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zerothi / sisl

Electronic structure Python package for post analysis and large scale tight-binding DFT/NEGF calculations
https://zerothi.github.io/sisl
Mozilla Public License 2.0
181 stars 58 forks source link

Error building sisl #124

Closed brandimarte closed 5 years ago

brandimarte commented 5 years ago

Hi!

I'm facing the following error when building sisl, git version. I'm reporting as an issue because anaconda is a probable culprit here, but since many people uses this environment manager I though it was maybe worth to report. It's been actually a few months since this error starting to show up, so now I did a clean installation of the python environment in order to avoid having libraries inconsistencies, but the error persists.

Thanks!

Pedro

Here you are relevant info (please, let me know if you need something else):

gcc: 6.3.0 and 8.3.0 (same error with both) python: 3.7.3 (anaconda)

Output of the build:

$ rm - build
$ python setup.py build
sisl-install: using git revision
system_info:
  NOT AVAILABLE

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 py_modules sources
creating build
creating build/src.linux-x86_64-3.7
creating build/src.linux-x86_64-3.7/sisl
creating build/src.linux-x86_64-3.7/sisl/geom
creating build/src.linux-x86_64-3.7/sisl/io
creating build/src.linux-x86_64-3.7/sisl/io/bigdft
creating build/src.linux-x86_64-3.7/sisl/io/gulp
creating build/src.linux-x86_64-3.7/sisl/io/openmx
creating build/src.linux-x86_64-3.7/sisl/io/scaleup
creating build/src.linux-x86_64-3.7/sisl/io/siesta
creating build/src.linux-x86_64-3.7/sisl/io/tbtrans
creating build/src.linux-x86_64-3.7/sisl/io/vasp
creating build/src.linux-x86_64-3.7/sisl/io/wannier90
creating build/src.linux-x86_64-3.7/sisl/physics
creating build/src.linux-x86_64-3.7/sisl/linalg
creating build/src.linux-x86_64-3.7/sisl/shape
creating build/src.linux-x86_64-3.7/sisl/unit
creating build/src.linux-x86_64-3.7/sisl/utils
building extension "sisl._math_small" sources
building extension "sisl._indices" sources
building extension "sisl._supercell" sources
building extension "sisl._sparse" sources
building extension "sisl.io.siesta._siesta" sources
f2py options: []
f2py:> build/src.linux-x86_64-3.7/sisl/io/siesta/_siestamodule.c
Reading fortran codes...
    Reading file 'sisl/io/siesta/_src/io_m.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/siesta_sc_off.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/hsx_read.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/hsx_write.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/dm_read.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/dm_write.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/tshs_read.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/tshs_write.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/grid_read.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/grid_write.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/gf_read.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/gf_write.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/hs_read.f90' (format:free)
    Reading file 'sisl/io/siesta/_src/tsde_read.f90' (format:free)
Post-processing...
    Block: _siesta
            Block: io_m
                Block: open_file
                Block: iostat_reset
                Block: iostat_update
                Block: iostat_query
            Block: siesta_sc_off
            Block: read_hsx_sizes
            Block: read_hsx_hsx
            Block: read_hsx_s
            Block: write_hsx
            Block: read_dm_sizes
            Block: read_dm
            Block: write_dm
            Block: read_tshs_version
            Block: read_tshs_sizes
            Block: read_tshs_cell
            Block: read_tshs_geom
            Block: read_tshs_hs
            Block: read_tshs_s
            Block: write_tshs_hs
            Block: read_grid_sizes
            Block: read_grid_cell
            Block: read_grid
            Block: write_grid
            Block: read_open_gf
            Block: read_gf_sizes
            Block: read_gf_header
            Block: read_gf_hs
            Block: read_gf_se
            Block: write_open_gf
            Block: write_gf_header
            Block: write_gf_hs
            Block: write_gf_se
            Block: close_gf
            Block: read_hs_header
            Block: read_hs
            Block: read_tsde_sizes
            Block: read_tsde_dm
            Block: read_tsde_edm
Post-processing (stage 2)...
    Block: _siesta
        Block: unknown_interface
            Block: io_m
                Block: open_file
                Block: iostat_reset
                Block: iostat_update
                Block: iostat_query
            Block: siesta_sc_off
            Block: read_hsx_sizes
            Block: read_hsx_hsx
            Block: read_hsx_s
            Block: write_hsx
            Block: read_dm_sizes
            Block: read_dm
            Block: write_dm
            Block: read_tshs_version
            Block: read_tshs_sizes
            Block: read_tshs_cell
            Block: read_tshs_geom
            Block: read_tshs_hs
            Block: read_tshs_s
            Block: write_tshs_hs
            Block: read_grid_sizes
            Block: read_grid_cell
            Block: read_grid
            Block: write_grid
            Block: read_open_gf
            Block: read_gf_sizes
            Block: read_gf_header
            Block: read_gf_hs
            Block: read_gf_se
            Block: write_open_gf
            Block: write_gf_header
            Block: write_gf_hs
            Block: write_gf_se
            Block: close_gf
            Block: read_hs_header
            Block: read_hs
            Block: read_tsde_sizes
            Block: read_tsde_dm
            Block: read_tsde_edm
Building modules...
    Building module "_siesta"...
        Constructing wrapper function "siesta_sc_off"...
          isc = siesta_sc_off(nsa,nsb,nsc)
        Constructing wrapper function "read_hsx_sizes"...
          gamma,nspin,no_u,no_s,maxnh = read_hsx_sizes(fname)
        Constructing wrapper function "read_hsx_hsx"...
          numh,listh,h,s,xij = read_hsx_hsx(fname,gamma,nspin,no_u,no_s,maxnh)
        Constructing wrapper function "read_hsx_s"...
          numh,listh,s = read_hsx_s(fname,gamma,nspin,no_u,no_s,maxnh)
        Constructing wrapper function "write_hsx"...
          write_hsx(fname,gamma,no_s,numh,listhptr,listh,h,s,xij,qtot,temp,[no_u,nspin,maxnh])
        Constructing wrapper function "read_dm_sizes"...
          nspin,no_u,nsc,nnz = read_dm_sizes(fname)
        Constructing wrapper function "read_dm"...
          ncol,list_col,dm = read_dm(fname,nspin,no_u,nsc,nnz)
        Constructing wrapper function "write_dm"...
          write_dm(fname,nsc,ncol,list_col,dm,[nspin,no_u,nnz])
        Constructing wrapper function "read_tshs_version"...
          version = read_tshs_version(fname)
        Constructing wrapper function "read_tshs_sizes"...
          nspin,na_u,no_u,n_s,nnz = read_tshs_sizes(fname)
        Constructing wrapper function "read_tshs_cell"...
          nsc,cell,isc = read_tshs_cell(fname,n_s)
        Constructing wrapper function "read_tshs_geom"...
          xa,lasto = read_tshs_geom(fname,na_u)
        Constructing wrapper function "read_tshs_hs"...
          ncol,list_col,h,s = read_tshs_hs(fname,nspin,no_u,nnz)
        Constructing wrapper function "read_tshs_s"...
          ncol,list_col,s = read_tshs_s(fname,no_u,nnz)
        Constructing wrapper function "write_tshs_hs"...
          write_tshs_hs(fname,nsc1,nsc2,nsc3,cell,xa,lasto,ncol,list_col,h,s,isc,[nspin,na_u,no_u,nnz])
        Constructing wrapper function "read_grid_sizes"...
          nspin,mesh = read_grid_sizes(fname)
        Constructing wrapper function "read_grid_cell"...
          cell = read_grid_cell(fname)
        Constructing wrapper function "read_grid"...
          grid = read_grid(fname,nspin,mesh1,mesh2,mesh3)
        Constructing wrapper function "write_grid"...
          write_grid(fname,nspin,cell,grid,[mesh1,mesh2,mesh3])
        Constructing wrapper function "read_open_gf"...
          iu = read_open_gf(fname)
        Constructing wrapper function "read_gf_sizes"...
          nspin,no_u,nkpt,ne = read_gf_sizes(iu)
        Constructing wrapper function "read_gf_header"...
          kpt,e = read_gf_header(iu,nkpt,ne)
        Constructing wrapper function "read_gf_hs"...
          h,s = read_gf_hs(iu,no_u)
        Constructing wrapper function "read_gf_se"...
          se = read_gf_se(iu,no_u,ie)
        Constructing wrapper function "write_open_gf"...
          iu = write_open_gf(fname)
        Constructing wrapper function "write_gf_header"...
          write_gf_header(iu,nspin,cell,na_u,no_u,no_used,xa_used,lasto_used,bloch,pre_expand,mu,kpt,kw,e,[na_used,nkpt,ne])
        Constructing wrapper function "write_gf_hs"...
          write_gf_hs(iu,ik,ie,e,h,s,[no_u])
        Constructing wrapper function "write_gf_se"...
          write_gf_se(iu,ik,ie,e,se,[no_u])
        Constructing wrapper function "close_gf"...
          close_gf(iu)
        Constructing wrapper function "read_hs_header"...
          gamma,nspin,no_u,no_s,maxnh = read_hs_header(fname)
        Constructing wrapper function "read_hs"...
          numh,listhptr,listh,h,s,xij = read_hs(fname,gamma,nspin,no_u,no_s,maxnh)
        Constructing wrapper function "read_tsde_sizes"...
          nspin,no_u,nsc,nnz = read_tsde_sizes(fname)
        Constructing wrapper function "read_tsde_dm"...
          ncol,list_col,dm = read_tsde_dm(fname,nspin,no_u,nsc,nnz)
        Constructing wrapper function "read_tsde_edm"...
          ncol,list_col,edm = read_tsde_edm(fname,nspin,no_u,nsc,nnz)
        Constructing F90 module support for "io_m"...
            Constructing wrapper function "io_m.open_file"...
              unit = open_file(file,action,status,form)
            Constructing wrapper function "io_m.iostat_reset"...
              iostat_reset()
            Constructing wrapper function "io_m.iostat_update"...
              iostat = iostat_update(iostat)
            Constructing wrapper function "io_m.iostat_query"...
              iostat = iostat_query()
    Wrote C/API module "_siesta" to file "build/src.linux-x86_64-3.7/sisl/io/siesta/_siestamodule.c"
    Fortran 90 wrappers are saved to "build/src.linux-x86_64-3.7/sisl/io/siesta/_siesta-f2pywrappers2.f90"
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/sisl/io/siesta/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/sisl/io/siesta' to include_dirs.
creating build/src.linux-x86_64-3.7/build
creating build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7
creating build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/sisl
creating build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/sisl/io
creating build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/sisl/io/siesta
copying /home/pedro/local/opt/python/anaconda3/lib/python3.7/site-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/sisl/io/siesta
copying /home/pedro/local/opt/python/anaconda3/lib/python3.7/site-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-x86_64-3.7/build/src.linux-x86_64-3.7/sisl/io/siesta
  adding 'build/src.linux-x86_64-3.7/sisl/io/siesta/_siesta-f2pywrappers2.f90' to sources.
building extension "sisl.physics._bloch" sources
building extension "sisl.physics._phase" sources
building extension "sisl.physics._matrix_phase" sources
building extension "sisl.physics._matrix_phase_nc" sources
building extension "sisl.physics._matrix_phase_so" sources
building extension "sisl.physics._matrix_phase_nc_diag" sources
building extension "sisl.physics._matrix_k" sources
building extension "sisl.physics._matrix_phase3" sources
building extension "sisl.physics._matrix_dk" sources
building extension "sisl.physics._matrix_ddk" sources
building data_files sources
build_src: building npy-pkg config files
running build_py
creating build/lib.linux-x86_64-3.7
creating build/lib.linux-x86_64-3.7/sisl
copying sisl/info.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/__init__.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/grid.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/supercell.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/constant.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/orbital.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/geometry.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/oplist.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/_plot.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/_help.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/atom.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/conftest.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/_namedindex.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/_array.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/quaternion.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/sparse.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/messages.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/selector.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/setup.py -> build/lib.linux-x86_64-3.7/sisl
copying sisl/sparse_geometry.py -> build/lib.linux-x86_64-3.7/sisl
copying build/src.linux-x86_64-3.7/sisl/__config__.py -> build/lib.linux-x86_64-3.7/sisl
creating build/lib.linux-x86_64-3.7/sisl/utils
copying sisl/utils/mathematics.py -> build/lib.linux-x86_64-3.7/sisl/utils
copying sisl/utils/__init__.py -> build/lib.linux-x86_64-3.7/sisl/utils
copying sisl/utils/sdata.py -> build/lib.linux-x86_64-3.7/sisl/utils
copying sisl/utils/ranges.py -> build/lib.linux-x86_64-3.7/sisl/utils
copying sisl/utils/cmd.py -> build/lib.linux-x86_64-3.7/sisl/utils
copying sisl/utils/misc.py -> build/lib.linux-x86_64-3.7/sisl/utils
copying sisl/utils/setup.py -> build/lib.linux-x86_64-3.7/sisl/utils
copying build/src.linux-x86_64-3.7/sisl/utils/__config__.py -> build/lib.linux-x86_64-3.7/sisl/utils
creating build/lib.linux-x86_64-3.7/sisl/utils/tests
copying sisl/utils/tests/__init__.py -> build/lib.linux-x86_64-3.7/sisl/utils/tests
copying sisl/utils/tests/test_ranges.py -> build/lib.linux-x86_64-3.7/sisl/utils/tests
copying sisl/utils/tests/test_cmd.py -> build/lib.linux-x86_64-3.7/sisl/utils/tests
copying sisl/utils/tests/test_mathematics.py -> build/lib.linux-x86_64-3.7/sisl/utils/tests
copying sisl/utils/tests/test_misc.py -> build/lib.linux-x86_64-3.7/sisl/utils/tests
creating build/lib.linux-x86_64-3.7/sisl/linalg
copying sisl/linalg/__init__.py -> build/lib.linux-x86_64-3.7/sisl/linalg
copying sisl/linalg/base.py -> build/lib.linux-x86_64-3.7/sisl/linalg
copying sisl/linalg/setup.py -> build/lib.linux-x86_64-3.7/sisl/linalg
copying build/src.linux-x86_64-3.7/sisl/linalg/__config__.py -> build/lib.linux-x86_64-3.7/sisl/linalg
creating build/lib.linux-x86_64-3.7/sisl/linalg/tests
copying sisl/linalg/tests/__init__.py -> build/lib.linux-x86_64-3.7/sisl/linalg/tests
copying sisl/linalg/tests/test_eig.py -> build/lib.linux-x86_64-3.7/sisl/linalg/tests
copying sisl/linalg/tests/test_solve.py -> build/lib.linux-x86_64-3.7/sisl/linalg/tests
copying sisl/linalg/tests/test_inv.py -> build/lib.linux-x86_64-3.7/sisl/linalg/tests
creating build/lib.linux-x86_64-3.7/sisl/unit
copying sisl/unit/__init__.py -> build/lib.linux-x86_64-3.7/sisl/unit
copying sisl/unit/siesta.py -> build/lib.linux-x86_64-3.7/sisl/unit
copying sisl/unit/base.py -> build/lib.linux-x86_64-3.7/sisl/unit
copying sisl/unit/setup.py -> build/lib.linux-x86_64-3.7/sisl/unit
copying build/src.linux-x86_64-3.7/sisl/unit/__config__.py -> build/lib.linux-x86_64-3.7/sisl/unit
creating build/lib.linux-x86_64-3.7/sisl/unit/tests
copying sisl/unit/tests/__init__.py -> build/lib.linux-x86_64-3.7/sisl/unit/tests
copying sisl/unit/tests/test_unit.py -> build/lib.linux-x86_64-3.7/sisl/unit/tests
copying sisl/unit/tests/test_unit_siesta.py -> build/lib.linux-x86_64-3.7/sisl/unit/tests
creating build/lib.linux-x86_64-3.7/sisl/geom
copying sisl/geom/__init__.py -> build/lib.linux-x86_64-3.7/sisl/geom
copying sisl/geom/basic.py -> build/lib.linux-x86_64-3.7/sisl/geom
copying sisl/geom/nanotube.py -> build/lib.linux-x86_64-3.7/sisl/geom
copying sisl/geom/flat.py -> build/lib.linux-x86_64-3.7/sisl/geom
copying sisl/geom/special.py -> build/lib.linux-x86_64-3.7/sisl/geom
copying sisl/geom/setup.py -> build/lib.linux-x86_64-3.7/sisl/geom
copying build/src.linux-x86_64-3.7/sisl/geom/__config__.py -> build/lib.linux-x86_64-3.7/sisl/geom
creating build/lib.linux-x86_64-3.7/sisl/geom/tests
copying sisl/geom/tests/__init__.py -> build/lib.linux-x86_64-3.7/sisl/geom/tests
copying sisl/geom/tests/test_geom.py -> build/lib.linux-x86_64-3.7/sisl/geom/tests
creating build/lib.linux-x86_64-3.7/sisl/shape
copying sisl/shape/__init__.py -> build/lib.linux-x86_64-3.7/sisl/shape
copying sisl/shape/prism4.py -> build/lib.linux-x86_64-3.7/sisl/shape
copying sisl/shape/ellipsoid.py -> build/lib.linux-x86_64-3.7/sisl/shape
copying sisl/shape/base.py -> build/lib.linux-x86_64-3.7/sisl/shape
copying sisl/shape/setup.py -> build/lib.linux-x86_64-3.7/sisl/shape
copying build/src.linux-x86_64-3.7/sisl/shape/__config__.py -> build/lib.linux-x86_64-3.7/sisl/shape
creating build/lib.linux-x86_64-3.7/sisl/shape/tests
copying sisl/shape/tests/test_ellipsoid.py -> build/lib.linux-x86_64-3.7/sisl/shape/tests
copying sisl/shape/tests/__init__.py -> build/lib.linux-x86_64-3.7/sisl/shape/tests
copying sisl/shape/tests/test_shape.py -> build/lib.linux-x86_64-3.7/sisl/shape/tests
copying sisl/shape/tests/test_prism4.py -> build/lib.linux-x86_64-3.7/sisl/shape/tests
creating build/lib.linux-x86_64-3.7/sisl/io
copying sisl/io/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io
copying sisl/io/ham.py -> build/lib.linux-x86_64-3.7/sisl/io
copying sisl/io/molden.py -> build/lib.linux-x86_64-3.7/sisl/io
copying sisl/io/table.py -> build/lib.linux-x86_64-3.7/sisl/io
copying sisl/io/_help.py -> build/lib.linux-x86_64-3.7/sisl/io
copying sisl/io/xsf.py -> build/lib.linux-x86_64-3.7/sisl/io
copying sisl/io/sile.py -> build/lib.linux-x86_64-3.7/sisl/io
copying sisl/io/cube.py -> build/lib.linux-x86_64-3.7/sisl/io
copying sisl/io/xyz.py -> build/lib.linux-x86_64-3.7/sisl/io
copying sisl/io/pdb.py -> build/lib.linux-x86_64-3.7/sisl/io
copying sisl/io/setup.py -> build/lib.linux-x86_64-3.7/sisl/io
copying build/src.linux-x86_64-3.7/sisl/io/__config__.py -> build/lib.linux-x86_64-3.7/sisl/io
creating build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying sisl/io/tbtrans/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying sisl/io/tbtrans/phtproj.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying sisl/io/tbtrans/pht.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying sisl/io/tbtrans/tbt.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying sisl/io/tbtrans/_cdf.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying sisl/io/tbtrans/se.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying sisl/io/tbtrans/tbtproj.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying sisl/io/tbtrans/delta.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying sisl/io/tbtrans/sile.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying sisl/io/tbtrans/binaries.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying sisl/io/tbtrans/setup.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
copying build/src.linux-x86_64-3.7/sisl/io/tbtrans/__config__.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans
creating build/lib.linux-x86_64-3.7/sisl/io/tbtrans/tests
copying sisl/io/tbtrans/tests/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans/tests
copying sisl/io/tbtrans/tests/test_tbtproj.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans/tests
copying sisl/io/tbtrans/tests/test_tbt.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans/tests
copying sisl/io/tbtrans/tests/test_delta.py -> build/lib.linux-x86_64-3.7/sisl/io/tbtrans/tests
creating build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/fa.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/basis.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/transiesta_grid.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/kp.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/siesta_grid.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/pdos.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/fdf.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/_help.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/orb_indx.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/sile.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/xv.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/fc.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/siesta_nc.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/out.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/bands.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/binaries.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/eig.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying sisl/io/siesta/setup.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
copying build/src.linux-x86_64-3.7/sisl/io/siesta/__config__.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta
creating build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_orb_indx.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_fdf.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_grid.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_fa.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_tsde.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_fc.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_basis.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_eig.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_gf.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_hsx.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_pdos.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_siesta.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_kp.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_bands.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_xv.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_tshs.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
copying sisl/io/siesta/tests/test_dm.py -> build/lib.linux-x86_64-3.7/sisl/io/siesta/tests
creating build/lib.linux-x86_64-3.7/sisl/io/wannier90
copying sisl/io/wannier90/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/wannier90
copying sisl/io/wannier90/sile.py -> build/lib.linux-x86_64-3.7/sisl/io/wannier90
copying sisl/io/wannier90/seedname.py -> build/lib.linux-x86_64-3.7/sisl/io/wannier90
copying sisl/io/wannier90/setup.py -> build/lib.linux-x86_64-3.7/sisl/io/wannier90
copying build/src.linux-x86_64-3.7/sisl/io/wannier90/__config__.py -> build/lib.linux-x86_64-3.7/sisl/io/wannier90
creating build/lib.linux-x86_64-3.7/sisl/io/vasp
copying sisl/io/vasp/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp
copying sisl/io/vasp/eigenval.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp
copying sisl/io/vasp/car.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp
copying sisl/io/vasp/sile.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp
copying sisl/io/vasp/locpot.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp
copying sisl/io/vasp/doscar.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp
copying sisl/io/vasp/chg.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp
copying sisl/io/vasp/setup.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp
copying build/src.linux-x86_64-3.7/sisl/io/vasp/__config__.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp
creating build/lib.linux-x86_64-3.7/sisl/io/vasp/tests
copying sisl/io/vasp/tests/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp/tests
copying sisl/io/vasp/tests/test_car.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp/tests
copying sisl/io/vasp/tests/test_eigenval.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp/tests
copying sisl/io/vasp/tests/test_locpot.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp/tests
copying sisl/io/vasp/tests/test_chg.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp/tests
copying sisl/io/vasp/tests/test_doscar.py -> build/lib.linux-x86_64-3.7/sisl/io/vasp/tests
creating build/lib.linux-x86_64-3.7/sisl/io/bigdft
copying sisl/io/bigdft/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/bigdft
copying sisl/io/bigdft/ascii.py -> build/lib.linux-x86_64-3.7/sisl/io/bigdft
copying sisl/io/bigdft/sile.py -> build/lib.linux-x86_64-3.7/sisl/io/bigdft
copying sisl/io/bigdft/setup.py -> build/lib.linux-x86_64-3.7/sisl/io/bigdft
copying build/src.linux-x86_64-3.7/sisl/io/bigdft/__config__.py -> build/lib.linux-x86_64-3.7/sisl/io/bigdft
creating build/lib.linux-x86_64-3.7/sisl/io/openmx
copying sisl/io/openmx/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/openmx
copying sisl/io/openmx/omx.py -> build/lib.linux-x86_64-3.7/sisl/io/openmx
copying sisl/io/openmx/sile.py -> build/lib.linux-x86_64-3.7/sisl/io/openmx
copying sisl/io/openmx/setup.py -> build/lib.linux-x86_64-3.7/sisl/io/openmx
copying build/src.linux-x86_64-3.7/sisl/io/openmx/__config__.py -> build/lib.linux-x86_64-3.7/sisl/io/openmx
creating build/lib.linux-x86_64-3.7/sisl/io/gulp
copying sisl/io/gulp/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/gulp
copying sisl/io/gulp/got.py -> build/lib.linux-x86_64-3.7/sisl/io/gulp
copying sisl/io/gulp/sile.py -> build/lib.linux-x86_64-3.7/sisl/io/gulp
copying sisl/io/gulp/fc.py -> build/lib.linux-x86_64-3.7/sisl/io/gulp
copying sisl/io/gulp/setup.py -> build/lib.linux-x86_64-3.7/sisl/io/gulp
copying build/src.linux-x86_64-3.7/sisl/io/gulp/__config__.py -> build/lib.linux-x86_64-3.7/sisl/io/gulp
creating build/lib.linux-x86_64-3.7/sisl/io/gulp/tests
copying sisl/io/gulp/tests/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/gulp/tests
copying sisl/io/gulp/tests/test_gout.py -> build/lib.linux-x86_64-3.7/sisl/io/gulp/tests
creating build/lib.linux-x86_64-3.7/sisl/io/scaleup
copying sisl/io/scaleup/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/scaleup
copying sisl/io/scaleup/sile.py -> build/lib.linux-x86_64-3.7/sisl/io/scaleup
copying sisl/io/scaleup/orbocc.py -> build/lib.linux-x86_64-3.7/sisl/io/scaleup
copying sisl/io/scaleup/ref.py -> build/lib.linux-x86_64-3.7/sisl/io/scaleup
copying sisl/io/scaleup/rham.py -> build/lib.linux-x86_64-3.7/sisl/io/scaleup
copying sisl/io/scaleup/setup.py -> build/lib.linux-x86_64-3.7/sisl/io/scaleup
copying build/src.linux-x86_64-3.7/sisl/io/scaleup/__config__.py -> build/lib.linux-x86_64-3.7/sisl/io/scaleup
creating build/lib.linux-x86_64-3.7/sisl/io/tests
copying sisl/io/tests/test_table.py -> build/lib.linux-x86_64-3.7/sisl/io/tests
copying sisl/io/tests/__init__.py -> build/lib.linux-x86_64-3.7/sisl/io/tests
copying sisl/io/tests/test_xyz.py -> build/lib.linux-x86_64-3.7/sisl/io/tests
copying sisl/io/tests/test_cube.py -> build/lib.linux-x86_64-3.7/sisl/io/tests
copying sisl/io/tests/test_xsf.py -> build/lib.linux-x86_64-3.7/sisl/io/tests
copying sisl/io/tests/test_object.py -> build/lib.linux-x86_64-3.7/sisl/io/tests
copying sisl/io/tests/test_tb.py -> build/lib.linux-x86_64-3.7/sisl/io/tests
creating build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/state.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/phonon.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/__init__.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/energydensitymatrix.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/densitymatrix.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/distribution.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/brillouinzone.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/self_energy.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/spin.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/electron.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/hamiltonian.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/bloch.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/sparse.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/dynamicalmatrix.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying sisl/physics/setup.py -> build/lib.linux-x86_64-3.7/sisl/physics
copying build/src.linux-x86_64-3.7/sisl/physics/__config__.py -> build/lib.linux-x86_64-3.7/sisl/physics
creating build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/__init__.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/test_hamiltonian.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/test_bloch.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/test_dynamical_matrix.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/test_self_energy.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/test_state.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/test_density_matrix.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/test_distribution.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/test_spin.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/test_brillouinzone.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/test_energy_density_matrix.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
copying sisl/physics/tests/test_physics_sparse.py -> build/lib.linux-x86_64-3.7/sisl/physics/tests
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
customize Gnu95FCompiler
Found executable /home/pedro/local/opt/gcc/8.3.0/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'sisl._math_small' extension
compiling C sources
C compiler: gcc -pthread -B /home/pedro/local/opt/python/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC

creating build/temp.linux-x86_64-3.7/sisl
compile options: '-I/home/pedro/local/opt/python/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/home/pedro/local/opt/python/anaconda3/include/python3.7m -c'
gcc: sisl/_math_small.c
In file included from /home/pedro/local/opt/python/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824,
                 from /home/pedro/local/opt/python/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /home/pedro/local/opt/python/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sisl/_math_small.c:607:
/home/pedro/local/opt/python/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
gcc -pthread -shared -B /home/pedro/local/opt/python/anaconda3/compiler_compat -L/home/pedro/local/opt/python/anaconda3/lib -Wl,-rpath=/home/pedro/local/opt/python/anaconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/sisl/_math_small.o -o build/lib.linux-x86_64-3.7/sisl/_math_small.cpython-37m-x86_64-linux-gnu.so
/home/pedro/local/opt/python/anaconda3/compiler_compat/ld: build/temp.linux-x86_64-3.7/sisl/_math_small.o: unable to initialize decompress status for section .debug_info
/home/pedro/local/opt/python/anaconda3/compiler_compat/ld: build/temp.linux-x86_64-3.7/sisl/_math_small.o: unable to initialize decompress status for section .debug_info
/home/pedro/local/opt/python/anaconda3/compiler_compat/ld: build/temp.linux-x86_64-3.7/sisl/_math_small.o: unable to initialize decompress status for section .debug_info
/home/pedro/local/opt/python/anaconda3/compiler_compat/ld: build/temp.linux-x86_64-3.7/sisl/_math_small.o: unable to initialize decompress status for section .debug_info
build/temp.linux-x86_64-3.7/sisl/_math_small.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status
error: Command "gcc -pthread -shared -B /home/pedro/local/opt/python/anaconda3/compiler_compat -L/home/pedro/local/opt/python/anaconda3/lib -Wl,-rpath=/home/pedro/local/opt/python/anaconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/sisl/_math_small.o -o build/lib.linux-x86_64-3.7/sisl/_math_small.cpython-37m-x86_64-linux-gnu.so" failed with exit status 1
zerothi commented 5 years ago

I also have problems building sisl for newer numpy versions. This is apparently known in the community (which was why I made a comment here: https://github.com/conda-forge/sisl-feedstock/blob/061ea1e85f2200ff608ff21234883693e79caf0e/recipe/meta.yaml#L32)

If you do:

conda remove numpy scipy
conda install -c conda-forge numpy=1.15.3 scipy

and then run python setup.py build it should work (just tested).

Let me know if it works!

zerothi commented 5 years ago

Note, that this only affects conda installations. It should have been fixed in the latest numpy release, but apparently I still see the error...

I have to play a bit more with it. :)

For now, downgrading numpy seems to fix the issue.

brandimarte commented 5 years ago

Thanks!

I did what you proposed but still I got the same error. I also tried rebasing with conda-forge with:

conda config --add channels conda-forge
conda config --set channel_priority strict

And then installing scipy and numpy=1.15.3, but the error persisted... Then I removed again completely the anaconda installation, installed minconda, and the following steps:

conda install -c conda-forge scipy
conda install six netcdf4 setuptools pyparsing pytest matplotlib tqdm xarray
conda install -c conda-forge numpy=1.15.3

Again the same error as the message above.

zerothi commented 5 years ago

I basically did this:

<download and install Miniconda3.sh>
conda install -c conda-forge fortran-compiler
conda install -c conda-forge numpy=1.15.3 scipy matplotlib netcdf4

then it should work (xarray is not really needed).

When you install these packages from different channels they may also do problematic things. Especially since xarray and netcdf4 depends on numpy, so probably already before you installed numpy=1.15.3 it didn't work?

As

brandimarte commented 5 years ago

Thanks!

Installing fortran-compiler from conda-forge fixed the problem, with no need to downgrade numpy (1.16.3 here). I got a few warnings like:

gcc: sisl/physics/_matrix_ddk.c
In file included from /home/pedro/local/opt/python/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                 from /home/pedro/local/opt/python/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /home/pedro/local/opt/python/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from sisl/physics/_matrix_ddk.c:607:
/home/pedro/local/opt/python/miniconda3/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~

but I guess this will not affect the program, right?

zerothi commented 5 years ago

Ok, great! No these are warnings implicitly raised by numpy (i.e. they have nothing to do with sisl). :)