Make error

Question

Make error

Closed this issue 2 years ago · 14 comments

When attempting to mix deps.get I'm getting this error:

==> ex_faiss
Using cached faiss build...
g++ -I/opt/homebrew/Cellar/erlang/25.2.2/lib/erlang/erts-13.1.4/include -I/Users/jamilabreu/.cache/ex_faiss/faiss-19f7696deedc93615c3ee0ff4de22284b53e0243 -fPIC -O3 -shared -std=c++14 c_src/ex_faiss.cc c_src/ex_faiss/nif_util.cc c_src/ex_faiss/index.cc \
        c_src/ex_faiss/clustering.cc -o cache/libex_faiss.so -L/Users/jamilabreu/.cache/ex_faiss/faiss-19f7696deedc93615c3ee0ff4de22284b53e0243/build/faiss -lfaiss -flat_namespace -undefined suppress

ld: library not found for -lfaiss
collect2: error: ld returned 1 exit status
make: *** [Makefile:54: cache/libex_faiss.so] Error 1
could not compile dependency :ex_faiss, "mix compile" failed. Errors may have been logged above. You can recompile this dependency with "mix deps.compile ex_faiss", update it with "mix deps.update ex_faiss" or clean it with "mix deps.clean ex_faiss"

** (Mix) Could not compile with "make" (exit status: 2).
You need to have gcc and make installed. Try running the
commands "gcc --version" and / or "make --version". If these programs
are not installed, you will be prompted to install them.

gcc --version                                            
Apple clang version 14.0.0 (clang-1400.0.29.202)
Target: arm64-apple-darwin22.1.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

make --version
GNU Make 4.4
Built for aarch64-apple-darwin22.1.0
Copyright (C) 1988-2022 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

I'm on a new Apple M2, @seanmor5 any ideas?

Answer 1 · 2023-02-10T09:24:52.000Z

Added the following to my .zshrc file:

export CC="/opt/homebrew/bin/gcc-12"
export CXX="/opt/homebrew/bin/g++-12"

Now getting this error:

[100%] Linking CXX shared library libfaiss.dylib
Undefined symbols for architecture arm64:
  "__Z10vpaddq_f3213__Float32x4_tS_", referenced from:
      __ZN5faiss4haddERKNS_12simd8float32ES2_ in distances_simd.cpp.o
  "__Z10vqtbl1q_u812__Uint8x16_tS_", referenced from:
      __ZNK5faiss11simd32uint814lookup_2_lanesERKS0_ in pq4_fast_scan_search_1.cpp.o
      __ZNK5faiss11simd32uint814lookup_2_lanesERKS0_ in pq4_fast_scan_search_qbs.cpp.o
  "__Z11vdupq_n_u16t", referenced from:
      __ZN5faiss12simd16uint165clearEv in pq4_fast_scan_search_1.cpp.o
      __ZN5faiss12simd16uint165clearEv in pq4_fast_scan_search_qbs.cpp.o
  "__Z8vandq_u812__Uint8x16_tS_", referenced from:
      __ZNK5faiss11simd32uint8anIS0_LDnEEES0_RKT_ in pq4_fast_scan_search_1.cpp.o
      __ZNK5faiss11simd32uint8anIS0_LDnEEES0_RKT_ in pq4_fast_scan_search_qbs.cpp.o
  "__Z9vaddq_f3213__Float32x4_tS_", referenced from:
      __ZNK5faiss12simd8float32plERKS0_ in distances_simd.cpp.o
  "__Z9vaddq_u1612__Uint16x8_tS_", referenced from:
      __ZNK5faiss12simd16uint16plERKS0_ in pq4_fast_scan_search_1.cpp.o
      __ZNK5faiss12simd16uint16plERKS0_ in pq4_fast_scan_search_qbs.cpp.o
  "__Z9vcgeq_u1612__Uint16x8_tS_", referenced from:
      __ZN5faiss6detail7simdlibL8cmp_xe32IXadL_Z9vcgeq_u1612__Uint16x8_tS3_EEEEjRK12uint16x8x2_tS6_S6_ in pq4_fast_scan_search_1.cpp.o
      __ZN5faiss6detail7simdlibL8cmp_xe32IXadL_Z9vcgeq_u1612__Uint16x8_tS3_EEEEjRK12uint16x8x2_tS6_S6_ in pq4_fast_scan_search_qbs.cpp.o
  "__Z9vcleq_u1612__Uint16x8_tS_", referenced from:
      __ZN5faiss6detail7simdlibL8cmp_xe32IXadL_Z9vcleq_u1612__Uint16x8_tS3_EEEEjRK12uint16x8x2_tS6_S6_ in pq4_fast_scan_search_1.cpp.o
      __ZN5faiss6detail7simdlibL8cmp_xe32IXadL_Z9vcleq_u1612__Uint16x8_tS3_EEEEjRK12uint16x8x2_tS6_S6_ in pq4_fast_scan_search_qbs.cpp.o
  "__Z9vmaxq_u1612__Uint16x8_tS_", referenced from:
      __ZN5faiss12simd16uint168accu_maxERKS0_ in partitioning.cpp.o
  "__Z9vminq_u1612__Uint16x8_tS_", referenced from:
      __ZN5faiss12simd16uint168accu_minERKS0_ in partitioning.cpp.o
  "__Z9vmulq_f3213__Float32x4_tS_", referenced from:
      __ZNK5faiss12simd8float32mlERKS0_ in distances_simd.cpp.o
  "__Z9vmulq_u1612__Uint16x8_tS_", referenced from:
      __ZNK5faiss12simd16uint16mlERKS0_ in pq4_fast_scan_search_1.cpp.o
      __ZNK5faiss12simd16uint16mlERKS0_ in pq4_fast_scan_search_qbs.cpp.o
  "__Z9vsubq_f3213__Float32x4_tS_", referenced from:
      __ZNK5faiss12simd8float32miERKS0_ in distances_simd.cpp.o
  "__Z9vsubq_u1612__Uint16x8_tS_", referenced from:
      __ZNK5faiss12simd16uint16miERKS0_ in pq4_fast_scan_search_1.cpp.o
      __ZNK5faiss12simd16uint16miERKS0_ in pq4_fast_scan_search_qbs.cpp.o
ld: symbol(s) not found for architecture arm64
collect2: error: ld returned 1 exit status
make[4]: *** [faiss/libfaiss.dylib] Error 1
make[3]: *** [faiss/CMakeFiles/faiss.dir/all] Error 2
make[2]: *** [faiss/CMakeFiles/faiss.dir/rule] Error 2
make[1]: *** [faiss] Error 2
make: *** [faiss] Error 2

Answer 2 · 2023-02-10T14:10:10.000Z

@jamilabreu Are you able to build Faiss standalone and run the C++ API: https://github.com/facebookresearch/faiss/wiki/Installing-Faiss
https://github.com/facebookresearch/faiss/wiki/Getting-started

Just ruling out this is not a Faiss+M2 issue

Answer 3 · 2023-02-10T14:11:36.000Z

I was just able to get it work! But now getting this error on this line:

ExFaiss.Index.new(384, "IDMap,Flat")

** (UndefinedFunctionError) function ExFaiss.NIF.new_index/3 is undefined (module ExFaiss.NIF is not available)

Answer 4 · 2023-02-10T14:15:20.000Z

Oh that looks like the NIF shared library is failing to load, likely due to undefined symbols. This looks similar to: facebookresearch/faiss#2335 stating that ARM symbols require specific flags. It's possible the Faiss installation isn't compiled with the proper flags on ARM

Answer 5 · 2023-02-10T14:17:44.000Z

Maybe also related? facebookresearch/faiss#2111

Answer 6 · 2023-02-10T14:41:22.000Z

Tried adding the flags listed here:

https://github.com/facebookresearch/faiss/wiki/Installing-Faiss#compiling-faiss-on-arm

Know of any other resources like this I could try?

Answer 7 · 2023-02-11T02:01:09.000Z

Here's the iex error:

 [warning] The on_load function for module Elixir.ExFaiss.NIF returned:
{:error,
 {:load_failed,
  'Failed to load NIF library: \'dlopen(/Users/jamilabreu/Code/elixir/ash/_build/dev/lib/ex_faiss/priv/libex_faiss.so, 0x0002): Library not loaded: @rpath/libfaiss.dylib\n  Referenced from: <14C09AC7-074B-344B-9B95-5D99F3B2819E> /Users/jamilabreu/Code/elixir/ash/deps/ex_faiss/cache/libex_faiss.so\n  Reason: tried: \'/System/Volumes/Preboot/Cryptexes/OS@rpath/libfaiss.dylib\' (no such file), \'/usr/local/lib/libfaiss.dylib\' (no such file), \'/usr/lib/libfaiss.dylib\' (no such file, not in dyld cache)\''}}

Seems to be looking for libfaiss.dylib in the wrong place?

Answer 8 · 2023-02-12T10:15:19.000Z

Historically we needed to use rpath for things to work on Mac. You can try porting this code to ex_faiss Makefile:

https://github.com/elixir-nx/nx/blob/main/exla/Makefile#L30-L43

Answer 9 · 2023-03-09T11:40:18.000Z

I was just able to get it work!

@jamilabreu We're having the same issue you had here. What did you do to get it to get it past the ld: library not found for -lfaiss error? :)

Answer 10 · 2023-04-02T14:37:19.000Z

I've tried just about everything in this thread. Including reading the linked wiki's and I get the same errors:

==> ex_faiss
cp -a /Users/name/.cache/ex_faiss/faiss-19f7696deedc93615c3ee0ff4de22284b53e0243/build/faiss cache/lib
/opt/homebrew/bin/g++ -I/opt/homebrew/Cellar/erlang/25.3/lib/erlang/erts-13.2/include -I/Users/name/.cache/ex_faiss/faiss-19f7696deedc93615c3ee0ff4de22284b53e0243 -fPIC -O3 -shared -std=c++14 c_src/ex_faiss.cc c_src/ex_faiss/nif_util.cc c_src/ex_faiss/index.cc \
		c_src/ex_faiss/clustering.cc -o cache/libex_faiss.so -Lcache/lib -lfaiss -flat_namespace -undefined suppress
make: /opt/homebrew/bin/g++: No such file or directory
make: *** [cache/libex_faiss.so] Error 1
could not compile dependency :ex_faiss, "mix compile" failed. Errors may have been logged above. You can recompile this dependency with "mix deps.compile ex_faiss", update it with "mix deps.update ex_faiss" or clean it with "mix deps.clean ex_faiss"

Apple M1 Pro
mac 13.3 (22E252)

❯ gcc -v
Apple clang version 14.0.0 (clang-1400.0.29.202)
Target: arm64-apple-darwin22.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

I am able to brew instal faiss maybe a solution for mac's is to let us link to that instead? Faiss compilation issues are unfortunately common.

Answer 11 · 2023-04-02T16:06:25.000Z

@jeregrine why is it trying to use g++ instead of c++ that comes with your system? perhaps that's part of the issue? maybe you have an env var messing up with your environment?

Answer 12 · 2023-04-02T21:07:48.000Z

This was the result of the above comment suggesting it might work. I removed those exports and get the same issue.

Answer 13 · 2023-04-02T21:33:58.000Z

I see! We can definitely link against a system one. Torchx offers a similar option we can copy. PRs welcome!

Answer 14 · 2023-04-03T15:13:42.000Z

If anyone in this thread is still having issues please try my branch.

You will need make sure to make clean in the ex_faiss dir for a fresh build. If the Makefile fails to build ex_faiss it will never try and build it again because the files don't change in the .cache dir. My make-fu is not good enough to fix that issue in the makefile.

Steps:

cd deps/ex_faiss
make clean
cd ../../
<edit mix file>
mix do deps.get, deps.compile

And that should work!