manifest file 'fsps.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'fsps.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/fsps copying fsps/fsps.py -> build/lib.linux-x86_64-2.7/fsps copying fsps/filters.py -> build/lib.linux-x86_64-2.7/fsps copying fsps/tests.py -> build/lib.linux-x86_64-2.7/fsps copying fsps/init.py -> build/lib.linux-x86_64-2.7/fsps copying fsps/fsps.f90 -> build/lib.linux-x86_64-2.7/fsps creating build/lib.linux-x86_64-2.7/fsps/data copying fsps/data/filter_keys.txt -> build/lib.linux-x86_64-2.7/fsps/data running build_ext Reading fortran codes... Reading file 'fsps.f90' (format:free) Post-processing... Block: _fsps Block: driver In: :_fsps:fsps.f90:driver get_useparameters: no module sps_utils info used by driver In: :_fsps:fsps.f90:driver get_useparameters: no module sps_vars info used by driver In: :_fsps:fsps.f90:driver getarrlen:variable "ntfull" undefined In: :_fsps:fsps.f90:driver getarrlen:variable "nz" undefined Block: setup In: :_fsps:fsps.f90:driver:setup get_useparameters: no module sps_utils info used by setup In: :_fsps:fsps.f90:driver:setup get_useparameters: no module sps_vars info used by setup Block: set_ssp_params In: :_fsps:fsps.f90:driver:set_ssp_params get_useparameters: no module sps_utils info used by set_ssp_params In: :_fsps:fsps.f90:driver:set_ssp_params get_useparameters: no module sps_vars info used by set_ssp_params Block: set_csp_params In: :_fsps:fsps.f90:driver:set_csp_params get_useparameters: no module sps_utils info used by set_csp_params In: :_fsps:fsps.f90:driver:set_csp_params get_useparameters: no module sps_vars info used by set_csp_params Block: ssps In: :_fsps:fsps.f90:driver:ssps get_useparameters: no module sps_utils info used by ssps In: :_fsps:fsps.f90:driver:ssps get_useparameters: no module sps_vars info used by ssps Block: ssp In: :_fsps:fsps.f90:driver:ssp get_useparameters: no module sps_utils info used by ssp In: :_fsps:fsps.f90:driver:ssp get_useparameters: no module sps_vars info used by ssp Block: get_ssp_spec In: :_fsps:fsps.f90:driver:get_ssp_spec get_useparameters: no module sps_utils info used by get_ssp_spec In: :_fsps:fsps.f90:driver:get_ssp_spec get_useparameters: no module sps_vars info used by get_ssp_spec Block: interp_ssp In: :_fsps:fsps.f90:driver:interp_ssp get_useparameters: no module sps_utils info used by interp_ssp In: :_fsps:fsps.f90:driver:interp_ssp get_useparameters: no module sps_vars info used by interp_ssp Block: smooth_spectrum In: :_fsps:fsps.f90:driver:smooth_spectrum get_useparameters: no module sps_utils info used by smooth_spectrum In: :_fsps:fsps.f90:driver:smooth_spectrum get_useparameters: no module sps_vars info used by smooth_spectrum Block: compute In: :_fsps:fsps.f90:driver:compute get_useparameters: no module sps_utils info used by compute In: :_fsps:fsps.f90:driver:compute get_useparameters: no module sps_vars info used by compute Block: get_spec In: :_fsps:fsps.f90:driver:get_spec get_useparameters: no module sps_utils info used by get_spec In: :_fsps:fsps.f90:driver:get_spec get_useparameters: no module sps_vars info used by get_spec Block: get_mags In: :_fsps:fsps.f90:driver:get_mags get_useparameters: no module sps_utils info used by get_mags In: :_fsps:fsps.f90:driver:get_mags get_useparameters: no module sps_vars info used by get_mags Block: get_setup_vars In: :_fsps:fsps.f90:driver:get_setup_vars get_useparameters: no module sps_utils info used by get_setup_vars In: :_fsps:fsps.f90:driver:get_setup_vars get_useparameters: no module sps_vars info used by get_setup_vars Block: get_nz In: :_fsps:fsps.f90:driver:get_nz get_useparameters: no module sps_utils info used by get_nz In: :_fsps:fsps.f90:driver:get_nz get_useparameters: no module sps_vars info used by get_nz Block: get_zlegend In: :_fsps:fsps.f90:driver:get_zlegend get_useparameters: no module sps_utils info used by get_zlegend In: :_fsps:fsps.f90:driver:get_zlegend get_useparameters: no module sps_vars info used by get_zlegend Block: get_timefull In: :_fsps:fsps.f90:driver:get_timefull get_useparameters: no module sps_utils info used by get_timefull In: :_fsps:fsps.f90:driver:get_timefull get_useparameters: no module sps_vars info used by get_timefull Block: get_ntfull In: :_fsps:fsps.f90:driver:get_ntfull get_useparameters: no module sps_utils info used by get_ntfull In: :_fsps:fsps.f90:driver:get_ntfull get_useparameters: no module sps_vars info used by get_ntfull Block: get_nspec In: :_fsps:fsps.f90:driver:get_nspec get_useparameters: no module sps_utils info used by get_nspec In: :_fsps:fsps.f90:driver:get_nspec get_useparameters: no module sps_vars info used by get_nspec Block: get_nbands In: :_fsps:fsps.f90:driver:get_nbands get_useparameters: no module sps_utils info used by get_nbands In: :_fsps:fsps.f90:driver:get_nbands get_useparameters: no module sps_vars info used by get_nbands Block: get_lambda In: :_fsps:fsps.f90:driver:get_lambda get_useparameters: no module sps_utils info used by get_lambda In: :_fsps:fsps.f90:driver:get_lambda get_useparameters: no module sps_vars info used by get_lambda Block: get_isochrone_dimensions In: :_fsps:fsps.f90:driver:get_isochrone_dimensions get_useparameters: no module sps_utils info used by get_isochrone_dimensions In: :_fsps:fsps.f90:driver:get_isochrone_dimensions get_useparameters: no module sps_vars info used by get_isochrone_dimensions Block: get_nmass_isochrone In: :_fsps:fsps.f90:driver:get_nmass_isochrone get_useparameters: no module sps_utils info used by get_nmass_isochrone In: :_fsps:fsps.f90:driver:get_nmass_isochrone get_useparameters: no module sps_vars info used by get_nmass_isochrone Block: get_stats In: :_fsps:fsps.f90:driver:get_stats get_useparameters: no module sps_utils info used by get_stats In: :_fsps:fsps.f90:driver:get_stats get_useparameters: no module sps_vars info used by get_stats Block: get_isochrone In: :_fsps:fsps.f90:driver:get_isochrone get_useparameters: no module sps_utils info used by get_isochrone In: :_fsps:fsps.f90:driver:get_isochrone get_useparameters: no module sps_vars info used by get_isochrone In: :_fsps:fsps.f90:driver:get_isochrone getarrlen:variable "nbands" undefined In: :_fsps:fsps.f90:driver:get_isochrone getarrlen:variable "nm" undefined In: :_fsps:fsps.f90:driver:get_isochrone getarrlen:variable "nspec" undefined Block: write_isoc In: :_fsps:fsps.f90:driver:write_isoc get_useparameters: no module sps_utils info used by write_isoc In: :_fsps:fsps.f90:driver:write_isoc get_useparameters: no module sps_vars info used by write_isoc Post-processing (stage 2)... Block: _fsps Block: unknown_interface Block: driver Block: setup Block: set_ssp_params Block: set_csp_params Block: ssps Block: ssp Block: get_ssp_spec Block: interp_ssp Block: smooth_spectrum Block: compute Block: get_spec Block: get_mags Block: get_setup_vars Block: get_nz Block: get_zlegend Block: get_timefull Block: get_ntfull Block: get_nspec Block: get_nbands Block: get_lambda Block: get_isochrone_dimensions Block: get_nmass_isochrone Block: get_stats Block: get_isochrone Block: write_isoc Saving signatures to file "./fsps.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 "_fsps" sources creating /tmp/tmp7aJuAU/src.linux-x86_64-2.7 f2py options: [] f2py: fsps.pyf Reading fortran codes... Reading file 'fsps.pyf' (format:free) Post-processing... Block: _fsps Block: driver In: fsps.pyf:_fsps:unknown_interface:driver get_useparameters: no module sps_utils info used by driver In: fsps.pyf:_fsps:unknown_interface:driver get_useparameters: no module sps_vars info used by driver Block: setup In: fsps.pyf:_fsps:unknown_interface:driver:setup get_useparameters: no module sps_utils info used by setup In: fsps.pyf:_fsps:unknown_interface:driver:setup get_useparameters: no module sps_vars info used by setup Block: set_ssp_params In: fsps.pyf:_fsps:unknown_interface:driver:set_ssp_params get_useparameters: no module sps_utils info used by set_ssp_params In: fsps.pyf:_fsps:unknown_interface:driver:set_ssp_params get_useparameters: no module sps_vars info used by set_ssp_params Block: set_csp_params In: fsps.pyf:_fsps:unknown_interface:driver:set_csp_params get_useparameters: no module sps_utils info used by set_csp_params In: fsps.pyf:_fsps:unknown_interface:driver:set_csp_params get_useparameters: no module sps_vars info used by set_csp_params Block: ssps In: fsps.pyf:_fsps:unknown_interface:driver:ssps get_useparameters: no module sps_utils info used by ssps In: fsps.pyf:_fsps:unknown_interface:driver:ssps get_useparameters: no module sps_vars info used by ssps Block: ssp In: fsps.pyf:_fsps:unknown_interface:driver:ssp get_useparameters: no module sps_utils info used by ssp In: fsps.pyf:_fsps:unknown_interface:driver:ssp get_useparameters: no module sps_vars info used by ssp Block: get_ssp_spec In: fsps.pyf:_fsps:unknown_interface:driver:get_ssp_spec get_useparameters: no module sps_utils info used by get_ssp_spec In: fsps.pyf:_fsps:unknown_interface:driver:get_ssp_spec get_useparameters: no module sps_vars info used by get_ssp_spec Block: interp_ssp In: fsps.pyf:_fsps:unknown_interface:driver:interp_ssp get_useparameters: no module sps_utils info used by interp_ssp In: fsps.pyf:_fsps:unknown_interface:driver:interp_ssp get_useparameters: no module sps_vars info used by interp_ssp Block: smooth_spectrum In: fsps.pyf:_fsps:unknown_interface:driver:smooth_spectrum get_useparameters: no module sps_utils info used by smooth_spectrum In: fsps.pyf:_fsps:unknown_interface:driver:smooth_spectrum get_useparameters: no module sps_vars info used by smooth_spectrum Block: compute In: fsps.pyf:_fsps:unknown_interface:driver:compute get_useparameters: no module sps_utils info used by compute In: fsps.pyf:_fsps:unknown_interface:driver:compute get_useparameters: no module sps_vars info used by compute Block: get_spec In: fsps.pyf:_fsps:unknown_interface:driver:get_spec get_useparameters: no module sps_utils info used by get_spec In: fsps.pyf:_fsps:unknown_interface:driver:get_spec get_useparameters: no module sps_vars info used by get_spec Block: get_mags In: fsps.pyf:_fsps:unknown_interface:driver:get_mags get_useparameters: no module sps_utils info used by get_mags In: fsps.pyf:_fsps:unknown_interface:driver:get_mags get_useparameters: no module sps_vars info used by get_mags Block: get_setup_vars In: fsps.pyf:_fsps:unknown_interface:driver:get_setup_vars get_useparameters: no module sps_utils info used by get_setup_vars In: fsps.pyf:_fsps:unknown_interface:driver:get_setup_vars get_useparameters: no module sps_vars info used by get_setup_vars Block: get_nz In: fsps.pyf:_fsps:unknown_interface:driver:get_nz get_useparameters: no module sps_utils info used by get_nz In: fsps.pyf:_fsps:unknown_interface:driver:get_nz get_useparameters: no module sps_vars info used by get_nz Block: get_zlegend In: fsps.pyf:_fsps:unknown_interface:driver:get_zlegend get_useparameters: no module sps_utils info used by get_zlegend In: fsps.pyf:_fsps:unknown_interface:driver:get_zlegend get_useparameters: no module sps_vars info used by get_zlegend Block: get_timefull In: fsps.pyf:_fsps:unknown_interface:driver:get_timefull get_useparameters: no module sps_utils info used by get_timefull In: fsps.pyf:_fsps:unknown_interface:driver:get_timefull get_useparameters: no module sps_vars info used by get_timefull Block: get_ntfull In: fsps.pyf:_fsps:unknown_interface:driver:get_ntfull get_useparameters: no module sps_utils info used by get_ntfull In: fsps.pyf:_fsps:unknown_interface:driver:get_ntfull get_useparameters: no module sps_vars info used by get_ntfull Block: get_nspec In: fsps.pyf:_fsps:unknown_interface:driver:get_nspec get_useparameters: no module sps_utils info used by get_nspec In: fsps.pyf:_fsps:unknown_interface:driver:get_nspec get_useparameters: no module sps_vars info used by get_nspec Block: get_nbands In: fsps.pyf:_fsps:unknown_interface:driver:get_nbands get_useparameters: no module sps_utils info used by get_nbands In: fsps.pyf:_fsps:unknown_interface:driver:get_nbands get_useparameters: no module sps_vars info used by get_nbands Block: get_lambda In: fsps.pyf:_fsps:unknown_interface:driver:get_lambda get_useparameters: no module sps_utils info used by get_lambda In: fsps.pyf:_fsps:unknown_interface:driver:get_lambda get_useparameters: no module sps_vars info used by get_lambda Block: get_isochrone_dimensions In: fsps.pyf:_fsps:unknown_interface:driver:get_isochrone_dimensions get_useparameters: no module sps_utils info used by get_isochrone_dimensions In: fsps.pyf:_fsps:unknown_interface:driver:get_isochrone_dimensions get_useparameters: no module sps_vars info used by get_isochrone_dimensions Block: get_nmass_isochrone In: fsps.pyf:_fsps:unknown_interface:driver:get_nmass_isochrone get_useparameters: no module sps_utils info used by get_nmass_isochrone In: fsps.pyf:_fsps:unknown_interface:driver:get_nmass_isochrone get_useparameters: no module sps_vars info used by get_nmass_isochrone Block: get_stats In: fsps.pyf:_fsps:unknown_interface:driver:get_stats get_useparameters: no module sps_utils info used by get_stats In: fsps.pyf:_fsps:unknown_interface:driver:get_stats get_useparameters: no module sps_vars info used by get_stats Block: get_isochrone In: fsps.pyf:_fsps:unknown_interface:driver:get_isochrone get_useparameters: no module sps_utils info used by get_isochrone In: fsps.pyf:_fsps:unknown_interface:driver:get_isochrone get_useparameters: no module sps_vars info used by get_isochrone Block: write_isoc In: fsps.pyf:_fsps:unknown_interface:driver:write_isoc get_useparameters: no module sps_utils info used by write_isoc In: fsps.pyf:_fsps:unknown_interface:driver:write_isoc get_useparameters: no module sps_vars info used by write_isoc Post-processing (stage 2)... Block: _fsps Block: unknown_interface Block: driver Block: setup Block: set_ssp_params Block: set_csp_params Block: ssps Block: ssp Block: get_ssp_spec Block: interp_ssp Block: smooth_spectrum Block: compute Block: get_spec Block: get_mags Block: get_setup_vars Block: get_nz Block: get_zlegend Block: get_timefull Block: get_ntfull Block: get_nspec Block: get_nbands Block: get_lambda Block: get_isochrone_dimensions Block: get_nmass_isochrone Block: get_stats Block: get_isochrone Block: write_isoc Building modules... Building module "_fsps"... Constructing F90 module support for "driver"... Variables: is_setup Constructing wrapper function "driver.setup"... setup(compute_vega_mags0,redshift_colors0,smooth_velocity0,add_stellar_remnants0,add_neb_emission0,add_dust_emission0,add_agb_dust_model0,tpagb_norm_type0) Constructing wrapper function "driver.set_ssp_params"... set_ssp_params(imf_type0,imf1,imf2,imf3,vdmc,mdave,dell,delt,sbss,fbhb,pagb,agb_dust,redgb,masscut,fcstar,evtype) Constructing wrapper function "driver.set_csp_params"... set_csp_params(dust_type0,zmet,sfh,wgp1,wgp2,wgp3,tau,const_bn,tage,fburst,tburst,dust1,dust2,logzsol,zred,pmetals,dust_clumps,frac_nodust,dust_index,dust_tesc,frac_obrun,uvb,mwr,dust1_index,sf_start,sf_trunc,sf_theta,duste_gamma,duste_umin,duste_qpah,sigma_smooth,min_wave_smooth,max_wave_smooth) Constructing wrapper function "driver.ssps"... ssps() Constructing wrapper function "driver.ssp"... ssp(zi) Constructing wrapper function "driver.get_ssp_spec"... get_ssp_spec(ssp_spec_out,ssp_mass_out,ssp_lbol_out,[ns,n_age,n_z]) Constructing wrapper function "driver.interp_ssp"... interp_ssp(zpos,tpos,spec,mass,lbol,[ns]) Constructing wrapper function "driver.smooth_spectrum"... smooth_spectrum(wave,spec,sigma_broad,minw,maxw,[ns]) Constructing wrapper function "driver.compute"... compute() Constructing wrapper function "driver.get_spec"... spec_out = get_spec(ns,n_age) Constructing wrapper function "driver.get_mags"... mags = get_mags(n_age,z_red,mc,[n_bands]) Constructing wrapper function "driver.get_setup_vars"... cvms,rcolors,svel,asr,ane,ade,agbd,agbn = get_setup_vars() Constructing wrapper function "driver.get_nz"... n_z = get_nz() Constructing wrapper function "driver.get_zlegend"... z_legend = get_zlegend(n_z) Constructing wrapper function "driver.get_timefull"... timefull = get_timefull(n_age) Constructing wrapper function "driver.get_ntfull"... n_age = get_ntfull() Constructing wrapper function "driver.get_nspec"... ns = get_nspec() Constructing wrapper function "driver.get_nbands"... nb = get_nbands() Constructing wrapper function "driver.get_lambda"... lambda = get_lambda(ns) Constructing wrapper function "driver.get_isochrone_dimensions"... n_age,n_mass = get_isochrone_dimensions() Constructing wrapper function "driver.get_nmass_isochrone"... nmass = get_nmass_isochrone(zz,tt) Constructing wrapper function "driver.get_stats"... age,mass_csp,lbol_csp,sfr,mdust = get_stats(n_age) Constructing wrapper function "driver.get_isochrone"... time_out,z_out,mass_init_out,logl_out,logt_out,logg_out,ffco_out,phase_out,wght_out,mags_out = get_isochrone(zz,tt,n_mass,n_mags) Constructing wrapper function "driver.write_isoc"... write_isoc(outfile) Wrote C/API module "_fsps" to file "/tmp/tmp7aJuAU/src.linux-x86_64-2.7/_fspsmodule.c" Fortran 90 wrappers are saved to "/tmp/tmp7aJuAU/src.linux-x86_64-2.7/_fsps-f2pywrappers2.f90" adding '/tmp/tmp7aJuAU/src.linux-x86_64-2.7/fortranobject.c' to sources. adding '/tmp/tmp7aJuAU/src.linux-x86_64-2.7' to include_dirs. copying /home/data/bdr244/anaconda/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmp7aJuAU/src.linux-x86_64-2.7 copying /home/data/bdr244/anaconda/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmp7aJuAU/src.linux-x86_64-2.7 adding '/tmp/tmp7aJuAU/src.linux-x86_64-2.7/_fsps-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 customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building '_fsps' extension compiling C sources C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating /tmp/tmp7aJuAU/tmp creating /tmp/tmp7aJuAU/tmp/tmp7aJuAU creating /tmp/tmp7aJuAU/tmp/tmp7aJuAU/src.linux-x86_64-2.7 compile options: '-I/home/data/bdr244/Desktop/fsps-read-only/src -I/tmp/tmp7aJuAU/src.linux-x86_64-2.7 -I/home/data/bdr244/anaconda/lib/python2.7/site-packages/numpy/core/include -I/home/data/bdr244/anaconda/include/python2.7 -c' gcc: /tmp/tmp7aJuAU/src.linux-x86_64-2.7/_fspsmodule.c In file included from /home/data/bdr244/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804, from /home/data/bdr244/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /home/data/bdr244/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/tmp7aJuAU/src.linux-x86_64-2.7/fortranobject.h:13, from /tmp/tmp7aJuAU/src.linux-x86_64-2.7/_fspsmodule.c:18: /home/data/bdr244/anaconda/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" /tmp/tmp7aJuAU/src.linux-x86_64-2.7/_fspsmodule.c:144: warning: ‘f2py_size’ defined but not used gcc: /tmp/tmp7aJuAU/src.linux-x86_64-2.7/fortranobject.c In file included from /home/data/bdr244/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804, from /home/data/bdr244/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /home/data/bdr244/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/tmp7aJuAU/src.linux-x86_64-2.7/fortranobject.h:13, from /tmp/tmp7aJuAU/src.linux-x86_64-2.7/fortranobject.c:2: /home/data/bdr244/anaconda/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" 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 -fPIC -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -fPIC -O3 -funroll-loops compile options: '-I/home/data/bdr244/Desktop/fsps-read-only/src -I/tmp/tmp7aJuAU/src.linux-x86_64-2.7 -I/home/data/bdr244/anaconda/lib/python2.7/site-packages/numpy/core/include -I/home/data/bdr244/anaconda/include/python2.7 -c' extra options: '-J/tmp/tmp7aJuAU/ -I/tmp/tmp7aJuAU/' gfortran:f90: fsps.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 -fPIC -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -fPIC -O3 -funroll-loops compile options: '-I/home/data/bdr244/Desktop/fsps-read-only/src -I/tmp/tmp7aJuAU/src.linux-x86_64-2.7 -I/home/data/bdr244/anaconda/lib/python2.7/site-packages/numpy/core/include -I/home/data/bdr244/anaconda/include/python2.7 -c' extra options: '-J/tmp/tmp7aJuAU/ -I/tmp/tmp7aJuAU/' gfortran:f90: /tmp/tmp7aJuAU/src.linux-x86_64-2.7/_fsps-f2pywrappers2.f90 /usr/bin/gfortran -Wall -g -Wall -g -shared /tmp/tmp7aJuAU/tmp/tmp7aJuAU/src.linux-x86_64-2.7/_fspsmodule.o /tmp/tmp7aJuAU/tmp/tmp7aJuAU/src.linux-x86_64-2.7/fortranobject.o /tmp/tmp7aJuAU/fsps.o /tmp/tmp7aJuAU/tmp/tmp7aJuAU/src.linux-x86_64-2.7/_fsps-f2pywrappers2.o /home/data/bdr244/Desktop/fsps-read-only/src/tsum.o /home/data/bdr244/Desktop/fsps-read-only/src/sps_setup.o /home/data/bdr244/Desktop/fsps-read-only/src/vacairconv.o /home/data/bdr244/Desktop/fsps-read-only/src/imf_weight.o /home/data/bdr244/Desktop/fsps-read-only/src/igm_absorb.o /home/data/bdr244/Desktop/fsps-read-only/src/write_isochrone.o /home/data/bdr244/Desktop/fsps-read-only/src/linterparr.o /home/data/bdr244/Desktop/fsps-read-only/src/getmags.o /home/data/bdr244/Desktop/fsps-read-only/src/smoothspec.o /home/data/bdr244/Desktop/fsps-read-only/src/mod_gb.o /home/data/bdr244/Desktop/fsps-read-only/src/sbf.o /home/data/bdr244/Desktop/fsps-read-only/src/sfhstat.o /home/data/bdr244/Desktop/fsps-read-only/src/add_bs.o /home/data/bdr244/Desktop/fsps-read-only/src/ztinterp.o /home/data/bdr244/Desktop/fsps-read-only/src/add_nebular.o /home/data/bdr244/Desktop/fsps-read-only/src/sps_vars.o /home/data/bdr244/Desktop/fsps-read-only/src/pz_convol.o /home/data/bdr244/Desktop/fsps-read-only/src/funcint.o /home/data/bdr244/Desktop/fsps-read-only/src/add_dust.o /home/data/bdr244/Desktop/fsps-read-only/src/get_lumdist.o /home/data/bdr244/Desktop/fsps-read-only/src/add_remnants.o /home/data/bdr244/Desktop/fsps-read-only/src/linterp.o /home/data/bdr244/Desktop/fsps-read-only/src/mod_hb.o /home/data/bdr244/Desktop/fsps-read-only/src/compsp.o /home/data/bdr244/Desktop/fsps-read-only/src/getspec.o /home/data/bdr244/Desktop/fsps-read-only/src/sps_utils.o /home/data/bdr244/Desktop/fsps-read-only/src/getindx.o /home/data/bdr244/Desktop/fsps-read-only/src/imf.o /home/data/bdr244/Desktop/fsps-read-only/src/add_agb_dust.o /home/data/bdr244/Desktop/fsps-read-only/src/ssp_gen.o /home/data/bdr244/Desktop/fsps-read-only/src/locate.o /home/data/bdr244/Desktop/fsps-read-only/src/get_tuniv.o -L/home/data/bdr244/anaconda/lib -lpython2.7 -lgfortran -o ./_fsps.so /usr/bin/ld: /home/data/bdr244/Desktop/fsps-read-only/src/sps_setup.o: relocation R_X86_64_32S against .rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /home/data/bdr244/Desktop/fsps-read-only/src/sps_setup.o: could not read symbols: Bad value collect2: ld returned 1 exit status /usr/bin/ld: /home/data/bdr244/Desktop/fsps-read-only/src/sps_setup.o: relocation R_X86_64_32S against.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC /home/data/bdr244/Desktop/fsps-read-only/src/sps_setup.o: could not read symbols: Bad value collect2: ld returned 1 exit status Running: cd fsps;f2py fsps.f90 -m _fsps -h fsps.pyf --overwrite-signature Running: cd fsps;f2py -c -I/home/data/bdr244/Desktop/fsps-read-only/src /home/data/bdr244/Desktop/fsps-read-only/src/tsum.o /home/data/bdr244/Desktop/fsps-read-only/src/sps_setup.o /home/data/bdr244/Desktop/fsps-read-only/src/vacairconv.o /home/data/bdr244/Desktop/fsps-read-only/src/imf_weight.o /home/data/bdr244/Desktop/fsps-read-only/src/igm_absorb.o /home/data/bdr244/Desktop/fsps-read-only/src/write_isochrone.o /home/data/bdr244/Desktop/fsps-read-only/src/linterparr.o /home/data/bdr244/Desktop/fsps-read-only/src/getmags.o /home/data/bdr244/Desktop/fsps-read-only/src/smoothspec.o /home/data/bdr244/Desktop/fsps-read-only/src/mod_gb.o /home/data/bdr244/Desktop/fsps-read-only/src/sbf.o /home/data/bdr244/Desktop/fsps-read-only/src/sfhstat.o /home/data/bdr244/Desktop/fsps-read-only/src/add_bs.o /home/data/bdr244/Desktop/fsps-read-only/src/ztinterp.o /home/data/bdr244/Desktop/fsps-read-only/src/add_nebular.o /home/data/bdr244/Desktop/fsps-read-only/src/sps_vars.o /home/data/bdr244/Desktop/fsps-read-only/src/pz_convol.o /home/data/bdr244/Desktop/fsps-read-only/src/funcint.o /home/data/bdr244/Desktop/fsps-read-only/src/add_dust.o /home/data/bdr244/Desktop/fsps-read-only/src/get_lumdist.o /home/data/bdr244/Desktop/fsps-read-only/src/add_remnants.o /home/data/bdr244/Desktop/fsps-read-only/src/linterp.o /home/data/bdr244/Desktop/fsps-read-only/src/mod_hb.o /home/data/bdr244/Desktop/fsps-read-only/src/compsp.o /home/data/bdr244/Desktop/fsps-read-only/src/getspec.o /home/data/bdr244/Desktop/fsps-read-only/src/sps_utils.o /home/data/bdr244/Desktop/fsps-read-only/src/getindx.o /home/data/bdr244/Desktop/fsps-read-only/src/imf.o /home/data/bdr244/Desktop/fsps-read-only/src/add_agb_dust.o /home/data/bdr244/Desktop/fsps-read-only/src/ssp_gen.o /home/data/bdr244/Desktop/fsps-read-only/src/locate.o /home/data/bdr244/Desktop/fsps-read-only/src/get_tuniv.o fsps.f90 fsps.pyf --f90flags=-cpp --f90flags=-fPIC Moving /home/data/bdr244/python-fsps/fsps/_fsps.so to /home/data/bdr244/python-fsps/build/lib.linux-x86_64-2.7/fsps/_fsps.so

bd-j commented 9 years ago

there is a line can not be used when making a shared object; recompile with -fPIC in your log You can try recompiling FSPS with the -fPIC compiler flag, hopefully that will solve the problem. Do this by changing the FSPS Makefile in fsps/src/ to add the compiler flag, then typing make clean and then make all.

Let us know if that works!

bdr244 commented 9 years ago

That nailed it - I just had to add that flag to the FSPS compilation. Thank you!