make python not working
Closed this issue · 2 comments
WangHaiYang874 commented
Dear Manas,
make python works fine on my laptops. But it failed on the CIMS compute servers. Would you help me with this? Thanks!
Here's the terminal output:
[hw1927@access1]~/pkg/fmm2d% make python
ar rcs libfmm2d.a src/common/cdjseval2d.o src/common/dfft.o src/common/fmmcommon2d.o src/common/next235.o src/common/prini.o src/common/tree_routs2d.o src/common/pts_tree2d.o src/common/cumsum.o src/common/hank103.o src/helmholtz/h2dcommon.o src/helmholtz/h2dterms.o src/helmholtz/helmrouts2d.o src/helmholtz/hfmm2d.o src/helmholtz/hfmm2dwrap.o src/helmholtz/wideband2d.o src/helmholtz/hfmm2dwrap_vec.o src/helmholtz/hndiv2d.o src/helmholtz/hfmm2d_ndiv.o src/helmholtz/hfmm2d_mps.o src/helmholtz/hfmm2d_mps_ndiv.o src/helmholtz/helmkernels2d.o src/laplace/l2dterms.o src/laplace/laprouts2d.o src/laplace/lfmm2d.o src/laplace/lfmm2dwrap.o src/laplace/lfmm2dwrap_vec.o src/laplace/cfmm2d.o src/laplace/cfmm2dwrap.o src/laplace/cfmm2dwrap_vec.o src/laplace/rfmm2d.o src/laplace/rfmm2dwrap.o src/laplace/rfmm2dwrap_vec.o src/laplace/lndiv2d.o src/laplace/rfmm2d_ndiv.o src/laplace/lfmm2d_ndiv.o src/laplace/cfmm2d_ndiv.o src/laplace/lapkernels2d.o src/laplace/rlapkernels2d.o src/laplace/cauchykernels2d.o src/biharmonic/bh2dterms.o src/biharmonic/bhrouts2d.o src/biharmonic/bhfmm2d.o src/biharmonic/bhndiv2d.o src/biharmonic/bhkernels2d.o src/stokes/stfmm2d.o src/stokes/stokkernels2d.o
mv libfmm2d.a lib-static/
cd python && \
FMM_FLIBS='-lm -lgomp -fopenmp' python -m pip install -e .
Obtaining file:///home/hw1927/pkg/fmm2d/python
Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages (from fmm2dpy==0.0.5) (1.23.3)
Requirement already satisfied: pytest in /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages (from fmm2dpy==0.0.5) (7.1.3)
Requirement already satisfied: attrs>=19.2.0 in /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages (from pytest->fmm2dpy==0.0.5) (22.1.0)
Requirement already satisfied: iniconfig in /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages (from pytest->fmm2dpy==0.0.5) (1.1.1)
Requirement already satisfied: packaging in /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages (from pytest->fmm2dpy==0.0.5) (21.3)
Requirement already satisfied: pluggy<2.0,>=0.12 in /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages (from pytest->fmm2dpy==0.0.5) (1.0.0)
Requirement already satisfied: py>=1.8.2 in /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages (from pytest->fmm2dpy==0.0.5) (1.11.0)
Requirement already satisfied: tomli>=1.0.0 in /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages (from pytest->fmm2dpy==0.0.5) (2.0.1)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages (from packaging->pytest->fmm2dpy==0.0.5) (3.0.9)
Installing collected packages: fmm2dpy
Running setup.py develop for fmm2dpy
error: subprocess-exited-with-error
× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [97 lines of output]
/home/hw1927/pkg/fmm2d/python/setup.py:4: DeprecationWarning:
`numpy.distutils` is deprecated since NumPy 1.23.0, as a result
of the deprecation of `distutils` itself. It will be removed for
Python >= 3.12. For older Python versions it will remain present.
It is recommended to use `setuptools < 60.0` for those Python versions.
For more details, see:
https://numpy.org/devdocs/reference/distutils_status_migration.html
from numpy.distutils.core import setup
running develop
/home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
/home/hw1927/miniconda3/envs/bim/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
INFO: build_src
INFO: building extension "fmm2dpy.hfmm2d_fortran" sources
INFO: f2py options: ['only:', 'hfmm2d_s_c_p', 'hfmm2d_s_c_g', 'hfmm2d_s_d_p', 'hfmm2d_s_d_g', 'hfmm2d_s_cd_p', 'hfmm2d_s_cd_g', 'hfmm2d_t_c_p', 'hfmm2d_t_c_g', 'hfmm2d_t_d_p', 'hfmm2d_t_d_g', 'hfmm2d_t_cd_p', 'hfmm2d_t_cd_g', 'hfmm2d_st_c_p', 'hfmm2d_st_c_g', 'hfmm2d_st_d_p', 'hfmm2d_st_d_g', 'hfmm2d_st_cd_p', 'hfmm2d_st_cd_g', 'hfmm2d_s_c_p_vec', 'hfmm2d_s_c_g_vec', 'hfmm2d_s_d_p_vec', 'hfmm2d_s_d_g_vec', 'hfmm2d_s_cd_p_vec', 'hfmm2d_s_cd_g_vec', 'hfmm2d_t_c_p_vec', 'hfmm2d_t_c_g_vec', 'hfmm2d_t_d_p_vec', 'hfmm2d_t_d_g_vec', 'hfmm2d_t_cd_p_vec', 'hfmm2d_t_cd_g_vec', 'hfmm2d_st_c_p_vec', 'hfmm2d_st_c_g_vec', 'hfmm2d_st_d_p_vec', 'hfmm2d_st_d_g_vec', 'hfmm2d_st_cd_p_vec', 'hfmm2d_st_cd_g_vec', 'h2d_directcp', 'h2d_directcg', 'h2d_directdp', 'h2d_directdg', 'h2d_directcdp', 'h2d_directcdg', ':']
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c' to sources.
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy' to include_dirs.
INFO: adding 'build/src.linux-x86_64-3.10/fmm2dpy/hfmm2d_fortran-f2pywrappers.f' to sources.
INFO: building extension "fmm2dpy.lfmm2d_fortran" sources
INFO: f2py options: ['only:', 'rfmm2d_s_c_p', 'lfmm2d_s_c_p', 'cfmm2d_s_c_p', 'rfmm2d_s_c_g', 'lfmm2d_s_c_g', 'cfmm2d_s_c_g', 'rfmm2d_s_c_h', 'lfmm2d_s_c_h', 'cfmm2d_s_c_h', 'rfmm2d_s_d_p', 'lfmm2d_s_d_p', 'cfmm2d_s_d_p', 'rfmm2d_s_d_g', 'lfmm2d_s_d_g', 'cfmm2d_s_d_g', 'rfmm2d_s_d_h', 'lfmm2d_s_d_h', 'cfmm2d_s_d_h', 'rfmm2d_s_cd_p', 'lfmm2d_s_cd_p', 'cfmm2d_s_cd_p', 'rfmm2d_s_cd_g', 'lfmm2d_s_cd_g', 'cfmm2d_s_cd_g', 'rfmm2d_s_cd_h', 'lfmm2d_s_cd_h', 'cfmm2d_s_cd_h', 'rfmm2d_t_c_p', 'lfmm2d_t_c_p', 'cfmm2d_t_c_p', 'rfmm2d_t_c_g', 'lfmm2d_t_c_g', 'cfmm2d_t_c_g', 'rfmm2d_t_c_h', 'lfmm2d_t_c_h', 'cfmm2d_t_c_h', 'rfmm2d_t_d_p', 'lfmm2d_t_d_p', 'cfmm2d_t_d_p', 'rfmm2d_t_d_g', 'lfmm2d_t_d_g', 'cfmm2d_t_d_g', 'rfmm2d_t_d_h', 'lfmm2d_t_d_h', 'cfmm2d_t_d_h', 'rfmm2d_t_cd_p', 'lfmm2d_t_cd_p', 'cfmm2d_t_cd_p', 'rfmm2d_t_cd_g', 'lfmm2d_t_cd_g', 'cfmm2d_t_cd_g', 'rfmm2d_t_cd_h', 'lfmm2d_t_cd_h', 'cfmm2d_t_cd_h', 'rfmm2d_st_c_p', 'lfmm2d_st_c_p', 'cfmm2d_st_c_p', 'rfmm2d_st_c_g', 'lfmm2d_st_c_g', 'cfmm2d_st_c_g', 'rfmm2d_st_c_h', 'lfmm2d_st_c_h', 'cfmm2d_st_c_h', 'rfmm2d_st_d_p', 'lfmm2d_st_d_p', 'cfmm2d_st_d_p', 'rfmm2d_st_d_g', 'lfmm2d_st_d_g', 'cfmm2d_st_d_g', 'rfmm2d_st_d_h', 'lfmm2d_st_d_h', 'cfmm2d_st_d_h', 'rfmm2d_st_cd_p', 'lfmm2d_st_cd_p', 'cfmm2d_st_cd_p', 'rfmm2d_st_cd_g', 'lfmm2d_st_cd_g', 'cfmm2d_st_cd_g', 'rfmm2d_st_cd_h', 'lfmm2d_st_cd_h', 'cfmm2d_st_cd_h', 'rfmm2d_s_c_p_vec', 'lfmm2d_s_c_p_vec', 'cfmm2d_s_c_p_vec', 'rfmm2d_s_c_g_vec', 'lfmm2d_s_c_g_vec', 'cfmm2d_s_c_g_vec', 'rfmm2d_s_c_h_vec', 'lfmm2d_s_c_h_vec', 'cfmm2d_s_c_h_vec', 'rfmm2d_s_d_p_vec', 'lfmm2d_s_d_p_vec', 'cfmm2d_s_d_p_vec', 'rfmm2d_s_d_g_vec', 'lfmm2d_s_d_g_vec', 'cfmm2d_s_d_g_vec', 'rfmm2d_s_d_h_vec', 'lfmm2d_s_d_h_vec', 'cfmm2d_s_d_h_vec', 'rfmm2d_s_cd_p_vec', 'lfmm2d_s_cd_p_vec', 'cfmm2d_s_cd_p_vec', 'rfmm2d_s_cd_g_vec', 'lfmm2d_s_cd_g_vec', 'cfmm2d_s_cd_g_vec', 'rfmm2d_s_cd_h_vec', 'lfmm2d_s_cd_h_vec', 'cfmm2d_s_cd_h_vec', 'rfmm2d_t_c_p_vec', 'lfmm2d_t_c_p_vec', 'cfmm2d_t_c_p_vec', 'rfmm2d_t_c_g_vec', 'lfmm2d_t_c_g_vec', 'cfmm2d_t_c_g_vec', 'rfmm2d_t_c_h_vec', 'lfmm2d_t_c_h_vec', 'cfmm2d_t_c_h_vec', 'rfmm2d_t_d_p_vec', 'lfmm2d_t_d_p_vec', 'cfmm2d_t_d_p_vec', 'rfmm2d_t_d_g_vec', 'lfmm2d_t_d_g_vec', 'cfmm2d_t_d_g_vec', 'rfmm2d_t_d_h_vec', 'lfmm2d_t_d_h_vec', 'cfmm2d_t_d_h_vec', 'rfmm2d_t_cd_p_vec', 'lfmm2d_t_cd_p_vec', 'cfmm2d_t_cd_p_vec', 'rfmm2d_t_cd_g_vec', 'lfmm2d_t_cd_g_vec', 'cfmm2d_t_cd_g_vec', 'rfmm2d_t_cd_h_vec', 'lfmm2d_t_cd_h_vec', 'cfmm2d_t_cd_h_vec', 'rfmm2d_st_c_p_vec', 'lfmm2d_st_c_p_vec', 'cfmm2d_st_c_p_vec', 'rfmm2d_st_c_g_vec', 'lfmm2d_st_c_g_vec', 'cfmm2d_st_c_g_vec', 'rfmm2d_st_c_h_vec', 'lfmm2d_st_c_h_vec', 'cfmm2d_st_c_h_vec', 'rfmm2d_st_d_p_vec', 'lfmm2d_st_d_p_vec', 'cfmm2d_st_d_p_vec', 'rfmm2d_st_d_g_vec', 'lfmm2d_st_d_g_vec', 'cfmm2d_st_d_g_vec', 'rfmm2d_st_d_h_vec', 'lfmm2d_st_d_h_vec', 'cfmm2d_st_d_h_vec', 'rfmm2d_st_cd_p_vec', 'lfmm2d_st_cd_p_vec', 'cfmm2d_st_cd_p_vec', 'rfmm2d_st_cd_g_vec', 'lfmm2d_st_cd_g_vec', 'cfmm2d_st_cd_g_vec', 'rfmm2d_st_cd_h_vec', 'lfmm2d_st_cd_h_vec', 'cfmm2d_st_cd_h_vec', 'r2d_directcp', 'l2d_directcp', 'c2d_directcp', 'r2d_directcg', 'l2d_directcg', 'c2d_directcg', 'r2d_directch', 'l2d_directch', 'c2d_directch', 'r2d_directdp', 'l2d_directdp', 'c2d_directdp', 'r2d_directdg', 'l2d_directdg', 'c2d_directdg', 'r2d_directdh', 'l2d_directdh', 'c2d_directdh', 'r2d_directcdp', 'l2d_directcdp', 'c2d_directcdp', 'r2d_directcdg', 'l2d_directcdg', 'c2d_directcdg', 'r2d_directcdh', 'l2d_directcdh', 'c2d_directcdh', ':']
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c' to sources.
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy' to include_dirs.
INFO: adding 'build/src.linux-x86_64-3.10/fmm2dpy/lfmm2d_fortran-f2pywrappers.f' to sources.
INFO: building extension "fmm2dpy.bhfmm2d_fortran" sources
INFO: f2py options: ['only:', 'bhfmm2d', 'bh2d_directcp', 'bh2d_directcg', 'bh2d_directdp', 'bh2d_directdg', 'bh2d_directcdp', 'bh2d_directcdg', ':']
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c' to sources.
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy' to include_dirs.
INFO: adding 'build/src.linux-x86_64-3.10/fmm2dpy/bhfmm2d_fortran-f2pywrappers.f' to sources.
INFO: build_src: building npy-pkg config files
writing fmm2dpy.egg-info/PKG-INFO
writing dependency_links to fmm2dpy.egg-info/dependency_links.txt
writing requirements to fmm2dpy.egg-info/requires.txt
writing top-level names to fmm2dpy.egg-info/top_level.txt
/home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/setuptools/command/egg_info.py:643: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'.
Please extend command classes from setuptools instead of distutils.
warnings.warn(
INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
reading manifest file 'fmm2dpy.egg-info/SOURCES.txt'
writing manifest file 'fmm2dpy.egg-info/SOURCES.txt'
running build_ext
INFO: customize UnixCCompiler
INFO: customize UnixCCompiler using build_ext
INFO: CCompilerOpt.__init__[813] : load cache from file -> /home/hw1927/pkg/fmm2d/python/build/temp.linux-x86_64-cpython-310/ccompiler_opt_cache_ext.py
INFO: CCompilerOpt.__init__[824] : hit the file cache
INFO: get_default_fcompiler: matching types: '['arm', 'gnu95', 'intel', 'lahey', 'pg', 'nv', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor', 'fujitsu']'
INFO: customize ArmFlangCompiler
WARN: Could not locate executable armflang
INFO: customize Gnu95FCompiler
INFO: Found executable /usr/bin/gfortran
INFO: customize Gnu95FCompiler
INFO: customize Gnu95FCompiler using build_ext
INFO: building 'fmm2dpy.hfmm2d_fortran' extension
INFO: compiling C sources
INFO: C compiler: gcc -pthread -B /home/hw1927/miniconda3/envs/bim/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hw1927/miniconda3/envs/bim/include -fPIC -O2 -isystem /home/hw1927/miniconda3/envs/bim/include -fPIC
INFO: compile options: '-Ibuild/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy -I/home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.10/numpy/distutils/include -I/home/hw1927/miniconda3/envs/bim/include/python3.10 -I/home/hw1927/miniconda3/envs/bim/include/python3.10 -c'
extra options: '-msse -msse2 -msse3'
INFO: gcc: build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c
In file included from /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948:0,
from /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/hw1927/miniconda3/envs/bim/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/fmm2dpy/fortranobject.h:13,
from build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c:2:
/home/hw1927/miniconda3/envs/bim/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/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c: In function ‘find_first_negative_dimension’:
build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c:707:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
for (int i = 0; i < rank; ++i) {
^
build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c:707:5: note: use option -std=c99 or -std=gnu99 to compile your code
error: Command "gcc -pthread -B /home/hw1927/miniconda3/envs/bim/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hw1927/miniconda3/envs/bim/include -fPIC -O2 -isystem /home/hw1927/miniconda3/envs/bim/include -fPIC -Ibuild/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy -I/home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.10/numpy/distutils/include -I/home/hw1927/miniconda3/envs/bim/include/python3.10 -I/home/hw1927/miniconda3/envs/bim/include/python3.10 -c build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c -o build/temp.linux-x86_64-cpython-310/build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.o -MMD -MF build/temp.linux-x86_64-cpython-310/build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.o.d -msse -msse2 -msse3" failed with exit status 1
INFO:
########### EXT COMPILER OPTIMIZATION ###########
INFO: Platform :
Architecture: x64
Compiler : gcc
CPU baseline :
Requested : 'min'
Enabled : SSE SSE2 SSE3
Flags : -msse -msse2 -msse3
Extra checks: none
CPU dispatch :
Requested : 'max -xop -fma4'
Enabled : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2
Generated : none
INFO: CCompilerOpt.cache_flush[857] : write cache to path -> /home/hw1927/pkg/fmm2d/python/build/temp.linux-x86_64-cpython-310/ccompiler_opt_cache_ext.py
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× python setup.py develop did not run successfully.
│ exit code: 1
╰─> [97 lines of output]
/home/hw1927/pkg/fmm2d/python/setup.py:4: DeprecationWarning:
`numpy.distutils` is deprecated since NumPy 1.23.0, as a result
of the deprecation of `distutils` itself. It will be removed for
Python >= 3.12. For older Python versions it will remain present.
It is recommended to use `setuptools < 60.0` for those Python versions.
For more details, see:
https://numpy.org/devdocs/reference/distutils_status_migration.html
from numpy.distutils.core import setup
running develop
/home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
/home/hw1927/miniconda3/envs/bim/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
INFO: build_src
INFO: building extension "fmm2dpy.hfmm2d_fortran" sources
INFO: f2py options: ['only:', 'hfmm2d_s_c_p', 'hfmm2d_s_c_g', 'hfmm2d_s_d_p', 'hfmm2d_s_d_g', 'hfmm2d_s_cd_p', 'hfmm2d_s_cd_g', 'hfmm2d_t_c_p', 'hfmm2d_t_c_g', 'hfmm2d_t_d_p', 'hfmm2d_t_d_g', 'hfmm2d_t_cd_p', 'hfmm2d_t_cd_g', 'hfmm2d_st_c_p', 'hfmm2d_st_c_g', 'hfmm2d_st_d_p', 'hfmm2d_st_d_g', 'hfmm2d_st_cd_p', 'hfmm2d_st_cd_g', 'hfmm2d_s_c_p_vec', 'hfmm2d_s_c_g_vec', 'hfmm2d_s_d_p_vec', 'hfmm2d_s_d_g_vec', 'hfmm2d_s_cd_p_vec', 'hfmm2d_s_cd_g_vec', 'hfmm2d_t_c_p_vec', 'hfmm2d_t_c_g_vec', 'hfmm2d_t_d_p_vec', 'hfmm2d_t_d_g_vec', 'hfmm2d_t_cd_p_vec', 'hfmm2d_t_cd_g_vec', 'hfmm2d_st_c_p_vec', 'hfmm2d_st_c_g_vec', 'hfmm2d_st_d_p_vec', 'hfmm2d_st_d_g_vec', 'hfmm2d_st_cd_p_vec', 'hfmm2d_st_cd_g_vec', 'h2d_directcp', 'h2d_directcg', 'h2d_directdp', 'h2d_directdg', 'h2d_directcdp', 'h2d_directcdg', ':']
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c' to sources.
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy' to include_dirs.
INFO: adding 'build/src.linux-x86_64-3.10/fmm2dpy/hfmm2d_fortran-f2pywrappers.f' to sources.
INFO: building extension "fmm2dpy.lfmm2d_fortran" sources
INFO: f2py options: ['only:', 'rfmm2d_s_c_p', 'lfmm2d_s_c_p', 'cfmm2d_s_c_p', 'rfmm2d_s_c_g', 'lfmm2d_s_c_g', 'cfmm2d_s_c_g', 'rfmm2d_s_c_h', 'lfmm2d_s_c_h', 'cfmm2d_s_c_h', 'rfmm2d_s_d_p', 'lfmm2d_s_d_p', 'cfmm2d_s_d_p', 'rfmm2d_s_d_g', 'lfmm2d_s_d_g', 'cfmm2d_s_d_g', 'rfmm2d_s_d_h', 'lfmm2d_s_d_h', 'cfmm2d_s_d_h', 'rfmm2d_s_cd_p', 'lfmm2d_s_cd_p', 'cfmm2d_s_cd_p', 'rfmm2d_s_cd_g', 'lfmm2d_s_cd_g', 'cfmm2d_s_cd_g', 'rfmm2d_s_cd_h', 'lfmm2d_s_cd_h', 'cfmm2d_s_cd_h', 'rfmm2d_t_c_p', 'lfmm2d_t_c_p', 'cfmm2d_t_c_p', 'rfmm2d_t_c_g', 'lfmm2d_t_c_g', 'cfmm2d_t_c_g', 'rfmm2d_t_c_h', 'lfmm2d_t_c_h', 'cfmm2d_t_c_h', 'rfmm2d_t_d_p', 'lfmm2d_t_d_p', 'cfmm2d_t_d_p', 'rfmm2d_t_d_g', 'lfmm2d_t_d_g', 'cfmm2d_t_d_g', 'rfmm2d_t_d_h', 'lfmm2d_t_d_h', 'cfmm2d_t_d_h', 'rfmm2d_t_cd_p', 'lfmm2d_t_cd_p', 'cfmm2d_t_cd_p', 'rfmm2d_t_cd_g', 'lfmm2d_t_cd_g', 'cfmm2d_t_cd_g', 'rfmm2d_t_cd_h', 'lfmm2d_t_cd_h', 'cfmm2d_t_cd_h', 'rfmm2d_st_c_p', 'lfmm2d_st_c_p', 'cfmm2d_st_c_p', 'rfmm2d_st_c_g', 'lfmm2d_st_c_g', 'cfmm2d_st_c_g', 'rfmm2d_st_c_h', 'lfmm2d_st_c_h', 'cfmm2d_st_c_h', 'rfmm2d_st_d_p', 'lfmm2d_st_d_p', 'cfmm2d_st_d_p', 'rfmm2d_st_d_g', 'lfmm2d_st_d_g', 'cfmm2d_st_d_g', 'rfmm2d_st_d_h', 'lfmm2d_st_d_h', 'cfmm2d_st_d_h', 'rfmm2d_st_cd_p', 'lfmm2d_st_cd_p', 'cfmm2d_st_cd_p', 'rfmm2d_st_cd_g', 'lfmm2d_st_cd_g', 'cfmm2d_st_cd_g', 'rfmm2d_st_cd_h', 'lfmm2d_st_cd_h', 'cfmm2d_st_cd_h', 'rfmm2d_s_c_p_vec', 'lfmm2d_s_c_p_vec', 'cfmm2d_s_c_p_vec', 'rfmm2d_s_c_g_vec', 'lfmm2d_s_c_g_vec', 'cfmm2d_s_c_g_vec', 'rfmm2d_s_c_h_vec', 'lfmm2d_s_c_h_vec', 'cfmm2d_s_c_h_vec', 'rfmm2d_s_d_p_vec', 'lfmm2d_s_d_p_vec', 'cfmm2d_s_d_p_vec', 'rfmm2d_s_d_g_vec', 'lfmm2d_s_d_g_vec', 'cfmm2d_s_d_g_vec', 'rfmm2d_s_d_h_vec', 'lfmm2d_s_d_h_vec', 'cfmm2d_s_d_h_vec', 'rfmm2d_s_cd_p_vec', 'lfmm2d_s_cd_p_vec', 'cfmm2d_s_cd_p_vec', 'rfmm2d_s_cd_g_vec', 'lfmm2d_s_cd_g_vec', 'cfmm2d_s_cd_g_vec', 'rfmm2d_s_cd_h_vec', 'lfmm2d_s_cd_h_vec', 'cfmm2d_s_cd_h_vec', 'rfmm2d_t_c_p_vec', 'lfmm2d_t_c_p_vec', 'cfmm2d_t_c_p_vec', 'rfmm2d_t_c_g_vec', 'lfmm2d_t_c_g_vec', 'cfmm2d_t_c_g_vec', 'rfmm2d_t_c_h_vec', 'lfmm2d_t_c_h_vec', 'cfmm2d_t_c_h_vec', 'rfmm2d_t_d_p_vec', 'lfmm2d_t_d_p_vec', 'cfmm2d_t_d_p_vec', 'rfmm2d_t_d_g_vec', 'lfmm2d_t_d_g_vec', 'cfmm2d_t_d_g_vec', 'rfmm2d_t_d_h_vec', 'lfmm2d_t_d_h_vec', 'cfmm2d_t_d_h_vec', 'rfmm2d_t_cd_p_vec', 'lfmm2d_t_cd_p_vec', 'cfmm2d_t_cd_p_vec', 'rfmm2d_t_cd_g_vec', 'lfmm2d_t_cd_g_vec', 'cfmm2d_t_cd_g_vec', 'rfmm2d_t_cd_h_vec', 'lfmm2d_t_cd_h_vec', 'cfmm2d_t_cd_h_vec', 'rfmm2d_st_c_p_vec', 'lfmm2d_st_c_p_vec', 'cfmm2d_st_c_p_vec', 'rfmm2d_st_c_g_vec', 'lfmm2d_st_c_g_vec', 'cfmm2d_st_c_g_vec', 'rfmm2d_st_c_h_vec', 'lfmm2d_st_c_h_vec', 'cfmm2d_st_c_h_vec', 'rfmm2d_st_d_p_vec', 'lfmm2d_st_d_p_vec', 'cfmm2d_st_d_p_vec', 'rfmm2d_st_d_g_vec', 'lfmm2d_st_d_g_vec', 'cfmm2d_st_d_g_vec', 'rfmm2d_st_d_h_vec', 'lfmm2d_st_d_h_vec', 'cfmm2d_st_d_h_vec', 'rfmm2d_st_cd_p_vec', 'lfmm2d_st_cd_p_vec', 'cfmm2d_st_cd_p_vec', 'rfmm2d_st_cd_g_vec', 'lfmm2d_st_cd_g_vec', 'cfmm2d_st_cd_g_vec', 'rfmm2d_st_cd_h_vec', 'lfmm2d_st_cd_h_vec', 'cfmm2d_st_cd_h_vec', 'r2d_directcp', 'l2d_directcp', 'c2d_directcp', 'r2d_directcg', 'l2d_directcg', 'c2d_directcg', 'r2d_directch', 'l2d_directch', 'c2d_directch', 'r2d_directdp', 'l2d_directdp', 'c2d_directdp', 'r2d_directdg', 'l2d_directdg', 'c2d_directdg', 'r2d_directdh', 'l2d_directdh', 'c2d_directdh', 'r2d_directcdp', 'l2d_directcdp', 'c2d_directcdp', 'r2d_directcdg', 'l2d_directcdg', 'c2d_directcdg', 'r2d_directcdh', 'l2d_directcdh', 'c2d_directcdh', ':']
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c' to sources.
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy' to include_dirs.
INFO: adding 'build/src.linux-x86_64-3.10/fmm2dpy/lfmm2d_fortran-f2pywrappers.f' to sources.
INFO: building extension "fmm2dpy.bhfmm2d_fortran" sources
INFO: f2py options: ['only:', 'bhfmm2d', 'bh2d_directcp', 'bh2d_directcg', 'bh2d_directdp', 'bh2d_directdg', 'bh2d_directcdp', 'bh2d_directcdg', ':']
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c' to sources.
INFO: adding 'build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy' to include_dirs.
INFO: adding 'build/src.linux-x86_64-3.10/fmm2dpy/bhfmm2d_fortran-f2pywrappers.f' to sources.
INFO: build_src: building npy-pkg config files
writing fmm2dpy.egg-info/PKG-INFO
writing dependency_links to fmm2dpy.egg-info/dependency_links.txt
writing requirements to fmm2dpy.egg-info/requires.txt
writing top-level names to fmm2dpy.egg-info/top_level.txt
/home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/setuptools/command/egg_info.py:643: SetuptoolsDeprecationWarning: Custom 'build_py' does not implement 'get_data_files_without_manifest'.
Please extend command classes from setuptools instead of distutils.
warnings.warn(
INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
reading manifest file 'fmm2dpy.egg-info/SOURCES.txt'
writing manifest file 'fmm2dpy.egg-info/SOURCES.txt'
running build_ext
INFO: customize UnixCCompiler
INFO: customize UnixCCompiler using build_ext
INFO: CCompilerOpt.__init__[813] : load cache from file -> /home/hw1927/pkg/fmm2d/python/build/temp.linux-x86_64-cpython-310/ccompiler_opt_cache_ext.py
INFO: CCompilerOpt.__init__[824] : hit the file cache
INFO: get_default_fcompiler: matching types: '['arm', 'gnu95', 'intel', 'lahey', 'pg', 'nv', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor', 'fujitsu']'
INFO: customize ArmFlangCompiler
WARN: Could not locate executable armflang
INFO: customize Gnu95FCompiler
INFO: Found executable /usr/bin/gfortran
INFO: customize Gnu95FCompiler
INFO: customize Gnu95FCompiler using build_ext
INFO: building 'fmm2dpy.hfmm2d_fortran' extension
INFO: compiling C sources
INFO: C compiler: gcc -pthread -B /home/hw1927/miniconda3/envs/bim/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hw1927/miniconda3/envs/bim/include -fPIC -O2 -isystem /home/hw1927/miniconda3/envs/bim/include -fPIC
INFO: compile options: '-Ibuild/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy -I/home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.10/numpy/distutils/include -I/home/hw1927/miniconda3/envs/bim/include/python3.10 -I/home/hw1927/miniconda3/envs/bim/include/python3.10 -c'
extra options: '-msse -msse2 -msse3'
INFO: gcc: build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c
In file included from /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948:0,
from /home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/hw1927/miniconda3/envs/bim/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/fmm2dpy/fortranobject.h:13,
from build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c:2:
/home/hw1927/miniconda3/envs/bim/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/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c: In function ‘find_first_negative_dimension’:
build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c:707:5: error: ‘for’ loop initial declarations are only allowed in C99 mode
for (int i = 0; i < rank; ++i) {
^
build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c:707:5: note: use option -std=c99 or -std=gnu99 to compile your code
error: Command "gcc -pthread -B /home/hw1927/miniconda3/envs/bim/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/hw1927/miniconda3/envs/bim/include -fPIC -O2 -isystem /home/hw1927/miniconda3/envs/bim/include -fPIC -Ibuild/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy -I/home/hw1927/miniconda3/envs/bim/lib/python3.10/site-packages/numpy/core/include -Ibuild/src.linux-x86_64-3.10/numpy/distutils/include -I/home/hw1927/miniconda3/envs/bim/include/python3.10 -I/home/hw1927/miniconda3/envs/bim/include/python3.10 -c build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.c -o build/temp.linux-x86_64-cpython-310/build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.o -MMD -MF build/temp.linux-x86_64-cpython-310/build/src.linux-x86_64-3.10/build/src.linux-x86_64-3.10/fmm2dpy/fortranobject.o.d -msse -msse2 -msse3" failed with exit status 1
INFO:
########### EXT COMPILER OPTIMIZATION ###########
INFO: Platform :
Architecture: x64
Compiler : gcc
CPU baseline :
Requested : 'min'
Enabled : SSE SSE2 SSE3
Flags : -msse -msse2 -msse3
Extra checks: none
CPU dispatch :
Requested : 'max -xop -fma4'
Enabled : SSSE3 SSE41 POPCNT SSE42 AVX F16C FMA3 AVX2
Generated : none
INFO: CCompilerOpt.cache_flush[857] : write cache to path -> /home/hw1927/pkg/fmm2d/python/build/temp.linux-x86_64-cpython-310/ccompiler_opt_cache_ext.py
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
make: *** [python] Error 1
lu1and10 commented
Hi Haiyang,
It seems that the default gcc version(4.8.5) is a bit low on cims access nodes.
You could try module load gcc-7.4 on cims nodes for a higer version gcc or specify C flag -std=c99 to f2py.
WangHaiYang874 commented
Hi Haiyang,
It seems that the default gcc version(4.8.5) is a bit low on cims access nodes. You could try
module load gcc-7.4on cims nodes for a higer version gcc or specify C flag-std=c99to f2py.
Hi Libin,
Thanks for your answer. The problem is solved.
Best,
Haiyang