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justin_brody
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Joined: 26 Jan 2005
Posts: 283
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 Posted: Sun Jun 24, 2018 8:52 am Post subject: numpy seems to want versions 3 and 4 of fortran |
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Hello,
I am unable to import numpy because it cannot find fortran 3:
| Code: |
$ python -c "import numpy as np" Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/lib64/python3.5/site-packages/numpy/__init__.py", line 142, in <module>
from . import add_newdocs
File "/usr/lib64/python3.5/site-packages/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "/usr/lib64/python3.5/site-packages/numpy/lib/__init__.py", line 19, in <module>
from .polynomial import *
File "/usr/lib64/python3.5/site-packages/numpy/lib/polynomial.py", line 20, in <module>
from numpy.linalg import eigvals, lstsq, inv
File "/usr/lib64/python3.5/site-packages/numpy/linalg/__init__.py", line 51, in <module>
from .linalg import *
File "/usr/lib64/python3.5/site-packages/numpy/linalg/linalg.py", line 30, in <module>
from numpy.linalg import lapack_lite, _umath_linalg
ImportError: libgfortran.so.3: cannot open shared object file: No such file or directory
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I do have libgfortran.so.4 installed on my system and numpy seems to find it:
| Code: |
$ ldd /usr/lib64/python2.7/site-packages/numpy/linalg/lapack_lite.so
linux-vdso.so.1 (0x00007ffc07cf7000)
liblapack.so.0 => /usr/lib64/liblapack.so.0 (0x00007fdf59e17000)
libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 (0x00007fdf59a36000)
libc.so.6 => /lib64/libc.so.6 (0x00007fdf59674000)
libblas.so.0 => /opt/openblas/lib/libblas.so.0 (0x00007fdf586cc000)
libgfortran.so.4 => /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgfortran.so.4 (0x00007fdf582f1000)
libm.so.6 => /lib64/libm.so.6 (0x00007fdf57f9f000)
libgcc_s.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgcc_s.so.1 (0x00007fdf57d88000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fdf57b68000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fdf57964000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007fdf57761000)
/lib64/ld-linux-x86-64.so.2 (0x00007fdf5a804000)
libgfortran.so.3 => not found
libgomp.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgomp.so.1 (0x00007fdf57533000)
libquadmath.so.0 => /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libquadmath.so.0 (0x00007fdf572f3000)
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Any ideas? I've re-emerged blas-reference, lapack-reference, cblas-reference, and numpy but am still getting this error.... |
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fedeliallalinea
Administrator
Joined: 08 Mar 2003
Posts: 30909
Location: here
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| Posted: Sun Jun 24, 2018 9:48 am Post subject: |
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You are sure to have compiled the right packages, because I tried in my system enabling lapack use flag on numpy and all linked correctly
| Code: | $ ldd /usr/lib64/python2.7/site-packages/numpy/linalg/lapack_lite.so
linux-vdso.so.1 (0x00007ffc993db000)
liblapack.so.0 => /usr/lib64/liblapack.so.0 (0x00007fef14a2e000)
libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 (0x00007fef1464d000)
libc.so.6 => /lib64/libc.so.6 (0x00007fef1428b000)
libblas.so.0 => /usr/lib64/blas/reference/libblas.so.0 (0x00007fef14035000)
libgfortran.so.4 => /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgfortran.so.4 (0x00007fef13c5a000)
libm.so.6 => /lib64/libm.so.6 (0x00007fef13917000)
libgcc_s.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgcc_s.so.1 (0x00007fef13700000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fef134e0000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fef132dc000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007fef130d9000)
/lib64/ld-linux-x86-64.so.2 (0x00007fef1541b000)
libquadmath.so.0 => /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libquadmath.so.0 (0x00007fef12e99000) |
Below packages compiled with lapack use flag
| Code: | [ebuild N ] virtual/cblas-1.0::gentoo 0 KiB
[ebuild N ] app-eselect/eselect-lapack-0.1::gentoo 0 KiB
[ebuild N ] app-eselect/eselect-blas-0.1::gentoo 0 KiB
[ebuild N ] sci-libs/blas-reference-20070226-r4::gentoo USE="-doc" 5,208 KiB
[ebuild N ] virtual/blas-1.0::gentoo 0 KiB
[ebuild N ] sci-libs/lapack-reference-3.2.1-r4::gentoo USE="-doc" 4,694 KiB
[ebuild N ] virtual/lapack-3.1::gentoo 0 KiB
[ebuild R ] dev-python/numpy-1.10.4::gentoo USE="lapack* -doc {-test}" PYTHON_TARGETS="python2_7 python3_6 -python3_4 -python3_5" 0 KiB |
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Questions are guaranteed in life; Answers aren't. |
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justin_brody
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Joined: 26 Jan 2005
Posts: 283
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| Posted: Sun Jun 24, 2018 9:52 am Post subject: numpy seems to want versions 3 and 4 of fortran [solvedISH] |
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| Thanks for this fedeliallalinea. It seemed to be lapack that was linking to gfortran 3. I couldn't get this to change by re-emerging, but I ended up bringing in openblas from the science overlay and after some mucking about all seems well. I unfortunatley can't give any systemic solution because I was really just trying a bunch of things but currently all seems well. |
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