MPFR 3.1.3 fails with "illegal thread local variable reference to regular symbol" on Mac + Intel 15 - macos

I downloaded MPFR 3.1.3 from http://www.mpfr.org/mpfr-current/ and attempted to compile with Intel 15 (icc --version returns icc (ICC) 15.0.3 20150408) on Mac Yosemite (10.10.4).
The build fails at this point:
jrhammon-mac01:build jrhammon$ make
Making all in doc
make[1]: Nothing to be done for `all'.
Making all in src
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-am
/bin/sh ../libtool --tag=CC --mode=link icc -Wall -Wmissing-prototypes -Wpointer-arith -fp_port -mp -wd1572 -wd265 -wd186 -wd239 -g -O2 -version-info 5:3:1 -Wl,-search_paths_first -o libmpfr.la -rpath /usr/local/lib exceptions.lo extract.lo uceil_exp2.lo uceil_log2.lo ufloor_log2.lo add.lo add1.lo add_ui.lo agm.lo clear.lo cmp.lo cmp_abs.lo cmp_si.lo cmp_ui.lo comparisons.lo div_2exp.lo div_2si.lo div_2ui.lo div.lo div_ui.lo dump.lo eq.lo exp10.lo exp2.lo exp3.lo exp.lo frac.lo frexp.lo get_d.lo get_exp.lo get_str.lo init.lo inp_str.lo isinteger.lo isinf.lo isnan.lo isnum.lo const_log2.lo log.lo modf.lo mul_2exp.lo mul_2si.lo mul_2ui.lo mul.lo mul_ui.lo neg.lo next.lo out_str.lo printf.lo vasprintf.lo const_pi.lo pow.lo pow_si.lo pow_ui.lo print_raw.lo print_rnd_mode.lo reldiff.lo round_prec.lo set.lo setmax.lo setmin.lo set_d.lo set_dfl_prec.lo set_exp.lo set_rnd.lo set_f.lo set_prc_raw.lo set_prec.lo set_q.lo set_si.lo set_str.lo set_str_raw.lo set_ui.lo set_z.lo sqrt.lo sqrt_ui.lo sub.lo sub1.lo sub_ui.lo rint.lo ui_div.lo ui_sub.lo urandom.lo urandomb.lo get_z_exp.lo swap.lo factorial.lo cosh.lo sinh.lo tanh.lo sinh_cosh.lo acosh.lo asinh.lo atanh.lo atan.lo cmp2.lo exp_2.lo asin.lo const_euler.lo cos.lo sin.lo tan.lo fma.lo fms.lo hypot.lo log1p.lo expm1.lo log2.lo log10.lo ui_pow.lo ui_pow_ui.lo minmax.lo dim.lo signbit.lo copysign.lo setsign.lo gmp_op.lo init2.lo acos.lo sin_cos.lo set_nan.lo set_inf.lo set_zero.lo powerof2.lo gamma.lo set_ld.lo get_ld.lo cbrt.lo volatile.lo fits_sshort.lo fits_sint.lo fits_slong.lo fits_ushort.lo fits_uint.lo fits_ulong.lo fits_uintmax.lo fits_intmax.lo get_si.lo get_ui.lo zeta.lo cmp_d.lo erf.lo inits.lo inits2.lo clears.lo sgn.lo check.lo sub1sp.lo version.lo mpn_exp.lo mpfr-gmp.lo mp_clz_tab.lo sum.lo add1sp.lo free_cache.lo si_op.lo cmp_ld.lo set_ui_2exp.lo set_si_2exp.lo set_uj.lo set_sj.lo get_sj.lo get_uj.lo get_z.lo iszero.lo cache.lo sqr.lo int_ceil_log2.lo isqrt.lo strtofr.lo pow_z.lo logging.lo mulders.lo get_f.lo round_p.lo erfc.lo atan2.lo subnormal.lo const_catalan.lo root.lo sec.lo csc.lo cot.lo eint.lo sech.lo csch.lo coth.lo round_near_x.lo constant.lo abort_prec_max.lo stack_interface.lo lngamma.lo zeta_ui.lo set_d64.lo get_d64.lo jn.lo yn.lo rem1.lo get_patches.lo add_d.lo sub_d.lo d_sub.lo mul_d.lo div_d.lo d_div.lo li2.lo rec_sqrt.lo min_prec.lo buildopt.lo digamma.lo bernoulli.lo isregular.lo set_flt.lo get_flt.lo scale2.lo set_z_exp.lo ai.lo gammaonethird.lo grandom.lo -lgmp
libtool: link: icc -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o .libs/libmpfr.4.dylib .libs/exceptions.o .libs/extract.o .libs/uceil_exp2.o .libs/uceil_log2.o .libs/ufloor_log2.o .libs/add.o .libs/add1.o .libs/add_ui.o .libs/agm.o .libs/clear.o .libs/cmp.o .libs/cmp_abs.o .libs/cmp_si.o .libs/cmp_ui.o .libs/comparisons.o .libs/div_2exp.o .libs/div_2si.o .libs/div_2ui.o .libs/div.o .libs/div_ui.o .libs/dump.o .libs/eq.o .libs/exp10.o .libs/exp2.o .libs/exp3.o .libs/exp.o .libs/frac.o .libs/frexp.o .libs/get_d.o .libs/get_exp.o .libs/get_str.o .libs/init.o .libs/inp_str.o .libs/isinteger.o .libs/isinf.o .libs/isnan.o .libs/isnum.o .libs/const_log2.o .libs/log.o .libs/modf.o .libs/mul_2exp.o .libs/mul_2si.o .libs/mul_2ui.o .libs/mul.o .libs/mul_ui.o .libs/neg.o .libs/next.o .libs/out_str.o .libs/printf.o .libs/vasprintf.o .libs/const_pi.o .libs/pow.o .libs/pow_si.o .libs/pow_ui.o .libs/print_raw.o .libs/print_rnd_mode.o .libs/reldiff.o .libs/round_prec.o .libs/set.o .libs/setmax.o .libs/setmin.o .libs/set_d.o .libs/set_dfl_prec.o .libs/set_exp.o .libs/set_rnd.o .libs/set_f.o .libs/set_prc_raw.o .libs/set_prec.o .libs/set_q.o .libs/set_si.o .libs/set_str.o .libs/set_str_raw.o .libs/set_ui.o .libs/set_z.o .libs/sqrt.o .libs/sqrt_ui.o .libs/sub.o .libs/sub1.o .libs/sub_ui.o .libs/rint.o .libs/ui_div.o .libs/ui_sub.o .libs/urandom.o .libs/urandomb.o .libs/get_z_exp.o .libs/swap.o .libs/factorial.o .libs/cosh.o .libs/sinh.o .libs/tanh.o .libs/sinh_cosh.o .libs/acosh.o .libs/asinh.o .libs/atanh.o .libs/atan.o .libs/cmp2.o .libs/exp_2.o .libs/asin.o .libs/const_euler.o .libs/cos.o .libs/sin.o .libs/tan.o .libs/fma.o .libs/fms.o .libs/hypot.o .libs/log1p.o .libs/expm1.o .libs/log2.o .libs/log10.o .libs/ui_pow.o .libs/ui_pow_ui.o .libs/minmax.o .libs/dim.o .libs/signbit.o .libs/copysign.o .libs/setsign.o .libs/gmp_op.o .libs/init2.o .libs/acos.o .libs/sin_cos.o .libs/set_nan.o .libs/set_inf.o .libs/set_zero.o .libs/powerof2.o .libs/gamma.o .libs/set_ld.o .libs/get_ld.o .libs/cbrt.o .libs/volatile.o .libs/fits_sshort.o .libs/fits_sint.o .libs/fits_slong.o .libs/fits_ushort.o .libs/fits_uint.o .libs/fits_ulong.o .libs/fits_uintmax.o .libs/fits_intmax.o .libs/get_si.o .libs/get_ui.o .libs/zeta.o .libs/cmp_d.o .libs/erf.o .libs/inits.o .libs/inits2.o .libs/clears.o .libs/sgn.o .libs/check.o .libs/sub1sp.o .libs/version.o .libs/mpn_exp.o .libs/mpfr-gmp.o .libs/mp_clz_tab.o .libs/sum.o .libs/add1sp.o .libs/free_cache.o .libs/si_op.o .libs/cmp_ld.o .libs/set_ui_2exp.o .libs/set_si_2exp.o .libs/set_uj.o .libs/set_sj.o .libs/get_sj.o .libs/get_uj.o .libs/get_z.o .libs/iszero.o .libs/cache.o .libs/sqr.o .libs/int_ceil_log2.o .libs/isqrt.o .libs/strtofr.o .libs/pow_z.o .libs/logging.o .libs/mulders.o .libs/get_f.o .libs/round_p.o .libs/erfc.o .libs/atan2.o .libs/subnormal.o .libs/const_catalan.o .libs/root.o .libs/sec.o .libs/csc.o .libs/cot.o .libs/eint.o .libs/sech.o .libs/csch.o .libs/coth.o .libs/round_near_x.o .libs/constant.o .libs/abort_prec_max.o .libs/stack_interface.o .libs/lngamma.o .libs/zeta_ui.o .libs/set_d64.o .libs/get_d64.o .libs/jn.o .libs/yn.o .libs/rem1.o .libs/get_patches.o .libs/add_d.o .libs/sub_d.o .libs/d_sub.o .libs/mul_d.o .libs/div_d.o .libs/d_div.o .libs/li2.o .libs/rec_sqrt.o .libs/min_prec.o .libs/buildopt.o .libs/digamma.o .libs/bernoulli.o .libs/isregular.o .libs/set_flt.o .libs/get_flt.o .libs/scale2.o .libs/set_z_exp.o .libs/ai.o .libs/gammaonethird.o .libs/grandom.o -lgmp -mp -g -O2 -Wl,-search_paths_first -mp -install_name /usr/local/lib/libmpfr.4.dylib -compatibility_version 6 -current_version 6.3 -Wl,-single_module
icc: command line remark #10148: option '-mp' not supported
icc: command line remark #10148: option '-mp' not supported
ld: illegal thread local variable reference to regular symbol __tls___mpfr_allocate_func for architecture x86_64
make[2]: *** [libmpfr.la] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1
I have never seen this error before. Is it a bug in MPFR, the Intel compiler or the Mac toolchain? I am using the system install of GMP (from Homebrew), which I assume is built with Clang, not Intel. Is there a C ABI incompatibility issue here with TLS?
I found https://github.com/feeley/gambit/issues/109 and https://trac.mpich.org/projects/mpich/ticket/1547, which suggest that it is a Mac issue, but I am able to build with CC=clang so I guess it has something to do with Intel.

I have got MPFR to build in the past with Intel compilers, but (apparently) had to apply this patch: https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/m/MPFR/MPFR_ictce_remove-deprecated-mp.patch .
Maybe the warnings you're getting aren't so harmless as they seem.

Related

How to indicate a list of dicts in pythran?

I don't know how to indicate a list of dicts in Pythran. Say I call the function dictest() in a pure python file. A list of dicts (here: ll) need to be provided as arguments:
import test_pythran as tp
dd = {
"ux": 10.0,
"uy": 5,
"uz": 3.4
}
ee = {
"ux": 11.0,
"uy": 7,
"uz": 2.4
}
ll = (dd,ee)
tp.dictest(ll)
The function dictest() is defined in a separate file (here: test.py), which is compiled by pythran test.py -o test_pythran.so:
#pythran export dictest(str:float dict list )
def dictest(ll):
print(ll["ux"], ll["uy"], ll["uz"])
Compilation gives a bunch of errors:
WARNING: Compilation error, trying hard to find its origin...
Compilation error, trying hard to find its origin...
WARNING: Nope, I'm going to flood you with C++ errors!
Nope, I'm going to flood you with C++ errors!
CRITICAL: Cover me Jack. Jack? Jaaaaack!!!!
E: error: Command "/usr/local/opt/gcc/bin/g++-12 -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -DENABLE_PYTHON_MODULE -D__PYTHRAN__=3 -DPYTHRAN_BLAS_OPENBLAS -I/usr/local/opt/openblas/include -I/usr/local/Cellar/pythran/0.12.0/libexec/lib/python3.10/site-packages/pythran -I/usr/local/opt/numpy/lib/python3.10/site-packages/numpy/core/include -I/usr/local/Cellar/pythran/0.12.0/libexec/include -I/usr/local/opt/python#3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c /var/folders/41/dj_cjw2977qbd4fqxf1c79tc0000gn/T/tmpctvfroxf.cpp -o /var/folders/41/dj_cjw2977qbd4fqxf1c79tc0000gn/T/tmp3ae2neiv/var/folders/41/dj_cjw2977qbd4fqxf1c79tc0000gn/T/tmpctvfroxf.o -std=c++11 -fno-math-errno -Wno-unused-function" failed with exit status 1
Cover me Jack. Jack? Jaaaaack!!!!
E: error: Command "/usr/local/opt/gcc/bin/g++-12 -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -DENABLE_PYTHON_MODULE -D__PYTHRAN__=3 -DPYTHRAN_BLAS_OPENBLAS -I/usr/local/opt/openblas/include -I/usr/local/Cellar/pythran/0.12.0/libexec/lib/python3.10/site-packages/pythran -I/usr/local/opt/numpy/lib/python3.10/site-packages/numpy/core/include -I/usr/local/Cellar/pythran/0.12.0/libexec/include -I/usr/local/opt/python#3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c /var/folders/41/dj_cjw2977qbd4fqxf1c79tc0000gn/T/tmpctvfroxf.cpp -o /var/folders/41/dj_cjw2977qbd4fqxf1c79tc0000gn/T/tmp3ae2neiv/var/folders/41/dj_cjw2977qbd4fqxf1c79tc0000gn/T/tmpctvfroxf.o -std=c++11 -fno-math-errno -Wno-unused-function" failed with exit status 1
I am sure that it is related to the way I need to indicate the list of dicts in the function definition: str:float dict list. How to do this in the proper way?
Thanks!
There are several issues in your example.
First, dictest takes a list of dict as input but you're indexing its argument through a string, maybe you meant
#pythran export dictest(str:float dict list )
def dictest(ll):
for l in ll:
print(l["ux"], l["uy"], l["uz"])
Second, at call site you're passing a tuple of dict and not a list of dict as input to dictest. You probably wants to type
ll = [dd, ee]

GCC Linking Error when Building Fast RCNN

I am trying to build the source code at https://github.com/craftGBD/craftGBD in order to achieve the same results of the published paper of authors to observe whether it is reproducible or not for my term project. I realized that I have to install Fast RCNN by running Makefile inside the craftGBD/evaluation/lib folder. However, I got following results when I run Makefile using make:
/cta/users/byaman/craftEnv/bin/python setup.py build_ext --inplace
python setup.py build_ext --inplace
running build_ext
cythoning utils/bbox.pyx to utils/bbox.c
/cta/users/byaman/craftEnv/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /cta/users/byaman/craftGBD/evaluation/lib/utils/bbox.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning nms/cpu_nms.pyx to nms/cpu_nms.c
/cta/users/byaman/craftEnv/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /cta/users/byaman/craftGBD/evaluation/lib/nms/cpu_nms.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning nms/gpu_nms.pyx to nms/gpu_nms.cpp
/cta/users/byaman/craftEnv/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /cta/users/byaman/craftGBD/evaluation/lib/nms/gpu_nms.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
skipping 'pycocotools/_mask.c' Cython extension (up-to-date)
building 'utils.cython_bbox' extension
['-Wno-cpp', '-Wno-unused-function'] .c ['-I/cta/users/byaman/craftEnv/lib/python2.7/site-packages/numpy/core/include', '-I/cta/users/byaman/craftEnv/include/python2.7', '-c'] ['-Wno-cpp', '-Wno-unused-function'] ['-I/cta/users/byaman/craftEnv/lib/python2.7/site-packages/numpy/core/include', '-I/cta/users/byaman/craftEnv/include/python2.7']
/cta/users/byaman/craftEnv/bin/x86_64-conda-linux-gnu-cc -fno-strict-aliasing -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /cta/users/byaman/craftEnv/include -I/cta/apps/opt/spack/linux-ubuntu18.04-cascadelake/gcc-10.2.0/cuda-10.0.130-zjercki4memwdfwjztmfkq2yio2jcev4/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /cta/users/byaman/craftEnv/include -I/cta/apps/opt/spack/linux-ubuntu18.04-cascadelake/gcc-10.2.0/cuda-10.0.130-zjercki4memwdfwjztmfkq2yio2jcev4/include -fPIC -I/cta/users/byaman/craftEnv/lib/python2.7/site-packages/numpy/core/include -I/cta/users/byaman/craftEnv/include/python2.7 -c utils/bbox.c -o build/temp.linux-x86_64-2.7/utils/bbox.o -Wno-cpp -Wno-unused-function
x86_64-conda_cos6-linux-gnu-gcc -pthread -shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/cta/users/byaman/craftEnv/lib -L/cta/users/byaman/craftEnv/lib -Wl,--no-as-needed -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/cta/users/byaman/craftEnv/lib -Wl,-rpath-link,/cta/users/byaman/craftEnv/lib -L/cta/users/byaman/craftEnv/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /cta/users/byaman/craftEnv/include -I/cta/apps/opt/spack/linux-ubuntu18.04-cascadelake/gcc-10.2.0/cuda-10.0.130-zjercki4memwdfwjztmfkq2yio2jcev4/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /cta/users/byaman/craftEnv/include -I/cta/apps/opt/spack/linux-ubuntu18.04-cascadelake/gcc-10.2.0/cuda-10.0.130-zjercki4memwdfwjztmfkq2yio2jcev4/include build/temp.linux-x86_64-2.7/utils/bbox.o -L/cta/users/byaman/craftEnv/lib -lpython2.7 -o /cta/users/byaman/craftGBD/evaluation/lib/utils/cython_bbox.so
/cta/users/byaman/craftEnv/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /cta/users/byaman/craftEnv/lib/libc.a(__stack_chk_fail.o): relocation R_X86_64_32 against symbol `__stack_chk_guard' can not be used when making a shared object; recompile with -fPIC
collect2: error: ld returned 1 exit status
error: command 'x86_64-conda_cos6-linux-gnu-gcc' failed with exit status 1
Makefile:2: recipe for target 'all' failed
make: *** [all] Error 1
Note that my username is byaman and I run the code inside the Conda environment, which is craftEnv.
The code that is run by Makefile is:
# --------------------------------------------------------
# Fast R-CNN
# Copyright (c) 2015 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ross Girshick
# --------------------------------------------------------
import os
from os.path import join as pjoin
from setuptools import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
import subprocess
import numpy as np
def find_in_path(name, path):
"Find a file in a search path"
# Adapted fom
# http://code.activestate.com/recipes/52224-find-a-file-given-a-search-path/
for dir in path.split(os.pathsep):
binpath = pjoin(dir, name)
if os.path.exists(binpath):
return os.path.abspath(binpath)
return None
def locate_cuda():
"""Locate the CUDA environment on the system
Returns a dict with keys 'home', 'nvcc', 'include', and 'lib64'
and values giving the absolute path to each directory.
Starts by looking for the CUDAHOME env variable. If not found, everything
is based on finding 'nvcc' in the PATH.
"""
# first check if the CUDAHOME env variable is in use
if 'CUDAHOME' in os.environ:
home = os.environ['CUDAHOME']
nvcc = pjoin(home, 'bin', 'nvcc')
else:
# otherwise, search the PATH for NVCC
default_path = pjoin(os.sep, 'usr', 'local', 'cuda', 'bin')
nvcc = find_in_path('nvcc', os.environ['PATH'] + os.pathsep + default_path)
if nvcc is None:
raise EnvironmentError('The nvcc binary could not be '
'located in your $PATH. Either add it to your path, or set $CUDAHOME')
home = os.path.dirname(os.path.dirname(nvcc))
cudaconfig = {'home':home, 'nvcc':nvcc,
'include': pjoin(home, 'include'),
'lib64': pjoin(home, 'lib64')}
for k, v in cudaconfig.iteritems():
if not os.path.exists(v):
raise EnvironmentError('The CUDA %s path could not be located in %s' % (k, v))
return cudaconfig
CUDA = locate_cuda()
# Obtain the numpy include directory. This logic works across numpy versions.
try:
numpy_include = np.get_include()
except AttributeError:
numpy_include = np.get_numpy_include()
def customize_compiler_for_nvcc(self):
"""inject deep into distutils to customize how the dispatch
to gcc/nvcc works.
If you subclass UnixCCompiler, it's not trivial to get your subclass
injected in, and still have the right customizations (i.e.
distutils.sysconfig.customize_compiler) run on it. So instead of going
the OO route, I have this. Note, it's kindof like a wierd functional
subclassing going on."""
# tell the compiler it can processes .cu
self.src_extensions.append('.cu')
# save references to the default compiler_so and _comple methods
default_compiler_so = self.compiler_so
super = self._compile
# now redefine the _compile method. This gets executed for each
# object but distutils doesn't have the ability to change compilers
# based on source extension: we add it.
def _compile(obj, src, ext, cc_args, extra_postargs, pp_opts):
if os.path.splitext(src)[1] == '.cu':
# use the cuda for .cu files
self.set_executable('compiler_so', CUDA['nvcc'])
# use only a subset of the extra_postargs, which are 1-1 translated
# from the extra_compile_args in the Extension class
postargs = extra_postargs['nvcc']
else:
postargs = extra_postargs['gcc']
super(obj, src, ext, cc_args, postargs, pp_opts)
# reset the default compiler_so, which we might have changed for cuda
self.compiler_so = default_compiler_so
# inject our redefined _compile method into the class
self._compile = _compile
# run the customize_compiler
class custom_build_ext(build_ext):
def build_extensions(self):
customize_compiler_for_nvcc(self.compiler)
build_ext.build_extensions(self)
ext_modules = [
Extension(
"utils.cython_bbox",
["utils/bbox.pyx"],
extra_compile_args={'gcc': ["-Wno-cpp", "-Wno-unused-function"]},
include_dirs = [numpy_include]
),
Extension(
"nms.cpu_nms",
["nms/cpu_nms.pyx"],
extra_compile_args={'gcc': ["-Wno-cpp", "-Wno-unused-function"]},
include_dirs = [numpy_include]
),
Extension('nms.gpu_nms',
['nms/nms_kernel.cu', 'nms/gpu_nms.pyx'],
library_dirs=[CUDA['lib64']],
libraries=['cudart'],
language='c++',
runtime_library_dirs=[CUDA['lib64']],
# this syntax is specific to this build system
# we're only going to use certain compiler args with nvcc and not with
# gcc the implementation of this trick is in customize_compiler() below
extra_compile_args={'gcc': ["-Wno-unused-function"],
'nvcc': ['-arch=sm_35',
'--ptxas-options=-v',
'-c',
'--compiler-options',
"'-fPIC'"]},
include_dirs = [numpy_include, CUDA['include']]
),
Extension(
'pycocotools._mask',
sources=['pycocotools/maskApi.c', 'pycocotools/_mask.pyx'],
include_dirs = [numpy_include, 'pycocotools'],
extra_compile_args={
'gcc': ['-Wno-cpp', '-Wno-unused-function', '-std=c99']},
),
]
setup(
name='fast_rcnn',
ext_modules=ext_modules,
# inject our custom trigger
cmdclass={'build_ext': custom_build_ext},
)
I don't know how to solve this problem even though I investigated following questions/answers:
"relocation R_X86_64_32S against " linking Error
How to recompile with -fPIC
Cython wrapping a class that uses another library

GCC : undefined reference to "__asan_init_v1"

I want to compile my C99 project with the flag -fsanitize=address. I need to use CMake and to compile with gcc on a Centos 7 distribution.
I currently have gcc 7.3.1 and cmake 3.13.4.
I added the -fsanitize=address flag in the compilation flags list and in the linker, but it still fails to compile with the following error:
[ 6%] Building C object CMakeFiles/last.dir/src/ast/ast.c.o
[ 13%] Building C object CMakeFiles/last.dir/src/ast/ast_printer.c.o
[ 20%] Building C object CMakeFiles/last.dir/src/ast/cleaner.c.o
[ 26%] Linking C static library liblast.a
[ 26%] Built target last
[ 33%] Building C object CMakeFiles/lexecution.dir/src/execution/exec_parser.c.o
[ 40%] Building C object CMakeFiles/lexecution.dir/src/execution/exec_utils.c.o
[ 46%] Building C object CMakeFiles/lexecution.dir/src/execution/exec_func.c.o
[ 53%] Building C object CMakeFiles/lexecution.dir/src/execution/exec_parser_options.c.o
[ 60%] Linking C static library liblexecution.a
[ 60%] Built target lexecution
[ 66%] Building C object CMakeFiles/lutils.dir/tests/utils/utils.c.o
[ 73%] Linking C static library liblutils.a
[ 73%] Built target lutils
[ 80%] Building C object CMakeFiles/lhist.dir/src/history/history.c.o
[ 86%] Linking C static library liblhist.a
[ 86%] Built target lhist
[ 93%] Building C object CMakeFiles/42sh.dir/src/execution/exec_42sh.c.o
[100%] Linking C executable 42sh
/usr/lib/gcc/x86_64-redhat-linux/4.8.5/libasan_preinit.o:(.preinit_array+0x0) : undefined reference to « __asan_init_v1 »
CMakeFiles/42sh.dir/src/execution/exec_42sh.c.o : In function « _GLOBAL__sub_I_00099_1_flag » :
/home/lyro/Documents/customshell/src/execution/exec_42sh.c:304 : undefined reference to « __asan_init_v1 »
liblexecution.a(exec_parser.c.o) : In function « _GLOBAL__sub_I_00099_1_parser_new_from_string » :
/home/lyro/Documents/customshell/src/execution/exec_parser.c:1105 : undefined reference to « __asan_init_v1 »
liblexecution.a(exec_utils.c.o) : In function « _GLOBAL__sub_I_00099_0_get_args_array » :
/home/lyro/Documents/customshell/src/execution/exec_utils.c:242 : undefined reference to « __asan_init_v1 »
liblexecution.a(exec_func.c.o) : In function « _GLOBAL__sub_I_00099_1_exec_ast » :
/home/lyro/Documents/customshell/src/execution/exec_func.c:187 : undefined reference to « __asan_init_v1 »
liblexecution.a(exec_parser_options.c.o):/home/lyro/Documents/customshell/src/execution/exec_parser_options.c:149 : more undefined references to « __asan_init_v1 »
collect2: error: ld returned 1 execution state code
make[2]: *** [42sh] Error 1
make[1]: *** [CMakeFiles/42sh.dir/all] Error 2
make: *** [all] Error 2
Here is my CMakeLists.txt file, I can't find what I am missing..
cmake_minimum_required(VERSION 3.0)
project(42SH LANGUAGES C)
add_compile_options(-Wall -Wextra -Werror -pedantic -fsanitize=address -g -std=c99)
add_library(last ${CMAKE_SOURCE_DIR}/src/ast/ast.c ${CMAKE_SOURCE_DIR}/src/ast/ast_printer.c ${CMAKE_SOURCE_DIR}/src/ast/cleaner.c)
target_include_directories(last PUBLIC ${CMAKE_SOURCE_DIR}/src/ast)
add_library(lutils ${CMAKE_SOURCE_DIR}/tests/utils/utils.c)
target_include_directories(lutils PUBLIC ${CMAKE_SOURCE_DIR}/tests/utils)
target_link_libraries(lutils -fsanitize=address lexecution)
add_library(lexecution ${CMAKE_SOURCE_DIR}/src/execution/exec_parser.c ${CMAKE_SOURCE_DIR}/src/execution/exec_utils.c ${CMAKE_SOURCE_DIR}/src/execution/exec_func.c ${CMAKE_SOURCE_DIR}/src/execution/exec_parser_options.c)
target_include_directories(lexecution PUBLIC ${CMAKE_SOURCE_DIR}/src/ast)
target_link_libraries(lexecution -fsanitize=address last)
add_library(lhist ${CMAKE_SOURCE_DIR}/src/history/history.c)
target_include_directories(lhist PUBLIC ${CMAKE_SOURCE_DIR}/src/history)
add_executable(42sh src/execution/exec_42sh.c)
target_link_libraries(42sh -fsanitize=address lexecution)
target_link_libraries(42sh -fsanitize=address lutils)
target_link_libraries(42sh -fsanitize=address last)
target_link_libraries(42sh -fsanitize=address lhist)
add_custom_target(submit
COMMENT "Compiled for submission. Sanitizers ON."
COMMENT "Don't use Valgrind on this executable. It will not work."
DEPENDS 42sh
)
add_custom_target(tests
COMMAND pytest ${CMAKE_SOURCE_DIR}/tests
COMMENT "Running testsuite..."
DEPENDS 42sh
)
add_custom_target(doc
COMMENT "Compiling documentation"
COMMAND doxygen ${CMAKE_SOURCE_DIR}/doc/Doxyfile
COMMENT "Compiled documentation"
)
Your toolchain is somewhat confused about which version of GCC it is and
the linkage failure is one consequence of that confusion.
You tell us you are using GCC 7.3.1, but the first of the unresolved references to __asan_init_v1:
/usr/lib/gcc/x86_64-redhat-linux/4.8.5/libasan_preinit.o:(.preinit_array+0x0) : undefined reference to « __asan_init_v1
shows that the gcc that invoked the linkage with -fsanitize=address linked the address santitizer initialization code
from your installation of GCC 4.8.5.
In GCC 7, the file libasan_preinit.o makes no references to __asan_init_v1, as seen on
the laptop I'm working on just now:
$ nm /usr/lib/gcc/x86_64-linux-gnu/7/libasan_preinit.o
U __asan_init
0000000000000000 D __local_asan_preinit
It calls __asan_init, which is indeed defined in the toolchain's libasan:
$ nm -D /usr/lib/gcc/x86_64-linux-gnu/7/libasan.so | grep __asan_init
00000000000ecdb0 T __asan_init
On the other hand, in GCC 4.8.5, libasan did not define the function __asan_init
and did define __asan_init_v1:
:~/Downloads/gcc-4.8.5$ grep -r '__asan_init_v'
gcc/ChangeLog: * sanitizer.def: Rename __asan_init to __asan_init_v1.
gcc/sanitizer.def:DEF_SANITIZER_BUILTIN(BUILT_IN_ASAN_INIT, "__asan_init_v1",
libsanitizer/asan/asan_interface_internal.h: void __asan_init_v1() SANITIZER_INTERFACE_ATTRIBUTE;
libsanitizer/asan/asan_interface_internal.h: #define __asan_init __asan_init_v1
There, __asan_init was just an internal #define aliasing the real function __asan_init_v1, as
per libsanitizer/asan/asan_interface_internal.h, but in that file in GCC 7
// This function should be called at the very beginning of the process,
// before any instrumented code is executed and before any call to malloc.
SANITIZER_INTERFACE_ATTRIBUTE void __asan_init();
it is a real function, as reported by nm.
So the thrust of the evidence is that you are linking against the libasan of GCC 7.3.1
but also linking the library initialization code of GCC 4.8.5. I have no visibility of
how you've landed in this GCC version mash-up - could be a packaging bug, for all I know - but
you'll have to fix that to solve these linkage failures.

Crosstool-ng g++ not compiling c++11 std::current_exception

I build a gcc toolchain using Crosstool-ng, but the resulting g++ does not compile and/or link C++11 exceptions.
If I try to compile:
#include <exception>
int main()
{
std::current_exception();
}
via:
arm-none-linux-gnueabihf-g++ -std=c++11 foo.cpp
I get:
foo.cpp: In function 'int main()':
foo.cpp:5:9: error: 'current_exception' is not a member of 'std'
std::current_exception();
^~~
However, if I additionally provide cortex-a9 as cpu the haviour changes:
arm-none-linux-gnueabihf-g++ -mcpu=cortex-a9 -std=c++11 foo.cpp
results in:
/tmp/cc13AEjE.o: In function `main':
foo.cpp:(.text+0x14): undefined reference to `std::current_exception()'
foo.cpp:(.text+0x20): undefined reference to
`std::__exception_ptr::exception_ptr::~exception_ptr()'
collect2: error: ld returned 1 exit status
I greped within the toolchain for current_exception and it seems good for me:
grep -r -e current_exception arm-none-linux-gnueabihf/
Binary file arm-none-linux-gnueabihf/arm-none-linux-gnueabihf/sysroot/lib/libstdc++.so.6.0.22 matches
Binary file arm-none-linux-gnueabihf/arm-none-linux-gnueabihf/sysroot/lib/libstdc++.a matches
Binary file arm-none-linux-gnueabihf/arm-none-linux-gnueabihf/sysroot/lib/libsupc++.a matches
arm-none-linux-gnueabihf/arm-none-linux-gnueabihf/include/c++/6.3.0/cxxabi.h: __cxa_current_exception_type() _GLIBCXX_NOTHROW __attribute__ ((__pure__));
arm-none-linux-gnueabihf/arm-none-linux-gnueabihf/include/c++/6.3.0/future: (*_M_result)->_M_error = current_exception();
arm-none-linux-gnueabihf/arm-none-linux-gnueabihf/include/c++/6.3.0/future: (*_M_result)->_M_error = current_exception();
arm-none-linux-gnueabihf/arm-none-linux-gnueabihf/include/c++/6.3.0/bits/exception_ptr.h: exception_ptr current_exception() _GLIBCXX_USE_NOEXCEPT;
arm-none-linux-gnueabihf/arm-none-linux-gnueabihf/include/c++/6.3.0/bits/exception_ptr.h: friend exception_ptr std::current_exception() _GLIBCXX_USE_NOEXCEPT;
arm-none-linux-gnueabihf/arm-none-linux-gnueabihf/include/c++/6.3.0/bits/exception_ptr.h: return current_exception();
arm-none-linux-gnueabihf/arm-none-linux- gnueabihf/include/c++/6.3.0/bits/nested_exception.h: nested_exception() noexcept : _M_ptr(current_exception()) { }
The settings I used for Crosstool-ng are:
arm-none-linux-gnueabihf/bin/arm-none-linux-gnueabihf-g++ -v
Using built-in specs.
COLLECT_GCC=x-tools/arm-none-linux-gnueabihf/bin/arm-none-linux-gnueabihf-g++
COLLECT_LTO_WRAPPER=/home/builduser/x-tools/arm-none-linux-gnueabihf/libexec/gcc/arm-none-linux-gnueabihf/6.3.0/lto-wrapper
Target: arm-none-linux-gnueabihf
Configured with: /home/builduser/build/.build/src/gcc-6.3.0/configure
--build=x86_64-build_pc-linux-gnu
--host=x86_64-build_pc-linux-gnu
--target=arm-none-linux-gnueabihf
--prefix=/home/builduser/x-tools/arm-none-linux-gnueabihf
--with-sysroot=/home/builduser/x-tools/arm-none-linux-gnueabihf/arm-none-linux-gnueabihf/sysroot
--enable-languages=c,c++
--with-float=hard
--with-pkgversion='crosstool-NG crosstool-ng-1.23.0'
--disable-sjlj-exceptions
--enable-__cxa_atexit
--disable-libmudflap
--disable-libgomp
--disable-libssp
--disable-libquadmath
--disable-libquadmath-support
--disable-libsanitizer
--disable-libmpx
--with-gmp=/home/builduser/build/.build/arm-none-linux-gnueabihf/buildtools
--with-mpfr=/home/builduser/build/.build/arm-none-linux-gnueabihf/buildtools
--with-mpc=/home/builduser/build/.build/arm-none-linux-gnueabihf/buildtools
--with-isl=/home/builduser/build/.build/arm-none-linux-gnueabihf/buildtools
--disable-lto
--with-host-libstdcxx='-static-libgcc -Wl,-Bstatic,-lstdc++ -lm'
--enable-threads=posix
--enable-target-optspace
--disable-plugin
--disable-nls
--disable-multilib
--with-local-prefix=/home/builduser/x-tools/arm-none-linux-gnueabihf/arm-none-linux-gnueabihf/sysroot
--enable-long-long
Thread model: posix
gcc version 6.3.0 (crosstool-NG crosstool-ng-1.23.0)
Building a std::array example works fine.
EDIT:
If I include the CT_ARCH_CPU="cortex-a9" option to my crostool-ng configuration (which leads to a --with-cpu=cortex-a9 within g++) the std::current_exception example works fine.
So the question is:
Why does the cpu variant the compiler should generate code for and the way the cpu variant is told to the toolchain (-mcpu at runtime vs. inbuild --with-cpu) is influencing the ability to compile/link std::current_exception?

sparse - Fixing build warnings

I'm compiling the sparse - linux kernel checking tool.
But it throws the following warning:
lovegcy#knltest-VirtualBox:~/git_root/sparse$ make
GEN version.h
/bin/sh: 1: llvm-config: not found
Makefile:63: Your system does not have libxml, disabling c2xml
Makefile:75: Your system does not have libgtk2, disabling test-inspect
Makefile:79: Your system does not have llvm, disabling sparse-llvm
CC test-lexing.o
CC target.o
CC parse.o
CC tokenize.o
CC pre-process.o
CC symbol.o
CC lib.o
CC scope.o
CC expression.o
CC show-parse.o
CC evaluate.o
CC expand.o
CC inline.o
CC linearize.o
CC char.o
CC sort.o
CC allocate.o
CC compat-linux.o
CC ptrlist.o
CC flow.o
CC cse.o
CC simplify.o
CC memops.o
CC liveness.o
CC storage.o
CC unssa.o
CC dissect.o
AR libsparse.a
LINK test-lexing
CC test-parsing.o
LINK test-parsing
CC obfuscate.o
LINK obfuscate
CC compile.o
CC compile-i386.o
compile-i386.c: In function ‘emit_insn_atom’:
compile-i386.c:719:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
LINK compile
CC graph.o
LINK graph
CC sparse.o
LINK sparse
CC test-linearize.o
LINK test-linearize
CC example.o
LINK example
CC test-unssa.o
LINK test-unssa
CC test-dissect.o
LINK test-dissect
CC ctags.o
LINK ctags
GEN sparse.pc
Fix the following
Makefile:63: Your system does not have libxml, disabling c2xml
Makefile:75: Your system does not have libgtk2, disabling test-inspect
by:
$ sudo apt-get install libxml2-dev libgtk2.0-dev
For
/bin/sh: 1: llvm-config: not found
Makefile:79: Your system does not have llvm, disabling sparse-llvm
the llvm-3.2-dev is installed, but it is still there.
I still donot know how to fix the following warning too:
compile-i386.c: In function ‘emit_insn_atom’:
compile-i386.c:719:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
Could anyone give some suggestions?
Thank you very much!
Update : Following TheCodeArtist's suggestion, here is the build error log after llvm installed.
lovegcy#knltest-VirtualBox:~/git_root/sparse$ make
CC test-lexing.o
CC target.o
CC parse.o
CC tokenize.o
CC pre-process.o
CC symbol.o
CC lib.o
CC scope.o
CC expression.o
CC show-parse.o
CC evaluate.o
CC expand.o
CC inline.o
CC linearize.o
CC char.o
CC sort.o
CC allocate.o
CC compat-linux.o
CC ptrlist.o
CC flow.o
CC cse.o
CC simplify.o
CC memops.o
CC liveness.o
CC storage.o
CC unssa.o
CC dissect.o
AR libsparse.a
LINK test-lexing
CC test-parsing.o
LINK test-parsing
CC obfuscate.o
LINK obfuscate
CC compile.o
CC compile-i386.o
compile-i386.c: In function ‘emit_insn_atom’:
compile-i386.c:719:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
LINK compile
CC graph.o
LINK graph
CC sparse.o
LINK sparse
CC test-linearize.o
LINK test-linearize
CC example.o
LINK example
CC test-unssa.o
LINK test-unssa
CC test-dissect.o
LINK test-dissect
CC ctags.o
LINK ctags
CC c2xml.o
LINK c2xml
CC test-inspect.o
CC ast-model.o
CC ast-view.o
CC ast-inspect.o
LINK test-inspect
CC sparse-llvm.o
LINK sparse-llvm
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(Signals.o): In function PrintStackTrace(void*)':
(.text+0x74): undefined reference todladdr'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(Signals.o): In function PrintStackTrace(void*)':
(.text+0x1fe): undefined reference todladdr'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(Mutex.o): In function llvm::sys::MutexImpl::MutexImpl(bool)':
(.text+0x58): undefined reference topthread_mutexattr_init'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(Mutex.o): In function llvm::sys::MutexImpl::MutexImpl(bool)':
(.text+0x64): undefined reference topthread_mutexattr_settype'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(Mutex.o): In function llvm::sys::MutexImpl::MutexImpl(bool)':
(.text+0x74): undefined reference topthread_mutexattr_setpshared'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(Mutex.o): In function llvm::sys::MutexImpl::MutexImpl(bool)':
(.text+0x88): undefined reference topthread_mutexattr_destroy'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(Mutex.o): In function llvm::sys::MutexImpl::tryacquire()':
(.text+0x179): undefined reference topthread_mutex_trylock'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(RWMutex.o): In function llvm::sys::RWMutexImpl::RWMutexImpl()':
(.text+0x3e): undefined reference topthread_rwlock_init'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(RWMutex.o): In function llvm::sys::RWMutexImpl::~RWMutexImpl()':
(.text+0x80): undefined reference topthread_rwlock_destroy'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(RWMutex.o): In function llvm::sys::RWMutexImpl::reader_acquire()':
(.text+0xb9): undefined reference topthread_rwlock_rdlock'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(RWMutex.o): In function llvm::sys::RWMutexImpl::reader_release()':
(.text+0xe9): undefined reference topthread_rwlock_unlock'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(RWMutex.o): In function llvm::sys::RWMutexImpl::writer_acquire()':
(.text+0x119): undefined reference topthread_rwlock_wrlock'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(RWMutex.o): In function llvm::sys::RWMutexImpl::writer_release()':
(.text+0x149): undefined reference topthread_rwlock_unlock'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(ThreadLocal.o): In function llvm::sys::ThreadLocalImpl::~ThreadLocalImpl()':
(.text+0x25): undefined reference topthread_key_delete'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(ThreadLocal.o): In function llvm::sys::ThreadLocalImpl::ThreadLocalImpl()':
(.text+0xae): undefined reference topthread_key_create'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(ThreadLocal.o): In function llvm::sys::ThreadLocalImpl::setInstance(void const*)':
(.text+0xe2): undefined reference topthread_setspecific'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(ThreadLocal.o): In function llvm::sys::ThreadLocalImpl::getInstance()':
(.text+0x10a): undefined reference topthread_getspecific'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(Threading.o): In function llvm::llvm_execute_on_thread(void (*)(void*), void*, unsigned int)':
(.text+0x1c2): undefined reference topthread_create'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(Threading.o): In function llvm::llvm_execute_on_thread(void (*)(void*), void*, unsigned int)':
(.text+0x1da): undefined reference topthread_join'
/usr/lib/llvm-3.2/lib/libLLVMSupport.a(Threading.o): In function llvm::llvm_execute_on_thread(void (*)(void*), void*, unsigned int)':
(.text+0x20c): undefined reference topthread_attr_setstacksize'
collect2: error: ld returned 1 exit status
make: * [sparse-llvm] Error 1
Properly installing llvm :
During the build, for make to detect llvm on the system ,llvm-config is required to be installed on your system properly. On Ubuntu, the following command will download(~16MB packages) and install all the dependencies correctly
$ sudo apt-get install llvm
Download the latest source of sparse
$ git clone git://git.kernel.org/pub/scm/devel/sparse/sparse.git
Build and install sparse
$ cd sparse
$ make
$ make install
(Tested on Ubuntu 10.04)
Fixing the innocuous Warning :
The following error is harmless in the current context as we are not concerned with the result of the call to write() at line 719 of compile-i386.c
compile-i386.c:719:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
Fixing this error is as simple as modifying line 719 of compile-i386.c to
comment[0] = write(STDOUT_FILENO, s, strlen(s));
This warning is triggered during build due to the -Wall (Enable ALL warnings) flag passed to gcc at line 16 of the Makefile
CFLAGS += -Wall -Wwrite-strings

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