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Failed to install 1.2.1 by pip on Dell Optiplex 5050 («error: conflicting types for ‘_xgetbv’»). Probably problem in compiling if "avx2" in cpu_info["flags"] #398

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belonesox opened this issue Sep 20, 2019 · 8 comments
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Failed to install 1.2.1 by pip on Dell Optiplex 5050 («error: conflicting types for ‘_xgetbv’»). Probably problem in compiling if "avx2" in cpu_info["flags"] #398

belonesox opened this issue Sep 20, 2019 · 8 comments

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@belonesox
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belonesox commented Sep 20, 2019 •
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Failed to install 1.2.1 (also 1.2.0) by pip (pip3, python 3.7) on Fedora 30. —
«c-blosc/blosc/shuffle.c:170:1: error: conflicting types for ‘_xgetbv’»

ternal-complibs/zstd-1.3.4/common -Ic-blosc/internal-complibs/zstd-1.3.4/legacy -Ic-blosc/internal-complibs/zstd-1.3.4/decompress -Ic-blosc/internal-complibs/zstd-1.3.4/dictBuilder -Ic-blosc/internal-complibs/zstd-1.3.4/compress -I/usr/local/lib64/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c c-blosc/blosc/shuffle.c -o build/temp.linux-x86_64-3.7/c-blosc/blosc/shuffle.o -DSHUFFLE_SSE2_ENABLED -msse2 -DSHUFFLE_AVX2_ENABLED -mavx2
    c-blosc/blosc/shuffle.c:170:1: error: conflicting types for ‘_xgetbv’
      170 | _xgetbv(uint32_t xcr) {
          | ^~~~~~~
    In file included from /usr/lib/gcc/x86_64-redhat-linux/9/include/immintrin.h:43,
                     from c-blosc/blosc/blosc-common.h:77,
                     from c-blosc/blosc/shuffle.h:18,
                     from c-blosc/blosc/shuffle.c:10:
    /usr/lib/gcc/x86_64-redhat-linux/9/include/xsaveintrin.h:60:1: note: previous definition of ‘_xgetbv’ was here
       60 | _xgetbv (unsigned int __A)
          | ^~~~~~~
    In file included from c-blosc/blosc/shuffle.c:11:
    c-blosc/blosc/shuffle-generic.h:61:13: warning: ‘unshuffle_generic_inline’ defined but not used [-Wunused-function]
       61 | static void unshuffle_generic_inline(const size_t type_size,
          |             ^~~~~~~~~~~~~~~~~~~~~~~~
    c-blosc/blosc/shuffle-generic.h:32:13: warning: ‘shuffle_generic_inline’ defined but not used [-Wunused-function]
       32 | static void shuffle_generic_inline(const size_t type_size,
          |             ^~~~~~~~~~~~~~~~~~~~~~
    error: command 'gcc' failed with exit status 1
@belonesox belonesox changed the title Failed to install 1.2.1 by pip on Fedora 30 («error: conflicting types for ‘_xgetbv’») Failed to install 1.2.1 by pip on Dell Optiplex 5050 («error: conflicting types for ‘_xgetbv’») Sep 30, 2019
@belonesox
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Actually, the problem not in Linux Distro, but in target architecture.
I tried to install on Dell Optiplex 5050, and the problem in supporting "avx2" in cpu_info["flags"].
I cannot fix the bug, but found workaround (after enumeration all possible flags) → add to setup.py
after the block

# For guessing the capabilities of the CPU for C-Blosc
try:
    # Currently just Intel and some ARM archs are supported by cpuinfo module
    import cpuinfo
    cpu_info = cpuinfo.get_cpu_info()
except:
    cpu_info = {'flags': []}

something like this:

flags_ = cpu_info["flags"]
flags_.remove("avx2")

@belonesox belonesox changed the title Failed to install 1.2.1 by pip on Dell Optiplex 5050 («error: conflicting types for ‘_xgetbv’») Failed to install 1.2.1 by pip on Dell Optiplex 5050 («error: conflicting types for ‘_xgetbv’»). Probably problem in compiling if "avx2" in cpu_info["flags"] Sep 30, 2019
@simon-castano
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simon-castano commented Dec 6, 2019 •
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I confirm facing the same issue on a computer running Ubuntu 19.10 with Core™ i7-10510U CPU.
Note that bcolz v1.1.1 do compile without issue on the very same system.

jdavid added a commit to jdavid/reflexible that referenced this issue Jan 29, 2020
@jdavid
Do not require bcolz
cdc8666 
bcolz has build/install problems, e.g.
Blosc/bcolz#398
@javadr
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javadr commented Feb 7, 2020

I confirm the same issue with 1.2.2 (also all the other versions) by pip (pip3, python 3.7) on Fedora 31.
«c-blosc/blosc/shuffle.c:170:1: error: conflicting types for ‘_xgetbv’»

Is there any way to bypass the error and get installed the package?

Collecting bcolz
Using cached bcolz-1.2.1.tar.gz (1.5 MB)
Requirement already satisfied: numpy>=1.7 in /usr/local/lib64/python3.7/site-packages (from bcolz) (1.18.1)
Building wheels for collected packages: bcolz
Building wheel for bcolz (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-_dm1gcei/bcolz/setup.py'"'"'; __file__='"'"'/tmp/pip-install-_dm1gcei/bcolz/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-ckm5pl6i         
cwd: /tmp/pip-install-_dm1gcei/bcolz/                                                         
Complete output (86 lines):                                                                        
SSE2 detected                                                                                      
AVX2 detected                                                                                      
running bdist_wheel                                                                                
running build                                                                                      
running build_py                                                                                   
creating build                                                                                     
creating build/lib.linux-x86_64-3.7                                                                
creating build/lib.linux-x86_64-3.7/bcolz                                                          
copying bcolz/arrayprint.py -> build/lib.linux-x86_64-3.7/bcolz                                    
copying bcolz/py2help.py -> build/lib.linux-x86_64-3.7/bcolz                                       
copying bcolz/attrs.py -> build/lib.linux-x86_64-3.7/bcolz                                         
copying bcolz/defaults.py -> build/lib.linux-x86_64-3.7/bcolz                                      
copying bcolz/chunked_eval.py -> build/lib.linux-x86_64-3.7/bcolz                                  
copying bcolz/utils.py -> build/lib.linux-x86_64-3.7/bcolz                                         
copying bcolz/__init__.py -> build/lib.linux-x86_64-3.7/bcolz                                      
copying bcolz/ctable.py -> build/lib.linux-x86_64-3.7/bcolz                                        
copying bcolz/toplevel.py -> build/lib.linux-x86_64-3.7/bcolz                                      
copying bcolz/version.py -> build/lib.linux-x86_64-3.7/bcolz                                       
copying bcolz/py2help_tests.py -> build/lib.linux-x86_64-3.7/bcolz                                 
creating build/lib.linux-x86_64-3.7/bcolz/tests                                                    
copying bcolz/tests/test_carray.py -> build/lib.linux-x86_64-3.7/bcolz/tests                       
copying bcolz/tests/test_ctable.py -> build/lib.linux-x86_64-3.7/bcolz/tests                       
copying bcolz/tests/test_queries.py -> build/lib.linux-x86_64-3.7/bcolz/tests                      
copying bcolz/tests/common.py -> build/lib.linux-x86_64-3.7/bcolz/tests                            
copying bcolz/tests/all.py -> build/lib.linux-x86_64-3.7/bcolz/tests                               
copying bcolz/tests/__init__.py -> build/lib.linux-x86_64-3.7/bcolz/tests                          
copying bcolz/tests/test_attrs.py -> build/lib.linux-x86_64-3.7/bcolz/tests                        
copying bcolz/tests/test_carray_objects.py -> build/lib.linux-x86_64-3.7/bcolz/tests               
copying bcolz/tests/test_ndcarray.py -> build/lib.linux-x86_64-3.7/bcolz/tests                     
copying bcolz/carray_ext.pxd -> build/lib.linux-x86_64-3.7/bcolz                                   
running build_ext                                                                                  
skipping 'bcolz/carray_ext.c' Cython extension (up-to-date)                                        
building 'bcolz.carray_ext' extension                                                              
creating build/temp.linux-x86_64-3.7                                                               
creating build/temp.linux-x86_64-3.7/bcolz                                                         
creating build/temp.linux-x86_64-3.7/c-blosc                                                       
creating build/temp.linux-x86_64-3.7/c-blosc/blosc                                                 
creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs                                     
creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/lz4-1.8.1.2                         
creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/snappy-1.1.1                        
creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zlib-1.2.8                          
creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4                          
creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/deprecated               
creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/common                   
creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/legacy                   
creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/decompress               
creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/dictBuilder              
creating build/temp.linux-x86_64-3.7/c-blosc/internal-complibs/zstd-1.3.4/compress                 
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ibcolz -Ic-blosc/blosc -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/lz4-1.8.1.2 -Ic-blosc/internal-complibs/zstd-1.3.4-Ic-blosc/internal-complibs/zstd-1.3.4/deprecated -Ic-blosc/internal-complibs/zstd-1.3.4/dll -Ic-blosc/internal-complibs/zstd-1.3.4/common -Ic-blosc/internal-complibs/zstd-1.3.4/legacy -Ic-blosc/internal-complibs/zstd-1.3.4/decompress -Ic-blosc/internal-complibs/zstd-1.3.4/dictBuilder -Ic-blosc/internal-complibs/zstd-1.3.4/compress -I/usr/local/lib64/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c bcolz/carray_ext.c -o build/temp.linux-x86_64-3.7/bcolz/carray_ext.o -DSHUFFLE_SSE2_ENABLED -msse2 -DSHUFFLE_AVX2_ENABLED -mavx2                                                    
In file included from /usr/local/lib64/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832,                                                                                            
from /usr/local/lib64/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,                                                                                             
from /usr/local/lib64/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,                                                                                                
from bcolz/carray_ext.c:525:                                                      
/usr/local/lib64/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]                                                                                
17 | #warning "Using deprecated NumPy API, disable it with " \                                  
|  ^~~~~~~                                                                                   
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ibcolz -Ic-blosc/blosc -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/lz4-1.8.1.2 -Ic-blosc/internal-complibs/zstd-1.3.4-Ic-blosc/internal-complibs/zstd-1.3.4/deprecated -Ic-blosc/internal-complibs/zstd-1.3.4/dll -Ic-blosc/internal-complibs/zstd-1.3.4/common -Ic-blosc/internal-complibs/zstd-1.3.4/legacy -Ic-blosc/internal-complibs/zstd-1.3.4/decompress -Ic-blosc/internal-complibs/zstd-1.3.4/dictBuilder -Ic-blosc/internal-complibs/zstd-1.3.4/compress -I/usr/local/lib64/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c c-blosc/blosc/shuffle-generic.c -o build/temp.linux-x86_64-3.7/c-blosc/blosc/shuffle-generic.o -DSHUFFLE_SSE2_ENABLED -msse2 -DSHUFFLE_AVX2_ENABLED -mavx2                          
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ibcolz -Ic-blosc/blosc -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/lz4-1.8.1.2 -Ic-blosc/internal-complibs/zstd-1.3.4-Ic-blosc/internal-complibs/zstd-1.3.4/deprecated -Ic-blosc/internal-complibs/zstd-1.3.4/dll -Ic-blosc/internal-complibs/zstd-1.3.4/common -Ic-blosc/internal-complibs/zstd-1.3.4/legacy -Ic-blosc/internal-complibs/zstd-1.3.4/decompress -Ic-blosc/internal-complibs/zstd-1.3.4/dictBuilder -Ic-blosc/internal-complibs/zstd-1.3.4/compress -I/usr/local/lib64/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c c-blosc/blosc/blosclz.c -o build/temp.linux-x86_64-3.7/c-blosc/blosc/blosclz.o -DSHUFFLE_SSE2_ENABLED -msse2 -DSHUFFLE_AVX2_ENABLED -mavx2                                          
c-blosc/blosc/blosclz.c: In function ‘get_run_32’:                                                 
c-blosc/blosc/blosclz.c:148:35: warning: comparison of integer expressions of different signedness:‘int’ and ‘unsigned int’ [-Wsign-compare]                                                           
148 |     if (_mm256_movemask_epi8(cmp) != 0xFFFFFFFF) {                                         
|                                   ^~                                                       
c-blosc/blosc/blosclz.c: In function ‘get_match_32’:                                               
c-blosc/blosc/blosclz.c:219:35: warning: comparison of integer expressions of different signedness:‘int’ and ‘unsigned int’ [-Wsign-compare]                                                           
219 |     if (_mm256_movemask_epi8(cmp) != 0xFFFFFFFF) {                                         
|                                   ^~                                                       
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ibcolz -Ic-blosc/blosc -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/lz4-1.8.1.2 -Ic-blosc/internal-complibs/zstd-1.3.4-Ic-blosc/internal-complibs/zstd-1.3.4/deprecated -Ic-blosc/internal-complibs/zstd-1.3.4/dll -Ic-blosc/internal-complibs/zstd-1.3.4/common -Ic-blosc/internal-complibs/zstd-1.3.4/legacy -Ic-blosc/internal-complibs/zstd-1.3.4/decompress -Ic-blosc/internal-complibs/zstd-1.3.4/dictBuilder -Ic-blosc/internal-complibs/zstd-1.3.4/compress -I/usr/local/lib64/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c c-blosc/blosc/fastcopy.c -o build/temp.linux-x86_64-3.7/c-blosc/blosc/fastcopy.o -DSHUFFLE_SSE2_ENABLED -msse2 -DSHUFFLE_AVX2_ENABLED -mavx2                                        
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DHAVE_LZ4=1 -DHAVE_SNAPPY=1 -DHAVE_ZLIB=1 -DHAVE_ZSTD=1 -Ibcolz -Ic-blosc/blosc -Ic-blosc/internal-complibs/zlib-1.2.8 -Ic-blosc/internal-complibs/snappy-1.1.1 -Ic-blosc/internal-complibs/lz4-1.8.1.2 -Ic-blosc/internal-complibs/zstd-1.3.4-Ic-blosc/internal-complibs/zstd-1.3.4/deprecated -Ic-blosc/internal-complibs/zstd-1.3.4/dll -Ic-blosc/internal-complibs/zstd-1.3.4/common -Ic-blosc/internal-complibs/zstd-1.3.4/legacy -Ic-blosc/internal-complibs/zstd-1.3.4/decompress -Ic-blosc/internal-complibs/zstd-1.3.4/dictBuilder -Ic-blosc/internal-complibs/zstd-1.3.4/compress -I/usr/local/lib64/python3.7/site-packages/numpy/core/include -I/usr/include/python3.7m -c c-blosc/blosc/shuffle.c -o build/temp.linux-x86_64-3.7/c-blosc/blosc/shuffle.o -DSHUFFLE_SSE2_ENABLED -msse2 -DSHUFFLE_AVX2_ENABLED -mavx2                                          
c-blosc/blosc/shuffle.c:170:1: error: conflicting types for ‘_xgetbv’                              
170 | _xgetbv(uint32_t xcr) {                                                                    
| ^~~~~~~                                                                                    
In file included from /usr/lib/gcc/x86_64-redhat-linux/9/include/immintrin.h:43,                   
from c-blosc/blosc/blosc-common.h:77,                                             
from c-blosc/blosc/shuffle.h:18,                                                  
from c-blosc/blosc/shuffle.c:10:                                                  
/usr/lib/gcc/x86_64-redhat-linux/9/include/xsaveintrin.h:60:1: note: previous definition of ‘_xgetbv’ was here                                                                                          
60 | _xgetbv (unsigned int __A)                                                                 
| ^~~~~~~                                                                                    
In file included from c-blosc/blosc/shuffle.c:11:                                                  
c-blosc/blosc/shuffle-generic.h:61:13: warning: ‘unshuffle_generic_inline’ defined but not used [-Wunused-function]                                                                                     
61 | static void unshuffle_generic_inline(const size_t type_size,                               
|             ^~~~~~~~~~~~~~~~~~~~~~~~                                                       
c-blosc/blosc/shuffle-generic.h:32:13: warning: ‘shuffle_generic_inline’ defined but not used [-Wunused-function]                                                                                       
32 | static void shuffle_generic_inline(const size_t type_size,                                 
|             ^~~~~~~~~~~~~~~~~~~~~~                                                         
error: command 'gcc' failed with exit status 1                                                     
----------------------------------------                                                           
ERROR: Failed building wheel for bcolz

@belonesox
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Is there any way to bypass the error and get installed the package?

My workaround → #398 (comment)

@e0lithic
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@belonesox I tried using your workaround. However that results in the following error

cythoning bcolz/carray_ext.pyx to bcolz/carray_ext.c
    /tmp/pip-req-build-8dm5a1w2/.eggs/Cython-3.0a5-py3.6.egg/Cython/Compiler/Main.py:344: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-req-build-8dm5a1w2/bcolz/carray_ext.pxd
      tree = Parsing.p_module(s, pxd, full_module_name)
    
    Error compiling Cython file:
    ------------------------------------------------------------
    ...
            # Create the final container and fill it
            out = carray([], dtype=newdtype, cparams=self.cparams,
                           expectedlen=newlen,
                           rootdir=rootdir, mode='w')
            if newlen < ilen:
                rsize = isize / newlen
                             ^
    ------------------------------------------------------------
    bcolz/carray_ext.pyx:1685:26: Cannot assign type 'double' to 'npy_intp'

@nevezhyn
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nevezhyn commented Sep 25, 2020 •
edited
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I had the same issue on Dell Latitude 4790 (Ubuntu 20.04).
I was able to install the package v1.2.1 with the following commands:

export DISABLE_BCOLZ_AVX2=true
python setup.py build_ext --inplace

@H-steven
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H-steven commented Oct 2, 2020

I had the same issue on Dell Latitude 4790 (Ubuntu 20.04).
I was able to install the package v1.2.1 with the following commands:

export DISABLE_BCOLZ_AVX2=true
python setup.py build_ext --inplace

Thank you. It works

@sanromd
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sanromd commented Dec 4, 2020

I had the same issue on Dell Latitude 4790 (Ubuntu 20.04).
I was able to install the package v1.2.1 with the following commands:

export DISABLE_BCOLZ_AVX2=true
python setup.py build_ext --inplace

@nevezhyn thanks. this solved it for me in an MSI laptop (Pop OS 20.10)

shlomiku added a commit to shlomiku/zipline-trader that referenced this issue Dec 20, 2020
@shlomiku
ci:: bcolz on mac. trying to disable AVX2
8c29985 
Blosc/bcolz#398
@agroszer agroszer mentioned this issue Jan 16, 2021
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@sanromd @javadr @belonesox @e0lithic @H-steven @nevezhyn @simon-castano