Missing dependency on a foreign library

[noughtmare]

I have installed arrayfire 3.6.4 from https://arrayfire.com/download/ to /opt/arrayfire as described on http://arrayfire.org/docs/installing.htm#Linux.

Running cabal install arrayfire yields the following error message:

Build profile: -w ghc-8.8.1 -O1
In order, the following will be built (use -v for more details):
 - arrayfire-0.1.0.0 (lib:arrayfire, exe:gen, exe:main) (requires build)
Starting     arrayfire-0.1.0.0 (all, legacy fallback)

Failed to build arrayfire-0.1.0.0. The failure occurred during the configure
step.
Build log (
/home/jaro/.cabal/logs/ghc-8.8.1/arrayfire-0.1.0.0-5e7527530ca25ab12a051fd4d0f7055fae7a4dba9f99268656d18fb873a6c8ce.log
):
[1 of 1] Compiling Main             ( /tmp/cabal-install.-22655/dist-newstyle/tmp/src-22655/arrayfire-0.1.0.0/dist/setup/setup.hs, /tmp/cabal-install.-22655/dist-newstyle/tmp/src-22655/arrayfire-0.1.0.0/dist/setup/Main.o )
Linking /tmp/cabal-install.-22655/dist-newstyle/tmp/src-22655/arrayfire-0.1.0.0/dist/setup/setup ...
Configuring arrayfire-0.1.0.0...
setup: Missing dependency on a foreign library:
* Missing (or bad) C library: af
This problem can usually be solved by installing the system package that
provides this library (you may need the "-dev" version). If the library is
already installed but in a non-standard location then you can use the flags
--extra-include-dirs= and --extra-lib-dirs= to specify where it is.If the
library file does exist, it may contain errors that are caught by the C
compiler at the preprocessing stage. In this case you can re-run configure
with the verbosity flag -v3 to see the error messages.

cabal: Failed to build arrayfire-0.1.0.0. See the build log above for details.

[lehins]

@noughtmare Looks like you need to build from source in order to be able to use the bindings:

For general usage of ArrayFire, we recommend the installer binaries. However, if you wish to dev on ArrayFire, you will need to build the source code.

https://github.com/arrayfire/arrayfire/wiki#build-instructions

[noughtmare]

I think that "dev on ArrayFire" means modifying the ArrayFire library itself. I just want to use it, so the binaries should be enough (the binaries include the /opt/arrayfire/lib64 and /opt/arrayfire/include directories). But I will try compiling from source to be sure.

[noughtmare]

I have finished building from source and I still get the same error.

[chessai]

Have you tried using the flags it tells you to? --extra-lib-dirs and/or --extra-include-dirs? You shouldnt need to build from source at all.

[noughtmare]

Yes

[noughtmare]

This fixes it for me:

diff --git a/arrayfire.cabal b/arrayfire.cabal
index 1f53125..8c4e1f9 100644
--- a/arrayfire.cabal
+++ b/arrayfire.cabal
@@ -96,7 +96,7 @@ library
     extra-lib-dirs:
       /opt/arrayfire/lib
     ld-options:
-      -Wl -rpath /opt/arrayfire/lib
+      -Wl,-rpath /opt/arrayfire/lib

[chessai]

Glad that works. Instead of a patch, it should be passed to cabal as --ghc-options (since we can't assume how arrayfire was installed on the system).

[noughtmare]

I think it is just an error in your .cabal file. AFAIK there should always be a comma after -Wl and not a space.

[chessai]

Ah, makes sense. Looking back I just realised that those linker flags are already there. Perhaps they shouldn't be.

[chessai]

I think @dmjio and myself haven't noticed because we use nix. I think we should add a travis setup for Ubuntu

[chessai]

Actually, opt is a standard enough place to let that be for non-NixOS. We should just document that, and apply the fix you gave @noughtmare. I'm on mobile right now so I can't do that.

[dmjio]

@noughtmare nice catch, strange that error didn't manifest on OSX for me (when I wasn't using nix). I can make a PR for this.

[9prady9]

I had a similar problem with ArrayFire installed to a custom location. We (me and @dmjio ) are working on figuring out the cause of it. Passing custom location using --extra-lib-dirs and --extra-include-dirs didn't resolve the issue.

[chessai]

I had a similar problem with ArrayFire installed to a custom location. We (me and @dmjio ) are working on figuring out the cause of it. Passing custom location using --extra-lib-dirs and --extra-include-dirs didn't resolve the issue.

what was the actual error?

[9prady9]

stack install --extra-lib-dirs=$AF_PATH/lib64 --extra-include-dirs=$AF_PATH/include arrayfire
arrayfire> configure
arrayfire> [1 of 2] Compiling Main             ( /tmp/stack-e44f53084a6bc144/arrayfire-0.1.0.0/Setup.hs, /tmp/stack-e44f53084a6bc144/arrayfire-0.1.0.0/.stack-work/dist/x86_64-linux-tinfo6/Cabal-2.4.0.1/setup/Main.o )
arrayfire> [2 of 2] Compiling StackSetupShim   ( /home/pradeep/.stack/setup-exe-src/setup-shim-mPHDZzAJ.hs, /tmp/stack-e44f53084a6bc144/arrayfire-0.1.0.0/.stack-work/dist/x86_64-linux-tinfo6/Cabal-2.4.0.1/setup/StackSetupShim.o )
arrayfire> Linking /tmp/stack-e44f53084a6bc144/arrayfire-0.1.0.0/.stack-work/dist/x86_64-linux-tinfo6/Cabal-2.4.0.1/setup/setup ...
arrayfire> Configuring arrayfire-0.1.0.0...
arrayfire> setup: Missing dependency on a foreign library:
arrayfire> * Missing (or bad) C library: af
arrayfire> This problem can usually be solved by installing the system package that
arrayfire> provides this library (you may need the "-dev" version). If the library is
arrayfire> already installed but in a non-standard location then you can use the flags
arrayfire> --extra-include-dirs= and --extra-lib-dirs= to specify where it is.If the
arrayfire> library file does exist, it may contain errors that are caught by the C
arrayfire> compiler at the preprocessing stage. In this case you can re-run configure
arrayfire> with the verbosity flag -v3 to see the error messages.
arrayfire> 

--  While building package arrayfire-0.1.0.0 using:
      /tmp/stack-e44f53084a6bc144/arrayfire-0.1.0.0/.stack-work/dist/x86_64-linux-tinfo6/Cabal-2.4.0.1/setup/setup --builddir=.stack-work/dist/x86_64-linux-tinfo6/Cabal-2.4.0.1 configure --user --package-db=clear --package-db=global --package-db=/home/pradeep/.stack/snapshots/x86_64-linux-tinfo6/8096d5c493ca1014d2da8250c11e63731bfe2fe6565556a6aa8a501eadfda3c2/8.6.5/pkgdb --libdir=/home/pradeep/.stack/snapshots/x86_64-linux-tinfo6/8096d5c493ca1014d2da8250c11e63731bfe2fe6565556a6aa8a501eadfda3c2/8.6.5/lib --bindir=/home/pradeep/.stack/snapshots/x86_64-linux-tinfo6/8096d5c493ca1014d2da8250c11e63731bfe2fe6565556a6aa8a501eadfda3c2/8.6.5/bin --datadir=/home/pradeep/.stack/snapshots/x86_64-linux-tinfo6/8096d5c493ca1014d2da8250c11e63731bfe2fe6565556a6aa8a501eadfda3c2/8.6.5/share --libexecdir=/home/pradeep/.stack/snapshots/x86_64-linux-tinfo6/8096d5c493ca1014d2da8250c11e63731bfe2fe6565556a6aa8a501eadfda3c2/8.6.5/libexec --sysconfdir=/home/pradeep/.stack/snapshots/x86_64-linux-tinfo6/8096d5c493ca1014d2da8250c11e63731bfe2fe6565556a6aa8a501eadfda3c2/8.6.5/etc --docdir=/home/pradeep/.stack/snapshots/x86_64-linux-tinfo6/8096d5c493ca1014d2da8250c11e63731bfe2fe6565556a6aa8a501eadfda3c2/8.6.5/doc/arrayfire-0.1.0.0 --htmldir=/home/pradeep/.stack/snapshots/x86_64-linux-tinfo6/8096d5c493ca1014d2da8250c11e63731bfe2fe6565556a6aa8a501eadfda3c2/8.6.5/doc/arrayfire-0.1.0.0 --haddockdir=/home/pradeep/.stack/snapshots/x86_64-linux-tinfo6/8096d5c493ca1014d2da8250c11e63731bfe2fe6565556a6aa8a501eadfda3c2/8.6.5/doc/arrayfire-0.1.0.0 --dependency=Cabal=Cabal-2.4.1.0-3JC906oWQ73Ah7bYkIcI4J --dependency=base=base-4.12.0.0 --dependency=cabal-doctest=cabal-doctest-1.0.8-40Ym5zAcLNVCMmwzciX9Qk --dependency=directory=directory-1.3.3.0 --dependency=filepath=filepath-1.4.2.1 --dependency=parsec=parsec-3.1.14.0-8t8UKeFouAo5hdmomuIjPj --dependency=text=text-1.2.3.1 --dependency=vector=vector-0.12.0.3-LfvlcMFJAcY18uD1Y2O5Ig -f-disable-default-paths --extra-include-dirs=/home/pradeep/gitroot/ArrayFireWorkspace/worktrees/v3.6/build/pkg/include --extra-lib-dirs=/home/pradeep/gitroot/ArrayFireWorkspace/worktrees/v3.6/build/pkg/lib64 --exact-configuration --ghc-option=-fhide-source-paths
    Process exited with code: ExitFailure 1

[noughtmare]

@9prady9 I think your problem is that the line:

https://github.com/arrayfire/arrayfire-haskell/blob/65bdf727def2bef77c47786585d19ba9050bd860/arrayfire.cabal#L99

Still links to the wrong directory. So it will fail with something like (if you pass -v3 to cabal somehow):

/usr/bin/gcc returned ExitFailure 1 with error message:
gcc: error: /opt/arrayfire/lib: No such file or directory

I have tried building with that line removed and that still works, so maybe that line should just be removed completely.

Another way to fix it for your case is to pass the disable-default-paths flag to arrayfire.

[9prady9]

@9prady9 I think your problem is that the line:

https://github.com/arrayfire/arrayfire-haskell/blob/65bdf727def2bef77c47786585d19ba9050bd860/arrayfire.cabal#L99

Still links to the wrong directory. So it will fail with something like (if you pass -v3 to cabal somehow):

/usr/bin/gcc returned ExitFailure 1 with error message:
gcc: error: /opt/arrayfire/lib: No such file or directory

I have tried building with that line removed and that still works, so maybe that line should just be removed completely.

Another way to fix it for your case is to pass the disable-default-paths flag to arrayfire.

If that is the case, why I do I still see the paths I am passing via command line in the command output I shared earlier ?

Also, when I pass extra options via command line, the following appears in the command output

-f-disable-default-paths --extra-include-dirs=/home/pradeep/gitroot/ArrayFireWorkspace/worktrees/v3.6/build/pkg/include --extra-lib-dirs=/home/pradeep/gitroot/ArrayFireWorkspace/worktrees/v3.6/build/pkg/lib64

no default paths are being disabled if I am not wrong. Please correct me if I am understanding it incorrectly.

[noughtmare]

If that is the case, why I do I still see the paths I am passing via command line in the command output I shared earlier ?

The correct paths do get passed to gcc, but it will also pass the wrong paths which do not exist.

-f-disable-default-paths

I think this means that the flag is disabled (I think this is explaned here in the cabal documentation), but you want to enable it. In the stack documentation I read that that is done using:

--flag arrayfire:disable-default-paths

[9prady9]

Adding that additional flag did carry the build process much further, the following command did finish successfully. @noughtmare thank you.

stack install --flag arrayfire:disable-default-paths \
--extra-lib-dirs=$AF_PATH/lib64 --extra-include-dirs=$AF_PATH/include arrayfire

I think it worked as it copied couple of binaries into $HOME/.local/bin, gen and main, I was able to run main. Is it possible to place them somewhere local in a build sort of directory ? Or is this the normal to place haskell binaries in .local/bin ?

@dmjio however nix-shell --run test-runner command fails. It's probably the same issue as above but with nix-shell or whatever it does. I am not familiar with nix-shell. I think the README guide could definitely use more improvements on the set of instructions required to use arrayfire-haskell via all three routes (as per my understanding) : cabal, stack , nix-shell.

[9prady9]

@dmjio what does gen executable do ? It is writing some files in the location where I ran the executable.

[noughtmare]

@9prady9

Is it possible to place them somewhere local in a build sort of directory ? Or is this the normal to place haskell binaries in .local/bin ?

stack build will put the executables in an obfuscated local (I mean local to the package not literally .local) folder somewhere in .stack-work (I think it prints the exact location to the command line). The executables can then be run with stack exec main for example.

[9prady9]

true, it is printing the path as $HOME/.local/bin.

I was concerned that this path doesn't always necessarily is present in PATH environment variable and the user needs to add it (although a one time thing) to run the executable via stack exec command.

Is there a way to control where stack generates the executable and lookup for executable ? something like a configuration option ?

[noughtmare]

There is a local bin path flag: https://docs.haskellstack.org/en/stable/yaml_configuration/#local-bin-path

stack install --local-bin-path="~/.bin" should work

[dmjio]

@9prady9 hmmm, nix-shell --run test-runner works for me on OSX and NixOS. Can you paste the error you're receiving and I can diagnose.

[dmjio]

@dmjio what does gen executable do ? It is writing some files in the location where I ran the executable.

@9prady9 gen is used to lex / parse the C headers into Haskell FFI declarations. Should only be ran when upgrading versions.

[9prady9]

It is same error message as earlier one with stack command.

On Wed, 6 Nov, 2019, 08:50 David Johnson, notifications@github.com wrote:

@9prady9 https://github.com/9prady9 hmmm, nix-shell --run test-runner works for me on OSX and NixOS. Can you paste the error you're receiving and I can diagnose.

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[9prady9]

Understood, thanks for the clarification

On Wed, 6 Nov, 2019, 09:12 David Johnson, notifications@github.com wrote:

@dmjio https://github.com/dmjio what does gen executable do ? It is writing some files in the location where I ran the executable.

gen is used to lex / parse the C headers in to Haskell FFI declarations. Should only be ran when upgrading versions.

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[dmjio]

when I run on OSX, I get:

λ Davids-MacBook-Pro arrayfire-haskell → λ git master* →       nix-shell --run test-runner
Resolving dependencies...
Configuring arrayfire-0.2.0.0...
Preprocessing library for arrayfire-0.2.0.0..
Building library for arrayfire-0.2.0.0..
Preprocessing test suite 'test' for arrayfire-0.2.0.0..
Building test suite 'test' for arrayfire-0.2.0.0..

ArrayFire.Algorithm
  Algorithm tests
    Should sum a scalar
    Should sum a vector
    Should sum a default value to replace NaN
    Should product a scalar
    Should product a vector
    Should product a default value to replace NaN
    Should take the minimum element of a vector
    Should find if all elements are true along dimension
    Should find if any elements are true along dimension
    Should get count of all elements
    Should get sum all elements
    Should get sum all elements
    Should product all elements in an Array
    Should product all elements in an Array
    Should find minimum value of an Array
    Should find maximum value of an Array
ArrayFire.Arith
  Arith tests
    Should negate scalar value
    Should negate a vector
    Should add two scalar arrays
    Should add two scalar bool arrays
    Should subtract two scalar arrays
    Should multiply two scalar arrays
    Should divide two scalar arrays
    Should add two matrices
    Should take cubed root
    Should take square root
    Should lt Array
    Should lte Array
    Should gte Array
    Should gt Array
    Should eq Array
    Should and Array
    Should and Array
    Should or Array
    Should not Array
    Should bitwise and array
    Should bitwise or array
    Should bitwise xor array
    Should bitwise shift left an array
    Should cast an array
    Should find the minimum of two arrays
    Should find the max of two arrays
    Should take the clamp of 3 arrays
    Should check if an array has positive or negative infinities
    Should check if an array has any NaN values
    Should check if an array has any Zero values
ArrayFire.Array
  Array tests
    Should perform Array tests
...
ArrayFire.Signal
  Signal spec
    Should do FFT in place
    Should do FFT
ArrayFire.Sparse
  Sparse spec
    Should create a sparse array
ArrayFire.Statistics
  Statistics spec
    Should find the mean
    Should find the weighted-mean
    Should find the variance
    Should find the weighted variance
    Should find the standard deviation
    Should find the covariance
    Should find the median
    Should find the mean of all elements across all dimensions
    Should find the weighted mean of all elements across all dimensions
    Should find the variance of all elements across all dimensions
    Should find the weighted variance of all elements across all dimensions
    Should find the stdev of all elements across all dimensions
    Should find the median of all elements across all dimensions
    Should find the correlation coefficient
    Should find the top k elements
ArrayFire.Util
  Util spec
    Should get size of
    Should get version
    Should get revision
    Should save / read array
ArrayFire.Vision
  Vision spec
    Should construct Features for fast feature detection

Finished in 6.2213 seconds
122 examples, 0 failures

what OS are you on?

[9prady9]

Arch Linux i can get you the Haskell version a bit later. I am not in front of the PC right now.

On Wed, 6 Nov, 2019, 10:36 David Johnson, notifications@github.com wrote:

when I run on OSX, I get:

λ Davids-MacBook-Pro arrayfire-haskell → λ git master* → ns --run test-runner

Resolving dependencies...

Configuring arrayfire-0.2.0.0...

Preprocessing library for arrayfire-0.2.0.0..

Building library for arrayfire-0.2.0.0..

Preprocessing test suite 'test' for arrayfire-0.2.0.0..

Building test suite 'test' for arrayfire-0.2.0.0..

ArrayFire.Algorithm

Algorithm tests

Should sum a scalar

Should sum a vector

Should sum a default value to replace NaN

Should product a scalar

Should product a vector

Should product a default value to replace NaN

Should take the minimum element of a vector

Should find if all elements are true along dimension

Should find if any elements are true along dimension

Should get count of all elements

Should get sum all elements

Should get sum all elements

Should product all elements in an Array

Should product all elements in an Array

Should find minimum value of an Array

Should find maximum value of an Array

ArrayFire.Arith

Arith tests

Should negate scalar value

Should negate a vector

Should add two scalar arrays

Should add two scalar bool arrays

Should subtract two scalar arrays

Should multiply two scalar arrays

Should divide two scalar arrays

Should add two matrices

Should take cubed root

Should take square root

Should lt Array

Should lte Array

Should gte Array

Should gt Array

Should eq Array

Should and Array

Should and Array

Should or Array

Should not Array

Should bitwise and array

Should bitwise or array

Should bitwise xor array

Should bitwise shift left an array

Should cast an array

Should find the minimum of two arrays

Should find the max of two arrays

Should take the clamp of 3 arrays

Should check if an array has positive or negative infinities

Should check if an array has any NaN values

Should check if an array has any Zero values

ArrayFire.Array

Array tests

Should perform Array tests

In function af::dim4 verifyDims(const unsigned int, const dim_t *const)

In file src/api/c/data.cpp:38

Invalid dimension for argument 2

Expected: dims[i] >= 1

Should fail to create 0 dimension arrays

In function af::dim4 verifyDims(const unsigned int, const dim_t *const)

In file src/api/c/data.cpp:38

Invalid dimension for argument 2

Expected: dims[i] >= 1

Should fail to create 0 length arrays

In function af::dim4 verifyDims(const unsigned int, const dim_t *const)

In file src/api/c/data.cpp:38

Invalid dimension for argument 2

Expected: dims[i] >= 1

Should fail to create 0 length arrays w/ 0 dimensions

Should create a column vector

Should create a row vector

Should create a vector

Should create a vector

Should copy an array

Should modify manual eval flag

Should return the number of elements

Should create a scalar array

Should get number of dims specified

Should get value of dims specified

Should test Sparsity

Should make a Bit array

Should make an integer array

Should make a Floating array

Should make a Complex array

Should make a Real array

Should make a Double precision array

Should make a Single precision array

Should make a Real floating array

Should get reference count

Should convert an array to a list

ArrayFire.Backend

Backend spec

Should get backend count

Should get available backends

Should set backend to CPU

ArrayFire.BLAS

BLAS spec

Should matmul two matrices

Should dot product two vectors

Should produce scalar dot product between two vectors as a Complex number

Should take the transpose of a matrix

Should take the transpose of a matrix in place

ArrayFire.Data

Data tests

Should create constant Array

ArrayFire.Device

Algorithm tests

ArrayFire v3.6.4 (OpenCL, 64-bit Mac OSX, build 1b8030c5)

[0] APPLE: AMD Radeon Pro 555X Compute Engine, 4096 MB

-1- APPLE: Intel(R) UHD Graphics 630, 1536 MB

Should show device info

Should show device init

Should get info string

Should get device

Should get and set device

ArrayFire.Features

Feautures tests

Should get features number an array

ArrayFire.Graphics

Graphics tests

Should create window

ArrayFire.Image

Image tests

Should test if Image I/O is available

ArrayFire.Index

Index spec

Should index into an array

ArrayFire.LAPACK

LAPACK spec

Should have LAPACK available

Should perform svd

Should perform svd in place

Should perform lu

Should perform qr

Should get determinant of Double

Should calculate inverse

ArrayFire.Random

Random engine spec

Should create random engine

Should set random engine

Should set and get seed

ArrayFire.Signal

Signal spec

Should do FFT in place

Should do FFT

ArrayFire.Sparse

Sparse spec

Should create a sparse array

ArrayFire.Statistics

Statistics spec

Should find the mean

Should find the weighted-mean

Should find the variance

Should find the weighted variance

Should find the standard deviation

Should find the covariance

Should find the median

Should find the mean of all elements across all dimensions

Should find the weighted mean of all elements across all dimensions

Should find the variance of all elements across all dimensions

Should find the weighted variance of all elements across all dimensions

Should find the stdev of all elements across all dimensions

Should find the median of all elements across all dimensions

Should find the correlation coefficient

Should find the top k elements

ArrayFire.Util

Util spec

Should get size of

Should get version

Should get revision

Should save / read array

ArrayFire.Vision

Vision spec

Should construct Features for fast feature detection

Finished in 6.2213 seconds

122 examples, 0 failures

what OS are you on?

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[dmjio]

I think the issue is that this ld-option should be removed.

-Wl,-rpath /opt/arrayfire/lib

It's presumptuous to assume we can always link with that directory even when the user is using the binary distribution (since it could be lib or lib64), and the failure always ends in compilation failure when its not found. Instead, we can add both

extra-lib-dirs:
   /opt/arrayfire/lib64 
   /opt/arrayfire/lib

And it will simply warn if one of the directories is missing w/o compilation failure. This should make a much better experience on initial install.

[9prady9]

What about the custom installation paths with nix-shell ? Please check my earlier messages for details.

[lehins]

Just in case anyone is looking for a simple workaround for this problem you can just use a symbolic link:

$ sudo ln -s /opt/arrayfire/lib64 /opt/arrayfire/lib
$ sudo bash -c 'echo /opt/arrayfire/lib > /etc/ld.so.conf.d/arrayfire.conf'
$ sudo ldconfig

[dmjio]

@lehins can you confirm if you install arrayfire with the binary installer on Linux that it creates /opt/arrayfire/lib64 and not /opt/arrayfire/lib (related to #46). Don't have ubuntu handy, and trying to make assumptions out here.

[lehins]

@dmjio That is correct, I can confirm this on Ubuntu.

[dmjio]

@lehins awesome! And not to be redundant, but can you also confirm that you did not install from source, but from the binary installer script ?

[lehins]

@dmjio lol. No worries. I did indeed install it from the downloadable Linux installer

[dmjio]

@lehins perfect ! then I'm going to go ahead and merge #46, since I think the default locations are accounted for on each platform. People who build from source will have to -f+disable-default-paths and --extra-lib-dirs=/path/to/arrayfire/lib and --extra-include-dirs=/path/to/arrayfire/include

[dmjio]

@noughtmare @9prady9 @chessai @lehins this issue should be solved in 0.6.0.0. (no more symbolic link required) If not, please re-open.

@9prady9 this issue is solved only in the case end-users are using the binary distribution of ArrayFire w/ the Haskell wrapper (not installing from source). I have an issue (and solution) to provide documentation for this case. #48