Failed to install ta-lib in AWS Arm Instance #514

2shou · 2022-04-17T15:06:06Z

Linux Dependencies has been installed. However, After I ran the command pip install TA-Lib, GCC Compile Errors happened.

(base) ➜  ta-lib pip install TA-Lib
Collecting TA-Lib
  Using cached TA-Lib-0.4.24.tar.gz (269 kB)
Requirement already satisfied: numpy in /home/ec2-user/anaconda3/lib/python3.9/site-packages (from TA-Lib) (1.20.3)
Building wheels for collected packages: TA-Lib
  Building wheel for TA-Lib (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/ec2-user/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-yubw63il/ta-lib_50b89ce5bffc4b918ebafdc561bef6c8/setup.py'"'"'; __file__='"'"'/tmp/pip-install-yubw63il/ta-lib_50b89ce5bffc4b918ebafdc561bef6c8/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'"'"'))' bdist_wheel -d /tmp/pip-wheel-9voq58u3
       cwd: /tmp/pip-install-yubw63il/ta-lib_50b89ce5bffc4b918ebafdc561bef6c8/
  Complete output (27 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-aarch64-cpython-39
  creating build/lib.linux-aarch64-cpython-39/talib
  copying talib/__init__.py -> build/lib.linux-aarch64-cpython-39/talib
  copying talib/abstract.py -> build/lib.linux-aarch64-cpython-39/talib
  copying talib/deprecated.py -> build/lib.linux-aarch64-cpython-39/talib
  copying talib/stream.py -> build/lib.linux-aarch64-cpython-39/talib
  copying talib/test_abstract.py -> build/lib.linux-aarch64-cpython-39/talib
  copying talib/test_data.py -> build/lib.linux-aarch64-cpython-39/talib
  copying talib/test_func.py -> build/lib.linux-aarch64-cpython-39/talib
  copying talib/test_pandas.py -> build/lib.linux-aarch64-cpython-39/talib
  copying talib/test_polars.py -> build/lib.linux-aarch64-cpython-39/talib
  copying talib/test_stream.py -> build/lib.linux-aarch64-cpython-39/talib
  running build_ext
  skipping 'talib/_ta_lib.c' Cython extension (up-to-date)
  building 'talib._ta_lib' extension
  creating build/temp.linux-aarch64-cpython-39
  creating build/temp.linux-aarch64-cpython-39/talib
  gcc -pthread -B /home/ec2-user/anaconda3/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -n1 .2-a+fp16+rcpc+dotprod+crypto -isystem /home/ec2-user/anaconda3/include -I/home/ec2-user/anaconda3/include -fPIC -O2 -n1 .2-a+fp16+rcpc+dotprod+crypto -isystem /home/ec2-user/anaconda3/include -fPIC -I/usr/include -I/usr/local/include -I/opt/include -I/opt/local/include -I/opt/homebrew/include -I/opt/homebrew/opt/ta-lib/include -I/home/ec2-user/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/home/ec2-user/anaconda3/include/python3.9 -c talib/_ta_lib.c -o build/temp.linux-aarch64-cpython-39/talib/_ta_lib.o
  gcc: Error: .2-a+fp16+rcpc+dotprod+crypto：No such file or directory
  gcc: Error: .2-a+fp16+rcpc+dotprod+crypto：No such file or directory
  gcc: Error: unrecognized command line option ‘-n1’; did you mean ‘-n’?
  gcc: Error: unrecognized command line option ‘-n1’; did you mean ‘-n’?
  error: command '/usr/bin/gcc' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for TA-Lib

The text was updated successfully, but these errors were encountered:

mrjbq7 · 2022-04-17T15:09:40Z

I haven't seen that gcc error before -- perhaps check and make sure you have the latest setuptools?

mrjbq7 · 2022-04-17T15:12:01Z

It's also possible that it's related to PEP 517?

https://peps.python.org/pep-0517/

2shou · 2022-04-17T15:38:12Z

I haven't seen that gcc error before -- perhaps check and make sure you have the latest setuptools?

Yes. I have updated setuptools to 62.1.0 but all the same.

2shou · 2022-04-17T15:45:50Z

Switch my Linux system to Debian but all the same.

trufanov-nok · 2022-04-17T15:50:37Z

There was a similar issue: #505
I'm suspecting that CFLAGS variable gets some wierd input and malformed, but can't debug to verify.

2shou · 2022-04-17T16:03:16Z

There was a similar issue: #505 I'm suspecting that CFLAGS variable gets some wierd input and malformed, but can't debug to verify.

So how to fix the CFLAGS variable?

trufanov-nok · 2022-04-17T17:54:33Z

Could you execute in python:

import distutils.sysconfig
distutils.sysconfig.get_config_vars()

and show the output? Upload it to pastebin if too long.

2shou · 2022-04-18T01:57:46Z

Could you execute in python:
import distutils.sysconfig
distutils.sysconfig.get_config_vars()
and show the output? Upload it to pastebin if too long.

{'prefix': '/home/ec2-user/anaconda3', 'exec_prefix': '/home/ec2-user/anaconda3', 'py_version': '3.9.7', 'py_version_short': '3.9', 'py_version_nodot': '39', 'installed_base': '/home/ec2-user/anaconda3', 'base': '/home/ec2-user/anaconda3', 'installed_platbase': '/home/ec2-user/anaconda3', 'platbase': '/home/ec2-user/anaconda3', 'projectbase': '/home/ec2-user/anaconda3/bin', 'platlibdir': 'lib', 'abiflags': '', 'ABIFLAGS': '', 'AC_APPLE_UNIVERSAL_BUILD': 0, 'AIX_BUILDDATE': 0, 'AIX_GENUINE_CPLUSPLUS': 0, 'ALT_SOABI': 0, 'ANDROID_API_LEVEL': 0, 'AR': 'ar', 'ARFLAGS': 'rcs', 'BASECFLAGS': '-Wno-unused-result -Wsign-compare', 'BASECPPFLAGS': '-IObjects -IInclude -IPython', 'BASEMODLIBS': '', 'BINDIR': '/home/ec2-user/anaconda3/bin', 'BINLIBDEST': '/home/ec2-user/anaconda3/lib/python3.9', 'BLDLIBRARY': 'libpython3.9.a', 'BLDSHARED': 'gcc -pthread -B /home/ec2-user/anaconda3/compiler_compat -shared -Wl,-rpath,/home/ec2-user/anaconda3/lib -Wl,-rpath-link,/home/ec2-user/anaconda3/lib -L/home/ec2-user/anaconda3/lib -L/home/ec2-user/anaconda3/lib -Wl,-rpath,/home/ec2-user/anaconda3/lib -Wl,-rpath-link,/home/ec2-user/anaconda3/lib -L/home/ec2-user/anaconda3/lib', 'BUILDEXE': '', 'BUILDPYTHON': 'python', 'BUILD_GNU_TYPE': 'aarch64-conda_cos7-linux-gnu', 'BYTESTR_DEPS': '\', 'CC': 'gcc -pthread -B /home/ec2-user/anaconda3/compiler_compat', 'CCSHARED': '-fPIC', 'CFLAGS': '-Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -n1 .2-a+fp16+rcpc+dotprod+crypto -isystem /home/ec2-user/anaconda3/include -I/home/ec2-user/anaconda3/include -fPIC -O2 -n1 .2-a+fp16+rcpc+dotprod+crypto -isystem /home/ec2-user/anaconda3/include ', 'CFLAGSFORSHARED': '', 'CFLAGS_ALIASING': '', 'CONFIGFILES': 'configure configure.ac acconfig.h pyconfig.h.in Makefile.pre.in', 'CONFIGURE_CFLAGS': ' -fPIC -O2 -n1 .2-a+fp16+rcpc+dotprod+crypto -isystem /home/ec2-user/anaconda3/include -I/home/ec2-user/anaconda3/include', 'CONFIGURE_CFLAGS_NODIST': ' -g -std=c99 -Wextra -Wno-unused-result 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'--with-openssl=/home/ec2-user/anaconda3' 'PKG_CONFIG_LIBDIR=/home/ec2-user/anaconda3/lib' 'PKG_CONFIG_PATH=/home/ec2-user/anaconda3/lib' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/ec2-user/anaconda3/include -I/home/ec2-user/anaconda3/include -I/home/ec2-user/anaconda3/include' 'CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -fPIC -O2 -n1 .2-a+fp16+rcpc+dotprod+crypto -isystem /home/ec2-user/anaconda3/include -I/home/ec2-user/anaconda3/include' 'CFLAGS= -fPIC -O2 -n1 .2-a+fp16+rcpc+dotprod+crypto -isystem /home/ec2-user/anaconda3/include -I/home/ec2-user/anaconda3/include' 'LDFLAGS= -Wl,-rpath,/home/ec2-user/anaconda3/lib -Wl,-rpath-link,/home/ec2-user/anaconda3/lib -L/home/ec2-user/anaconda3/lib -L/home/ec2-user/anaconda3/lib' 'CC= gcc' 'CXX=g++''--with-lto' '--enable-optimizations' '-oldincludedir=/usr/include' '--disable-shared''PROFILE_TASK=-m test --pgo' 'build_alias=aarch64-conda_cos7-linux-gnu' 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trufanov-nok · 2022-04-18T05:47:04Z

What's the output for: python --version and gcc -v ?

2shou · 2022-04-18T06:04:03Z

What's the output for: python --version and gcc -v ?

(base) ➜  ~ python --version
Python 3.9.7
(base) ➜  ~ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-redhat-linux/7/lto-wrapper
Target: aarch64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,objc,obj-c++,fortran,ada,go,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --disable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl --disable-libmpx --enable-libsanitizer --enable-gnu-indirect-function --disable-libcilkrts --enable-libatomic --disable-libquadmath --enable-libitm --build=aarch64-redhat-linux
Thread model: posix
gcc version 7.3.1 20180712 (Red Hat 7.3.1-13) (GCC)

trufanov-nok · 2022-04-18T06:29:21Z

Well, it would be interesting to dig into this further, but it's too inconvenient without access to the system. Anyway, as you can see there are a lot of " -n1 .2-a+fp16+rcpc+dotprod+crypto " right in distutils.sysconfig.get_config_vars() output which means a Python itself is misconfigured. Probably this build of Anaconda3 is misconfigured. The problem is deep inside and I guess setuptools doesn't allow to override these flags, just to add something to them. So it can't be workarounded.

There is a helpful discussion re this problem here: https://githubhelp.com/tuwien-cms/xprec/issues/1

It seems to be related to Graviton2 CPUs from Amazon. To enable " Arm Architecture Specific Features" this processor requires "-march=armv8.2-a+fp16+rcpc+dotprod+crypto" and "-mtune=neoverse-n1": https://github.com/aws/aws-graviton-getting-started/blob/main/c-c++.md

Probably Anaconda3 was configured with them but something went wrong after that.
It's hard to say there exactly the command line got broken. I guess a good point to start would be raising this issue for AWS support team as no any python module that requires C/CPP code compilation could be installed on their system.

2shou · 2022-04-18T07:03:58Z

ok, i will take issues to amazon support team. but, i tried to install xgboost today which also have c++ compiling and it worked finally. will another version of anaconda be useful?

trufanov-nok · 2022-04-18T07:35:47Z

Try

sudo pip uninstall xgboost
sudo pip install --no-binary :all: xgboost

this is supposed to skip prebuild binary and force installing via setup.py. What's the output?

will another version of anaconda be useful?

If AWS suggests other version or allows to replace it - you may try it. Or if there is a virtual machine with other CPU than Graviton2 - that might also help.

2shou · 2022-04-18T08:45:01Z

Try
sudo pip uninstall xgboost
sudo pip install --no-binary :all: xgboost
this is supposed to skip prebuild binary and force installing via setup.py. What's the output?

will another version of anaconda be useful?

If AWS suggests other version or allows to replace it - you may try it. Or if there is a virtual machine with other CPU than Graviton2 - that might also help.

It's OK for xgboost.

(base) ➜  ~ pip uninstall xgboost
Found existing installation: xgboost 2.0.0.dev0
Uninstalling xgboost-2.0.0.dev0:
  Would remove:
    /home/ec2-user/anaconda3/lib/python3.9/site-packages/xgboost
    /home/ec2-user/anaconda3/lib/python3.9/site-packages/xgboost-2.0.0.dev0-py3.9.egg-info
Proceed (Y/n)? y
  Successfully uninstalled xgboost-2.0.0.dev0
(base) ➜  ~ pip install --no-binary :all: xgboost
Collecting xgboost
  Downloading xgboost-1.6.0.tar.gz (775 kB)
     |████████████████████████████████| 775 kB 24.2 MB/s
Requirement already satisfied: numpy in ./anaconda3/lib/python3.9/site-packages (from xgboost) (1.20.3)
Requirement already satisfied: scipy in ./anaconda3/lib/python3.9/site-packages (from xgboost) (1.7.1)
Skipping wheel build for xgboost, due to binaries being disabled for it.
Installing collected packages: xgboost
    Running setup.py install for xgboost ... done
Successfully installed xgboost-1.6.0

feeloho · 2022-04-18T11:08:19Z

Me too

cat /etc/redhat-release CentOS Linux release 7.7.1908 (Core)

trufanov-nok · 2022-04-18T11:25:59Z

I'm not a python expert (I'm a c++ developer), but it looks like xgboost is working because they are not using C/CPP code in the wrapper at all. They are not using cython. They are using ctypes module to call C library functions. As for the core library itself (which is in C) - they're defined a custom build steps for setuptools and these build steps just call a cmake/make or a cmake/ninja, so CMake buildchain decides which arguments are needed to be passed to the compiler, and no any hardcoded defaults from sysinfo are used.

TA-Lib is built with CMake too, but it's distributed as an already built binary anyway. And the only problem is that wrapper uses C code and no any smart buildsystem is used to compile it - it just build with a setuptools' default compiler which uses default (hardcoded in python) arguments.

Does this have a sense @mrjbq7 ?

trufanov-nok · 2022-04-18T14:25:15Z

Perhaps I can suggest a workaround.

Find the right sysconfig.py for your python 3.9.7 with locate distutils/sysconfig.py.
Edit it (might require sudo) in a following way: find lines

        if 'CFLAGS' in os.environ:
            cflags = cflags + ' ' + os.environ['CFLAGS']
            ldshared = ldshared + ' ' + os.environ['CFLAGS']
        elif configure_cflags:
            cflags = cflags + ' ' + configure_cflags
            ldshared = ldshared + ' ' + configure_cflags
        if 'CPPFLAGS' in os.environ:
            cpp = cpp + ' ' + os.environ['CPPFLAGS']
            cflags = cflags + ' ' + os.environ['CPPFLAGS']
            ldshared = ldshared + ' ' + os.environ['CPPFLAGS']
        elif configure_cppflags:
            cpp = cpp + ' ' + configure_cppflags
            cflags = cflags + ' ' + configure_cppflags
            ldshared = ldshared + ' ' + configure_cppflags

And insert AFTER them lines

        if 'CFLAGS2' in os.environ:
            cflags = os.environ['CFLAGS2']

This will introduce CFLAGS2 environment variable that will completely override CFLAGS defaults.

Get a copy of TA-Lib wrapper sources with

git clone https://github.com/mrjbq7/ta-lib.git
cd ta-lib

Install the TA-Lib wrapper manually with
sudo CFLAGS2="-pthread -B /home/ec2-user/anaconda3/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -isystem /home/ec2-user/anaconda3/include -I/home/ec2-user/anaconda3/include" python setup.py install

This should work.

2shou · 2022-04-19T02:28:30Z

Finally I switched to System Python and installed ta-lib successfully.

mrjbq7 · 2022-07-27T10:22:59Z

Please let me know if there is anything I should document or change as a result of your issues here. In the meantime, I'm going to close this bug.

RaoTianlong · 2022-09-13T03:54:03Z

Perhaps I can suggest a workaround.

Find the right sysconfig.py for your python 3.9.7 with locate distutils/sysconfig.py.

Edit it (might require sudo) in a following way: find lines
        if 'CFLAGS' in os.environ:
            cflags = cflags + ' ' + os.environ['CFLAGS']
            ldshared = ldshared + ' ' + os.environ['CFLAGS']
        elif configure_cflags:
            cflags = cflags + ' ' + configure_cflags
            ldshared = ldshared + ' ' + configure_cflags
        if 'CPPFLAGS' in os.environ:
            cpp = cpp + ' ' + os.environ['CPPFLAGS']
            cflags = cflags + ' ' + os.environ['CPPFLAGS']
            ldshared = ldshared + ' ' + os.environ['CPPFLAGS']
        elif configure_cppflags:
            cpp = cpp + ' ' + configure_cppflags
            cflags = cflags + ' ' + configure_cppflags
            ldshared = ldshared + ' ' + configure_cppflags
And insert AFTER them lines
        if 'CFLAGS2' in os.environ:
            cflags = os.environ['CFLAGS2']
This will introduce CFLAGS2 environment variable that will completely override CFLAGS defaults.

Get a copy of TA-Lib wrapper sources with
git clone https://github.com/mrjbq7/ta-lib.git
cd ta-lib
Install the TA-Lib wrapper manually with
sudo CFLAGS2="-pthread -B /home/ec2-user/anaconda3/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -isystem /home/ec2-user/anaconda3/include -I/home/ec2-user/anaconda3/include" python setup.py install

This should work.

not work T^T

trufanov-nok · 2022-09-13T09:15:08Z

@RaoTianlong could you explain what exactly is not working?

geoffreyblake · 2022-12-11T15:30:29Z

This appears to be an anaconda python specific bug on AArch64.
See: ContinuumIO/anaconda-issues#13106
and: https://stackoverflow.com/questions/74739356/python-cant-install-ta-lib-in-oracle-arm64-vm-ubuntu-20-04/74749125#74749125
For more detailed explanation and workaround.

Short story is lib/python3.9/_sysconfigdata__linux_aarch64-linux-gnu.py is mal-formed with the latest Anaconda, if you edit that file to correct the mal-formed CFLAGS, everything will work.

timkpaine mentioned this issue Apr 24, 2022

Failed building wheel for bt issue pmorissette/bt#272

Closed

mrjbq7 closed this as completed Jul 27, 2022

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Failed to install ta-lib in AWS Arm Instance #514

Failed to install ta-lib in AWS Arm Instance #514

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Failed to install ta-lib in AWS Arm Instance #514

Failed to install ta-lib in AWS Arm Instance #514

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