macOS High Sierra Linking Fails

[bbrener1]

Encountering problems when building with ndarray-linalg as a dependency

Versions:

OSX: 10.13.4 (17E199)

clang: Apple LLVM version 9.1.0 (clang-902.0.39.2)
Target: x86_64-apple-darwin17.5.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

blas and openblas installed via conda, versions are:

blas 1.0 openblas anaconda
openblas 0.3.3 3 anaconda
openblas-devel 0.3.3 3 anaconda

gfortran was installed via homebrew:

boris@Boriss-MacBook-Pro-2:~/haxx/python/gravity_clustering$ gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/8.2.0/libexec/gcc/x86_64-apple-darwin17.7.0/8.2.0/lto-wrapper
Target: x86_64-apple-darwin17.7.0
Configured with: ../configure --build=x86_64-apple-darwin17.7.0 --prefix=/usr/local/Cellar/gcc/8.2.0 --libdir=/usr/local/Cellar/gcc/8.2.0/lib/gcc/8 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-8 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --enable-checking=release --with-pkgversion='Homebrew GCC 8.2.0' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --disable-nls
Thread model: posix
gcc version 8.2.0 (Homebrew GCC 8.2.0)

Error text is as follows:

error: linking with `cc` failed: exit code: 1
  |
  = note: "cc" "-m64" "-L" "/Users/boris/.rustup/toolchains/stable-x86_64-apple-darwin/lib/rustlib/x86_64-apple-darwin/lib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering0-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering1-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering10-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering11-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering12-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering13-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering14-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering15-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering2-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering3-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering4-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering5-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering6-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering7-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering8-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.gravity_clustering9-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o" "-o" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/gravity_clustering-af9a185107b464a2.crate.allocator.rcgu.o" "-Wl,-dead_strip" "-nodefaultlibs" "-L" "/Users/boris/haxx/python/gravity_clustering/target/release/deps" "-L" "/Users/boris/.rustup/toolchains/stable-x86_64-apple-darwin/lib/rustlib/x86_64-apple-darwin/lib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/librayon-4b02d786d1bd55a5.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/librayon_core-6ad42d4bfe037261.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libcrossbeam_deque-3e4d4acc829c5c73.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libcrossbeam_epoch-ca8363f9197e111f.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libscopeguard-b6ce87978007c9eb.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libmemoffset-19ba1fa21caf0388.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/liblazy_static-f9f2f60147bdfdf0.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libcrossbeam_utils-025f80d9e0908a5b.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libcfg_if-31e57d1f0d09db98.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libarrayvec-b72cb89b05274aca.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libnodrop-a40abb48bf76c4e6.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libndarray_linalg-b74f9ca68324d40e.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/liblapacke-4b6143a9e09368de.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/liblapacke_sys-fa7f00acac0e1073.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libndarray-9ae38c327d6212ae.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libnum_complex-e1f6eb9ac6503af6.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libnum_traits-03eef3ab8946d374.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libitertools-9016f082db60a7a7.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libeither-fcfc96e5a4db8cce.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libmatrixmultiply-817168ed32bf0403.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/librawpointer-d8a37321df43ac4b.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libblas_src-772e556da810a4d4.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libcblas_sys-9a2f33c41b92c395.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/libnum_cpus-eaf59e66f6f31242.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/librand-800929ac40d24603.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/liblibc-3c1946dd65acb4d1.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/librand_core-3b99e0cebd545167.rlib" "/Users/boris/haxx/python/gravity_clustering/target/release/deps/librand_core-d541ebf4a966e2be.rlib" "/Users/boris/.rustup/toolchains/stable-x86_64-apple-darwin/lib/rustlib/x86_64-apple-darwin/lib/libstd-03b901326ae24853.rlib" "/Users/boris/.rustup/toolchains/stable-x86_64-apple-darwin/lib/rustlib/x86_64-apple-darwin/lib/libpanic_unwind-6ff7c563e703aab0.rlib" "/Users/boris/.rustup/toolchains/stable-x86_64-apple-darwin/lib/rustlib/x86_64-apple-darwin/lib/liballoc_jemalloc-5bcc251fd166dc12.rlib" "/Users/boris/.rustup/toolchains/stable-x86_64-apple-darwin/lib/rustlib/x86_64-apple-darwin/lib/libunwind-3af07b1997da2eea.rlib" "/Users/boris/.rustup/toolchains/stable-x86_64-apple-darwin/lib/rustlib/x86_64-apple-darwin/lib/liballoc_system-f2d882c31340c020.rlib" "/Users/boris/.rustup/toolchains/stable-x86_64-apple-darwin/lib/rustlib/x86_64-apple-darwin/lib/liblibc-c27b8d1b261d1a71.rlib" "/Users/boris/.rustup/toolchains/stable-x86_64-apple-darwin/lib/rustlib/x86_64-apple-darwin/lib/liballoc-a8adffd320893f05.rlib" "/Users/boris/.rustup/toolchains/stable-x86_64-apple-darwin/lib/rustlib/x86_64-apple-darwin/lib/libcore-095d0e0c6f534dd1.rlib" "/Users/boris/.rustup/toolchains/stable-x86_64-apple-darwin/lib/rustlib/x86_64-apple-darwin/lib/libcompiler_builtins-5bd49e510cc11ed9.rlib" "-framework" "Security" "-lSystem" "-lresolv" "-lpthread" "-lc" "-lm"
  = note: Undefined symbols for architecture x86_64:
            "_LAPACKE_dgesvd", referenced from:
                _$LT$f64$u20$as$u20$ndarray_linalg..lapack_traits..svd..SVD_$GT$::svd::hfaf0e8598dff5bc2 in libndarray_linalg-b74f9ca68324d40e.rlib(ndarray_linalg-b74f9ca68324d40e.ndarray_linalg4-18283fb439679ae1ca7e2ec2221088bb.rs.rcgu.o)
            "_cblas_ddot", referenced from:
                ndarray::linalg::impl_linalg::_$LT$impl$u20$ndarray..ArrayBase$LT$S$C$$u20$ndarray..dimension..dim..Dim$LT$$u5b$usize$u3b$$u20$_$u5d$$GT$$GT$$GT$::dot::h714423fc9780e798 in gravity_clustering-af9a185107b464a2.gravity_clustering1-b7d3c0d45745af024f0794934bb8388b.rs.rcgu.o
          ld: symbol(s) not found for architecture x86_64
          clang: error: linker command failed with exit code 1 (use -v to see invocation)

Cargo.toml is:

[package]
name = "gravity_clustering"
version = "0.1.0"
authors = ["boris"]

[dependencies]
ndarray = "0.12"
ndarray-linalg = { version = "0.10", features = ["openblas"] }
#(I have tried this with "ndarray-linalg = "0.10"" as well)
rand = "0.5.5"
num_cpus = "1.8.0"
rayon = "1.0.2"

Please advise on options, so far I have solved this by creating a symlink in usr/local/bin for cc to link to G++-8, however this is terrifying and terrible, and I would like another way to solve. Issue doesn't appear to be platform dependent, as this build also fails on Ubuntu.

EDIT(by @termoshtt): Fix markdown

[termoshtt]

The feature "openblas" builds OpenBLAS in a temporal directory, which is not match for your use case. To link existing library, please link backend LAPACK library using openblas-src = { version = "*", features = ["system"]}.

[bbrener1]

I think I might be running into the issue noted here:
rust-lang/cargo#2888

I have produced a very minimal crate for which I have not been able to resolve compilation issues:

https://github.com/bbrener1/dylib_linking_test

Briefly, these are the only contents of the crate:

Cargo.toml:

[package]
name = "n_test"
version = "0.1.0"
authors = ["boris"]

[dependencies]
ndarray = "0.12"
#ndarray-linalg = { version = "0.10" }
ndarray-linalg = { version = "0.10", features = ["openblas"] }
#ndarray-linalg = { version = "0.10", features = ["intel-mkl"] }
openblas-src = { version = "0.6", features = ["system"] }
#intel-mkl-src = "0.2.5"
#blas = "*"
#netlib-src = { version = "0.6" }

src/main.rs:

extern crate ndarray;
extern crate ndarray_linalg;
// extern crate blas;
// extern crate netlib_src;
extern crate openblas_src;
// extern crate intel_mkl_src;

use ndarray::{Array,Ix2};
use ndarray_linalg::{Factorize,Inverse};

fn main() {

    let mut mtx: Array<f64,Ix2> = Array::from_shape_vec((2,2),vec![1.,2.,3.,4.]).unwrap();
    mtx.factorize().unwrap().inv();

    println!("Hello, world!");

}

Currently this returns the following error:

error: could not find native static library `openblas`, perhaps an -L flag is missing?

error: aborting due to previous error

error: Could not compile `openblas-src`.

To learn more, run the command again with --verbose.

Perhaps this is occurring because openblas is installed in ~/miniconda3/pkgs/... and cargo is changing LD_LIBRARY_PATH ?

I suspect this is the case because when I reconfigure this same crate to instead use intel-mkl-src, it compiles successfully, and moreover executes successfully using cargo run. However, if the executable itself is called, an error is returned stating

dyld: Library not loaded: @rpath/libmkl_intel_lp64.dylib
  Referenced from: /Users/boris/haxx/ndarray_linalg_test/dylib_linking_test/./target/debug/n_test
  Reason: image not found
Abort trap: 6

Thank you for your help

---

EDIT (by @termoshtt): Fix markdown

[termoshtt]

ndarray-linalg = { version = "0.10", features = ["openblas"] }

Please drop this feature

ndarray-linalg = { version = "0.10" }

Perhaps this is occurring because openblas is installed in ~/miniconda3/pkgs/... and cargo is changing LD_LIBRARY_PATH ?

Please add the library path in miniconda both LIBRARY_PATH and LD_LIBRARY_PATH. cargo build -vv will display the full link command, and the -L flag in it will help your debug.

[termoshtt]

Please reopen if not resolved