Installation issue when using gcc > version 7
louisl3grand opened this issue · comments
When trying to install lenscarf with a conda environment in python 3.10 I got this error.
It did not appear when using python 3.9.
>>> pip install -e .
Obtaining file:///global/u2/l/llegrand/lenscarf
Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /global/u2/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages (from lenscarf==0.0.1) (1.22.0)
Requirement already satisfied: pyfftw in /global/u2/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages (from lenscarf==0.0.1) (0.13.0)
Installing collected packages: lenscarf
Running setup.py develop for lenscarf
ERROR: Command errored out with exit status 1:
command: /global/homes/l/llegrand/.conda/envs/scarf6/bin/python3.1 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/global/u2/l/llegrand/lenscarf/setup.py'"'"'; __file__='"'"'/global/u2/l/llegrand/lenscarf/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
cwd: /global/u2/l/llegrand/lenscarf/
Complete output (53 lines):
running develop
/global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/setuptools/command/easy_install.py:156: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
/global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build_scripts
running egg_info
running build_src
/global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/setuptools/command/egg_info.py:624: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'.
Please extend command classes from setuptools instead of distutils.
warnings.warn(
writing manifest file 'lenscarf.egg-info/SOURCES.txt'
running build_ext
creating /tmp/tmp4uh9g_m7/global
creating /tmp/tmp4uh9g_m7/global/u2
creating /tmp/tmp4uh9g_m7/global/u2/l
creating /tmp/tmp4uh9g_m7/global/u2/l/llegrand
creating /tmp/tmp4uh9g_m7/global/u2/l/llegrand/.conda
creating /tmp/tmp4uh9g_m7/global/u2/l/llegrand/.conda/envs
creating /tmp/tmp4uh9g_m7/global/u2/l/llegrand/.conda/envs/scarf6
creating /tmp/tmp4uh9g_m7/global/u2/l/llegrand/.conda/envs/scarf6/lib
creating /tmp/tmp4uh9g_m7/global/u2/l/llegrand/.conda/envs/scarf6/lib/python3.10
creating /tmp/tmp4uh9g_m7/global/u2/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages
creating /tmp/tmp4uh9g_m7/global/u2/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/numpy
creating /tmp/tmp4uh9g_m7/global/u2/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/numpy/distutils
creating /tmp/tmp4uh9g_m7/global/u2/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/numpy/distutils/checks
WARN: Could not locate executable armflang
In file included from /global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
from /global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5,
from build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/lenscarf/fortran/fortranobject.h:13,
from build/src.linux-x86_64-3.10/lenscarf/fortran/remappingmodule.c:20:
/global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/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 " \
^~~~~~~
In file included from /global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
from /global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5,
from build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/lenscarf/fortran/fortranobject.h:13,
from build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/lenscarf/fortran/fortranobject.c:2:
/global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/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 " \
^~~~~~~
build/src.linux-x86_64-3.10/lenscarf/fortran/remappingmodule.c: In function 'f2py_rout_remapping_bicubic_eval':
build/src.linux-x86_64-3.10/lenscarf/fortran/remappingmodule.c:389:25: error: expected expression before ',' token
ftl_map_Dims[0]=1 + ,ftl_map_Dims[1]=1 + ;
^
build/src.linux-x86_64-3.10/lenscarf/fortran/remappingmodule.c:389:25: warning: left-hand operand of comma expression has no effect [-Wunused-value]
At top level:
build/src.linux-x86_64-3.10/lenscarf/fortran/remappingmodule.c:113:12: warning: 'f2py_size' defined but not used [-Wunused-function]
static int f2py_size(PyArrayObject* var, ...)
^~~~~~~~~
error: Command "gcc -pthread -B /global/homes/l/llegrand/.conda/envs/scarf6/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -fPIC -O2 -isystem /global/homes/l/llegrand/.conda/envs/scarf6/include -fPIC -O2 -isystem /global/homes/l/llegrand/.conda/envs/scarf6/include -fPIC -Ibuild/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/lenscarf/fortran -I/global/homes/l/llegrand/.conda/envs/scarf6/lib/python3.10/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.10/numpy/distutils/include -I/global/homes/l/llegrand/.conda/envs/scarf6/include/python3.10 -I/global/homes/l/llegrand/.conda/envs/scarf6/include/python3.10 -c build/src.linux-x86_64-3.10/lenscarf/fortran/remappingmodule.c -o build/temp.linux-x86_64-3.10/build/src.linux-x86_64-3.10/lenscarf/fortran/remappingmodule.o -MMD -MF build/temp.linux-x86_64-3.10/build/src.linux-x86_64-3.10/lenscarf/fortran/remappingmodule.o.d -msse -msse2 -msse3" failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /global/homes/l/llegrand/.conda/envs/scarf6/bin/python3.1 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/global/u2/l/llegrand/lenscarf/setup.py'"'"'; __file__='"'"'/global/u2/l/llegrand/lenscarf/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.
It seems that it is due to the f2py module.
When comparing line 389 of lenscarf/build/src.linux-x86_64-3.10/lenscarf/fortran/remappingmodule.c with line 373 of lenscarf/build/src.linux-x86_64-3.9/lenscarf/fortran/remappingmodule.c I see for the 3.10 version:
ftl_map_Dims[0]=1 + ,ftl_map_Dims[1]=1 + ;
and for the 3.9 version
ftl_map_Dims[0]=1,ftl_map_Dims[1]=1;
I observed the same problem using python 3.9.
It looks to me as though this is a gfortran version issue.
On my personal computer and using gcc version 11.2.1, I get the same error.
Adding extra f90 compile arguments such as -std=legacy, -fallow-argument-mismatch or -freal-4-real-8 did not resolve the issue.
However, I tried installing it in a docker container with gcc 7.0 and the installation worked.
Solved by #30