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JuliaLinearAlgebra / Arpack.jl

Julia Wrappers for the arpack-ng Fortran library
https://arpack.julialinearalgebra.org/stable
MIT License
69 stars 29 forks source link

Installation error when Julia is built from source #5

Closed yurivish closed 5 years ago

yurivish commented 6 years ago

I tried installing Arpack on 0.7 beta and saw this error trying to run eigs:

julia> A = Diagonal(1:4);
WARNING: Base.Diagonal is deprecated: it has been moved to the standard library package `LinearAlgebra`.
Add `using LinearAlgebra` to your imports.
 in module Main

julia> λ, ϕ = eigs(A, nev = 2);
ERROR: error compiling saupd: could not load library ""
dlopen(.dylib, 1): image not found
Stacktrace:
 [1] aupd_wrapper(::Any, ::getfield(Arpack, Symbol("#matvecA!#24")){LinearAlgebra.Diagonal{Float64,Array{Float64,1}}}, ::getfield(Arpack, Symbol("##18#25")), ::getfield(Arpack, Symbol("##19#26")), ::Int64, ::Bool, ::Bool, ::String, ::Int64, ::Int64, ::String, ::Float64, ::Int64, ::Int64, ::Array{Float64,1}) at /Users/yurivish/.julia/packages/Arpack/Rkbg/src/libarpack.jl:42
 [2] #_eigs#17(::Int64, ::Int64, ::Symbol, ::Float64, ::Int64, ::Nothing, ::Array{Float64,1}, ::Bool, ::Any, ::Any, ::Any) at /Users/yurivish/.julia/packages/Arpack/Rkbg/src/Arpack.jl:176
 [3] (::getfield(Arpack, Symbol("#kw##eigs")))(::NamedTuple{(:nev,),Tuple{Int64}}, ::typeof(eigs), ::LinearAlgebra.Diagonal{Int64,UnitRange{Int64}}) at ./none:0
 [4] top-level scope at none:0

To see if this was solved on master, I tried installing it. But this happens when I try to develop Arpack#master:

Error: Error building `Arpack`:
│ [ Info: Downloading https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-0.2.20/ArpackBuilder.x86_64-apple-darwin14.tar.gz to /Users/yurivish/.julia/dev/Arpack/deps/usr/downloads/ArpackBuilder.x86_64-apple-darwin14.tar.gz...
│ ┌ Warning: `wait(t::Task)` is deprecated, use `fetch(t)` instead.
│ │   caller = macro expansion at OutputCollector.jl:63 [inlined]
│ └ @ Core OutputCollector.jl:63
│ ┌ Warning: `wait(t::Task)` is deprecated, use `fetch(t)` instead.
│ │   caller = wait(::OutputCollector) at OutputCollector.jl:158
│ └ @ BinaryProvider OutputCollector.jl:158
│ ┌ Warning: `wait(t::Task)` is deprecated, use `fetch(t)` instead.
│ │   caller = wait(::OutputCollector) at OutputCollector.jl:159
│ └ @ BinaryProvider OutputCollector.jl:159
│ ┌ Warning: `wait(t::Task)` is deprecated, use `fetch(t)` instead.
│ │   caller = wait(::OutputCollector) at OutputCollector.jl:163
│ └ @ BinaryProvider OutputCollector.jl:163
│ ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack, "Prefix(/Users/yurivish/.julia/dev/Arpack/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] error at ./error.jl:33 [inlined]
│  [2] #write_deps_file#134(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /Users/yurivish/.julia/packages/BinaryProvider/2Hlv/src/Products.jl:389
│  [3] write_deps_file(::String, ::Array{LibraryProduct,1}) at /Users/yurivish/.julia/packages/BinaryProvider/2Hlv/src/Products.jl:376
│  [4] top-level scope at none:0
│  [5] include at ./boot.jl:317 [inlined]
│  [6] include_relative(::Module, ::String) at ./loading.jl:1075
│  [7] include(::Module, ::String) at ./sysimg.jl:29
│  [8] include(::String) at ./client.jl:393
│  [9] top-level scope at none:0
│ in expression starting at /Users/yurivish/.julia/dev/Arpack/deps/build.jl:40
julia> versioninfo()
Julia Version 0.7.0-beta.0
Commit f41b1ecaec (2018-06-24 01:32 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin16.7.0)
  CPU: Intel(R) Core(TM) i7-3615QM CPU @ 2.30GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.0 (ORCJIT, ivybridge)
Environment:
  JULIA_EDITOR = subl
galenlynch commented 6 years ago

I am trying what @klpn suggested on Fedora, but Julia seems to hang when invoking Pkg.build("Arpack").

galenlynch commented 6 years ago

I just removed some log files and it suddenly worked...?

galenlynch commented 6 years ago

Also just chiming in on the whole pre-built binaries debate in this thread: at least on Fedora, the pre-built binaries don't work well with PyCall and PyPlot. I invariably run into library problems, even if I let Julia keep its own version of anaconda. I think the problem stems from poor anaconda packaging. Anaconda's matplotlib simply doesn't work on Fedora.

The only way I can use Julia with plotting capabilities is to use distro packaged (or built from source) Julia as well as distro packaged python modules. If the official recommendation is to only use "official" Julia binaries, then I won't be able to make figures.

simonbyrne commented 6 years ago

Yeah, I'm not a big fan of depending on Conda either: for one thing its ARM support its pretty bad.

Could you open an issue on PyCall or PyPlot?

galenlynch commented 6 years ago

That certainly makes more sense than grousing about it here. I'll make an issue with PyPlot.

staticfloat commented 6 years ago

Once #43 is merged, this package will now provide GCC-multiversioned libraries, which means that from-source builds should work. Essentially, we have developed the capability to build against GCC 4.X, 7.X and 8.X (which correspond to the increments in gfortran version number), and so when you attempt to download the Arpack.jl binaries, it will download a libarpack that links against the proper libgfortran that already exists on your local system.

andreasnoack commented 6 years ago

I've merged #43 so it would be great if people could try out

pkg> add Arpack#master

and see if things work.

chriselrod commented 6 years ago 
(v1.0) pkg> add Arpack#master
  Updating git-repo `https://github.com/JuliaLinearAlgebra/Arpack.jl.git`
 Resolving package versions...
  Updating `~/.julia/environments/v1.0/Project.toml`
  [7d9fca2a] + Arpack v0.2.3+ #master (https://github.com/JuliaLinearAlgebra/Arpack.jl.git)
  Updating `~/.julia/environments/v1.0/Manifest.toml`
  [7d9fca2a] + Arpack v0.2.3+ #master (https://github.com/JuliaLinearAlgebra/Arpack.jl.git)

(v1.0) pkg> test Arpack
   Testing Arpack
    Status `/tmp/tmppMe5xd/Manifest.toml`
  [7d9fca2a] Arpack v0.2.3+ #master (https://github.com/JuliaLinearAlgebra/Arpack.jl.git)
  [b99e7846] BinaryProvider v0.5.0
  [2a0f44e3] Base64  [`@stdlib/Base64`]
  [ade2ca70] Dates  [`@stdlib/Dates`]
  [8ba89e20] Distributed  [`@stdlib/Distributed`]
  [b77e0a4c] InteractiveUtils  [`@stdlib/InteractiveUtils`]
  [76f85450] LibGit2  [`@stdlib/LibGit2`]
  [8f399da3] Libdl  [`@stdlib/Libdl`]
  [37e2e46d] LinearAlgebra  [`@stdlib/LinearAlgebra`]
  [56ddb016] Logging  [`@stdlib/Logging`]
  [d6f4376e] Markdown  [`@stdlib/Markdown`]
  [44cfe95a] Pkg  [`@stdlib/Pkg`]
  [de0858da] Printf  [`@stdlib/Printf`]
  [3fa0cd96] REPL  [`@stdlib/REPL`]
  [9a3f8284] Random  [`@stdlib/Random`]
  [ea8e919c] SHA  [`@stdlib/SHA`]
  [9e88b42a] Serialization  [`@stdlib/Serialization`]
  [6462fe0b] Sockets  [`@stdlib/Sockets`]
  [2f01184e] SparseArrays  [`@stdlib/SparseArrays`]
  [8dfed614] Test  [`@stdlib/Test`]
  [cf7118a7] UUIDs  [`@stdlib/UUIDs`]
  [4ec0a83e] Unicode  [`@stdlib/Unicode`]
Test Summary: | Pass  Total
eigs          |   56     56
Test Summary: | Pass  Total
real svds     |  189    189
Test Summary: | Pass  Total
complex svds  |    7      7
Test Summary: | Pass  Total
promotion     |    3      3
Test Summary:               | Pass  Total
svds for non-AbstractMatrix |    1      1
Test Summary: | Pass  Broken  Total
low rank      |   15       3     18
   Testing Arpack tests passed 

shell> gfortran --version
GNU Fortran (GCC) 8.2.1 20180831
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

julia> versioninfo()
Julia Version 1.0.2-pre.0
Commit 4aea3d2b7c (2018-09-30 15:02 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: AMD Ryzen Threadripper 1950X 16-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.0 (ORCJIT, znver1)
wehlutyk commented 6 years ago 
$ rm -rf .julia

Then in julia:

(v1.0) pkg> add Arpack#master
   Cloning default registries into /home/sl/.julia/registries
   Cloning registry General from "https://github.com/JuliaRegistries/General.git"
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
   Cloning git-repo `https://github.com/JuliaLinearAlgebra/Arpack.jl.git`
  Updating git-repo `https://github.com/JuliaLinearAlgebra/Arpack.jl.git`
 Resolving package versions...
 Installed BinaryProvider ─ v0.5.1
  Updating `~/.julia/environments/v1.0/Project.toml`
  [7d9fca2a] + Arpack v0.2.3+ #master (https://github.com/JuliaLinearAlgebra/Arpack.jl.git)
  Updating `~/.julia/environments/v1.0/Manifest.toml`
  [7d9fca2a] + Arpack v0.2.3+ #master (https://github.com/JuliaLinearAlgebra/Arpack.jl.git)
  [b99e7846] + BinaryProvider v0.5.1
  [2a0f44e3] + Base64 
  [ade2ca70] + Dates 
  [8ba89e20] + Distributed 
  [b77e0a4c] + InteractiveUtils 
  [76f85450] + LibGit2 
  [8f399da3] + Libdl 
  [37e2e46d] + LinearAlgebra 
  [56ddb016] + Logging 
  [d6f4376e] + Markdown 
  [44cfe95a] + Pkg 
  [de0858da] + Printf 
  [3fa0cd96] + REPL 
  [9a3f8284] + Random 
  [ea8e919c] + SHA 
  [9e88b42a] + Serialization 
  [6462fe0b] + Sockets 
  [2f01184e] + SparseArrays 
  [8dfed614] + Test 
  [cf7118a7] + UUIDs 
  [4ec0a83e] + Unicode 
  Building Arpack → `~/.julia/packages/Arpack/UiiMc/deps/build.log`
┌ Error: Error building `Arpack`: 
│ [ Info: Downloading https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-3/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz to /home/sl/.julia/packages/Arpack/UiiMc/deps/usr/downloads/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz...
│ ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack, "Prefix(/home/sl/.julia/packages/Arpack/UiiMc/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] #write_deps_file#152(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /home/sl/.julia/packages/BinaryProvider/cVlaj/src/Products.jl:408
│  [2] (::getfield(BinaryProvider, Symbol("#kw##write_deps_file")))(::NamedTuple{(:verbose,),Tuple{Bool}}, ::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at ./none:0
│  [3] top-level scope at none:0
│  [4] include(::String) at ./client.jl:388
│  [5] top-level scope at none:0
│ in expression starting at /home/sl/.julia/packages/Arpack/UiiMc/deps/build.jl:74
[10:39:47] ######################################################################## 100.0% 
└ @ Pkg.Operations /build/julia/src/julia/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1068
$ pacman -Ss '^gcc-libs$'
core/gcc-libs 8.2.1+20180831-1 (base) [installed]
    Runtime libraries shipped by GCC

$ pacman -Ql gcc-libs | grep libgfortran
gcc-libs /usr/lib/libgfortran.so
gcc-libs /usr/lib/libgfortran.so.5
gcc-libs /usr/lib/libgfortran.so.5.0.0

Am I missing something?

staticfloat commented 6 years ago

This is a complex problem that has to do with your library layout not matching that of a typical Julia installation; a typical Julia installation has libgfortran within Julia’s “private libdir” (in this case, probably “/usr/lib/julia”). A quick fix for you will probably be to create a symlink to libgfortran in that directory that points to your global gfortran. The next big chunk of work to be done is to make this process slightly more intelligent with Julia, however that work is held up by some other design decisions in the Pkg space, so it’s going to be weeks before it’s ready, not days.

On Thu, Oct 4, 2018 at 16:47 Sébastien Lerique notifications@github.com wrote:

$ rm -rf .julia

Then in julia:

(v1.0) pkg> add Arpack#master Cloning default registries into /home/sl/.julia/registries Cloning registry General from "https://github.com/JuliaRegistries/General.git" Updating registry at ~/.julia/registries/General Updating git-repo https://github.com/JuliaRegistries/General.git Cloning git-repo https://github.com/JuliaLinearAlgebra/Arpack.jl.git Updating git-repo https://github.com/JuliaLinearAlgebra/Arpack.jl.git Resolving package versions... Installed BinaryProvider ─ v0.5.1 Updating ~/.julia/environments/v1.0/Project.toml [7d9fca2a] + Arpack v0.2.3+ #master (https://github.com/JuliaLinearAlgebra/Arpack.jl.git) Updating ~/.julia/environments/v1.0/Manifest.toml [7d9fca2a] + Arpack v0.2.3+ #master (https://github.com/JuliaLinearAlgebra/Arpack.jl.git) [b99e7846] + BinaryProvider v0.5.1 [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [b77e0a4c] + InteractiveUtils [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [44cfe95a] + Pkg [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA [9e88b42a] + Serialization [6462fe0b] + Sockets [2f01184e] + SparseArrays [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode Building Arpack → ~/.julia/packages/Arpack/UiiMc/deps/build.log ┌ Error: Error building Arpack: │ [ Info: Downloading https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-3/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz to /home/sl/.julia/packages/Arpack/UiiMc/deps/usr/downloads/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz... │ ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack, "Prefix(/home/sl/.julia/packages/Arpack/UiiMc/deps/usr)") is not satisfied, cannot generate deps.jl! │ Stacktrace: │ [1] #write_deps_file#152(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /home/sl/.julia/packages/BinaryProvider/cVlaj/src/Products.jl:408 │ [2] (::getfield(BinaryProvider, Symbol("#kw##write_deps_file")))(::NamedTuple{(:verbose,),Tuple{Bool}}, ::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at ./none:0 │ [3] top-level scope at none:0 │ [4] include(::String) at ./client.jl:388 │ [5] top-level scope at none:0 │ in expression starting at /home/sl/.julia/packages/Arpack/UiiMc/deps/build.jl:74 [10:39:47] ######################################################################## 100.0% └ @ Pkg.Operations /build/julia/src/julia/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1068

$ pacman -Ss '^gcc-libs$' core/gcc-libs 8.2.1+20180831-1 (base) [installed] Runtime libraries shipped by GCC

$ pacman -Ql gcc-libs | grep libgfortran gcc-libs /usr/lib/libgfortran.so gcc-libs /usr/lib/libgfortran.so.5 gcc-libs /usr/lib/libgfortran.so.5.0.0

Am I missing something?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/JuliaLinearAlgebra/Arpack.jl/issues/5#issuecomment-426936591, or mute the thread https://github.com/notifications/unsubscribe-auth/AAH_aOTBGI-Nbj314p3OzqJDTd_m2rKuks5uhcs5gaJpZM4U1Wfr .

wehlutyk commented 6 years ago

Symlinking libgfortran to either /usr/lib/julia or ~/.julia/packages/Arpack/XXX/deps/usr/lib has no effect for me (but thanks for answering :) ). The workaround by @klpn above does work though, but I guess that just side-steps obtaining arpack through Arpack.jl.

staticfloat commented 6 years ago

Did you symlink just libgfortran.so, or did you do the versioned filenames as well?

wehlutyk commented 6 years ago

All of them:

 ~  sudo ln -s /usr/lib/libgfortran.so /usr/lib/julia/                       Thu 04 Oct 2018 23:40:57 CEST
[sudo] password for sl: 
 ~  sudo ln -s /usr/lib/libgfortran.so.5 /usr/lib/julia/            4931ms  Thu 04 Oct 2018 23:41:13 CEST
 ~  sudo ln -s /usr/lib/libgfortran.so.5.0.0  /usr/lib/julia/                Thu 04 Oct 2018 23:41:25 CEST
 ~  rm -rf .julia                                                            Thu 04 Oct 2018 23:41:34 CEST
 ~  julia                                                            173ms  Thu 04 Oct 2018 23:41:38 CEST
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.0.0 (2018-08-08)
 _/ |\__'_|_|_|\__'_|  |  
|__/                   |

(v1.0) pkg> add Arpack#master
   Cloning default registries into /home/sl/.julia/registries
   Cloning registry General from "https://github.com/JuliaRegistries/General.git"
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
   Cloning git-repo `https://github.com/JuliaLinearAlgebra/Arpack.jl.git`
  Updating git-repo `https://github.com/JuliaLinearAlgebra/Arpack.jl.git`
 Resolving package versions...
 Installed BinaryProvider ─ v0.5.1
  Updating `~/.julia/environments/v1.0/Project.toml`
  [7d9fca2a] + Arpack v0.2.3+ #master (https://github.com/JuliaLinearAlgebra/Arpack.jl.git)
  Updating `~/.julia/environments/v1.0/Manifest.toml`
  [7d9fca2a] + Arpack v0.2.3+ #master (https://github.com/JuliaLinearAlgebra/Arpack.jl.git)
  [b99e7846] + BinaryProvider v0.5.1
  [2a0f44e3] + Base64 
  [ade2ca70] + Dates 
  [8ba89e20] + Distributed 
  [b77e0a4c] + InteractiveUtils 
  [76f85450] + LibGit2 
  [8f399da3] + Libdl 
  [37e2e46d] + LinearAlgebra 
  [56ddb016] + Logging 
  [d6f4376e] + Markdown 
  [44cfe95a] + Pkg 
  [de0858da] + Printf 
  [3fa0cd96] + REPL 
  [9a3f8284] + Random 
  [ea8e919c] + SHA 
  [9e88b42a] + Serialization 
  [6462fe0b] + Sockets 
  [2f01184e] + SparseArrays 
  [8dfed614] + Test 
  [cf7118a7] + UUIDs 
  [4ec0a83e] + Unicode 
  Building Arpack → `~/.julia/packages/Arpack/UiiMc/deps/build.log`
┌ Error: Error building `Arpack`: 
│ [ Info: Downloading https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-3/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz to /home/sl/.julia/packages/Arpack/UiiMc/deps/usr/downloads/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz...
│ ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack, "Prefix(/home/sl/.julia/packages/Arpack/UiiMc/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] #write_deps_file#152(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /home/sl/.julia/packages/BinaryProvider/cVlaj/src/Products.jl:408
│  [2] (::getfield(BinaryProvider, Symbol("#kw##write_deps_file")))(::NamedTuple{(:verbose,),Tuple{Bool}}, ::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at ./none:0
│  [3] top-level scope at none:0
│  [4] include(::String) at ./client.jl:388
│  [5] top-level scope at none:0
│ in expression starting at /home/sl/.julia/packages/Arpack/UiiMc/deps/build.jl:74
[23:42:14] ######################################################################## 100.0% 
└ @ Pkg.Operations /build/julia/src/julia/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1068
staticfloat commented 6 years ago

Can you post the output of the following for me:

$ LD_DEBUG=libs julia -e 'using Pkg, Libdl; dlopen(Pkg.dir("Arpack", "deps", "usr", "lib", "libarpack.so"))'
wehlutyk commented 6 years ago

So running this right after the set of commands from above: https://gist.github.com/wehlutyk/77ded681c17d0cb8cf0be9312335f046.

Also:

 $ tree -lah .julia/packages/Arpack/UiiMc/deps/usr/lib/
.julia/packages/Arpack/UiiMc/deps/usr/lib/
├── [4.0K]  cmake
├── [  14]  libarpack.so -> libarpack.so.2
├── [  18]  libarpack.so.2 -> libarpack.so.2.0.0
└── [366K]  libarpack.so.2.0.0
staticfloat commented 6 years ago

Ah, so it did have an effect; it stopped complaining about libgfortran and instead started complaining about libopenblas64_.so.0. Do you have such a file on your computer? If not, what is your libopenblas called?

wehlutyk commented 6 years ago

Indeed, hadn't noticed that. I don't have a file named exactly that. My blas library was Arch's blas package (which provides /usr/lib/libblas.so, /usr/lib/libblas.so.3, /usr/lib/libblas.so.3.8.0, but no libopenblas), and installing openblas instead gives me:

/usr/lib/libblas.so
/usr/lib/libblas.so.3
/usr/lib/libopenblas.so
/usr/lib/libopenblas.so.3
/usr/lib/libopenblasp-r0.3.3.so

(And the debug ouput from julia is unchanged.)

I just noticed there's also a libopenblas in /usr/lib/julia, so installing a system-wide one wouldn't be necessary anyway:

 ls -l /usr/lib/julia/libopenblas*
-rwxr-xr-x 1 root root 29168800 Sep 17 06:46 /usr/lib/julia/libopenblas.so
lrwxrwxrwx 1 root root       14 Sep 17 06:46 /usr/lib/julia/libopenblas.so.0 -> libopenblas.so
staticfloat commented 6 years ago

Because your OpenBLAS is named libopenblas.so and not libopenblas64_.so, I'm guessing that it is not an ILP64 BLAS, (which means that the indices used in matrix operations in your library are 32-bit, not 64-bit). This means that your BLAS operations will be unable to deal with matrices with more than 4.5B elements along any single axis. This may seem like an unrealistic amount, but for many Julia users that is not an unrealistic size at all.

By default, we build all BLAS libraries as ILP64 on 64-bit platforms. Many distributions lag behind us in this, because they want to provide a single BLAS that can be used by all different kinds of numerical software, but unfortunately you cannot swap out a non-ILP64 library with an ILP64 library. We jump through all sorts of hoops in the Julia language because of this, renaming symbols within OpenBLAS so as to allow our ILP64 version of OpenBLAS to peacefully co-exist within a single process as another 3rd party binary that may need a non-ILP64 BLAS might link one in, and you don't want it to accidentally start calling ILP64 functions. (That's also why we name it libopenblas64_.so, to show that it's not the same thing as libopenblas.so).

There are two solutions for you here:

wehlutyk commented 6 years ago

That's a very useful piece of context, thank you!

4.5B elements doesn't seem too far from what I might be facing if I start migrating to Flux.jl fulltime, so I think I'll just go with option 0 and use the binaries from the Julia website since I also need a non-ILP64 implementation on my system.

Thanks for debugging this for me and for the explanations!

eli-schwartz commented 6 years ago

BTW as of today Arch Linux's julia package builds against the system openblas (I finally got it to work) so toggling ILP64 for the internal, vendored copy would not be a solution.

mindbound commented 6 years ago

When building Arpack.jl with Julia 1.0.1 on Arch Linux 4.18.12 x86_64 (latest update, community/julia 2:1.0.1-2), I'm getting the following error:

(v1.0) pkg> build Arpack
  Building Arpack → `~/.julia/packages/Arpack/WP3ru/deps/build.log`
┌ Error: Error building `Arpack`: 
│ ┌ Warning: platform_key() is deprecated, use platform_key_abi() from now on
│ │   caller = ip:0x0
│ └ @ Core :-1
│ ┌ Warning: Could not extract the platform key of https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-0.2.20/ArpackBuilder.x86_64-linux-gnu.tar.gz; continuing...
│ └ @ BinaryProvider ~/.julia/packages/BinaryProvider/cVlaj/src/Prefix.jl:185
│ ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack, "Prefix(/home/user/.julia/packages/Arpack/WP3ru/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] #write_deps_file#152(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /home/user/.julia/packages/BinaryProvider/cVlaj/src/Products.jl:408
│  [2] write_deps_file(::String, ::Array{LibraryProduct,1}) at /home/user/.julia/packages/BinaryProvider/cVlaj/src/Products.jl:395
│  [3] top-level scope at none:0
│  [4] include(::String) at ./client.jl:388
│  [5] top-level scope at none:0
│ in expression starting at /home/user/.julia/packages/Arpack/WP3ru/deps/build.jl:40
└ @ Pkg.Operations /build/julia/src/julia/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1069

Could it be related to this issue? If not, what could I be doing wrong? TIA.

staticfloat commented 6 years ago

We're currently testing the solution of this problem on the latest development version of Arpack.jl; you need to do pkg> add Arpack#master within the Pkg REPL mode to install the latest master version of Arpack within your package environment. (If you've already done that, then you need to pkg> update to get the latest version). This will no longer be necessary once a new version of Arpack is released, however there may be other considerations than just this fix before a new release is made, I'm not sure.

eli-schwartz commented 6 years ago

@mindbound, try repackaging Arpack.jl using a symlink to the libarpack.so provided by the Arch Linux system arpack package.

mindbound commented 6 years ago

Trying to use the latest development version unfortunately results in another error:

(v1.0) pkg> add Arpack#master
  Updating git-repo `https://github.com/JuliaLinearAlgebra/Arpack.jl.git`
 Resolving package versions...
  Updating `~/.julia/environments/v1.0/Project.toml`
  [7d9fca2a] + Arpack v0.2.3+ #master (https://github.com/JuliaLinearAlgebra/Arpack.jl.git)
  Updating `~/.julia/environments/v1.0/Manifest.toml`
 [no changes]
  Building Arpack → `~/.julia/packages/Arpack/UiiMc/deps/build.log`
┌ Error: Error building `Arpack`: 
│ [ Info: Downloading https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-3/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz to /home/user/.julia/packages/Arpack/UiiMc/deps/usr/downloads/Arpack.v3.5.0-3.x86_64-linux-gnu-gcc8.tar.gz...
│ ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack, "Prefix(/home/user/.julia/packages/Arpack/UiiMc/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] #write_deps_file#152(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /home/user/.julia/packages/BinaryProvider/cVlaj/src/Products.jl:408
│  [2] (::getfield(BinaryProvider, Symbol("#kw##write_deps_file")))(::NamedTuple{(:verbose,),Tuple{Bool}}, ::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at ./none:0
│  [3] top-level scope at none:0
│  [4] include(::String) at ./client.jl:388
│  [5] top-level scope at none:0
│ in expression starting at /home/user/.julia/packages/Arpack/UiiMc/deps/build.jl:74
[23:31:24] ######################################################################## 100.0% 
└ @ Pkg.Operations /build/julia/src/julia/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1069

@eli-schwartz, how do I do that? I tried finding something relevant in the Julia docs but failed.

homocomputeris commented 6 years ago

Basically, the same as what @mindbound has:

julia> versioninfo()
Julia Version 1.0.1
Commit 0d713926f8 (2018-09-29 19:05 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Core(TM) i5-6260U CPU @ 1.80GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.0 (ORCJIT, skylake)
julia> using DifferentialEquations
[ Info: Precompiling DifferentialEquations [0c46a032-eb83-5123-abaf-570d42b7fbaa]
ERROR: LoadError: No deps.jl file could be found. Please try running Pkg.build("Arpack").
Currently, the build command might fail when Julia has been built from source
and the recommendation is to use the official binaries from julialang.org.
For more info see https://github.com/JuliaLinearAlgebra/Arpack.jl/issues/5.

Stacktrace:
 [1] top-level scope at /home/user/.julia/packages/Arpack/WP3ru/src/Arpack.jl:19
 [2] top-level scope at none:2
in expression starting at /home/user/.julia/packages/Arpack/WP3ru/src/Arpack.jl:16
ERROR: LoadError: LoadError: Failed to precompile Arpack [7d9fca2a-8960-54d3-9f78-7d1dccf2cb97] to /home/user/.julia/compiled/v1.0/Arpack/X5VZL.ji.
Stacktrace:
 [1] include at ./boot.jl:317 [inlined]
 [2] include_relative(::Module, ::String) at ./loading.jl:1041
 [3] include at ./sysimg.jl:29 [inlined]
 [4] include(::String) at /home/user/.julia/packages/PDMats/mL7bX/src/PDMats.jl:3
 [5] top-level scope at /home/user/.julia/packages/PDMats/mL7bX/src/PDMats.jl:53
 [6] top-level scope at none:2
in expression starting at /home/user/.julia/packages/PDMats/mL7bX/src/pdsparsemat.jl:1
in expression starting at /home/user/.julia/packages/PDMats/mL7bX/src/PDMats.jl:52
ERROR: LoadError: Failed to precompile PDMats [90014a1f-27ba-587c-ab20-58faa44d9150] to /home/user/.julia/compiled/v1.0/PDMats/wuzEE.ji.
Stacktrace:
 [1] top-level scope at none:2
in expression starting at /home/user/.julia/packages/Distributions/WHjOk/src/Distributions.jl:3
ERROR: LoadError: Failed to precompile Distributions [31c24e10-a181-5473-b8eb-7969acd0382f] to /home/user/.julia/compiled/v1.0/Distributions/xILW0.ji.
Stacktrace:
 [1] top-level scope at none:2
in expression starting at /home/user/.julia/packages/LsqFit/IsCnQ/src/LsqFit.jl:10
ERROR: LoadError: Failed to precompile LsqFit [2fda8390-95c7-5789-9bda-21331edee243] to /home/user/.julia/compiled/v1.0/LsqFit/GCdY9.ji.
Stacktrace:
 [1] top-level scope at none:2
in expression starting at /home/user/.julia/packages/DiffEqParamEstim/FpD31/src/DiffEqParamEstim.jl:4
ERROR: LoadError: Failed to precompile DiffEqParamEstim [1130ab10-4a5a-5621-a13d-e4788d82bd4c] to /home/user/.julia/compiled/v1.0/DiffEqParamEstim/nWq0E.ji.
Stacktrace:
 [1] top-level scope at none:2
in expression starting at /home/user/.julia/packages/DifferentialEquations/88DSk/src/DifferentialEquations.jl:19
ERROR: Failed to precompile DifferentialEquations [0c46a032-eb83-5123-abaf-570d42b7fbaa] to /home/user/.julia/compiled/v1.0/DifferentialEquations/UQdwS.ji.

and 

julia> Pkg.build("Arpack")
  Building Arpack → `~/.julia/packages/Arpack/WP3ru/deps/build.log`
┌ Error: Error building `Arpack`: 
│ ┌ Warning: platform_key() is deprecated, use platform_key_abi() from now on
│ │   caller = ip:0x0
│ └ @ Core :-1
│ ┌ Warning: Could not extract the platform key of https://github.com/JuliaLinearAlgebra/ArpackBuilder/releases/download/v3.5.0-0.2.20/ArpackBuilder.x86_64-linux-gnu.tar.gz; continuing...
│ └ @ BinaryProvider ~/.julia/packages/BinaryProvider/cVlaj/src/Prefix.jl:185
│ ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack, "Prefix(/home/user/.julia/packages/Arpack/WP3ru/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] #write_deps_file#152(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /home/user/.julia/packages/BinaryProvider/cVlaj/src/Products.jl:408
│  [2] write_deps_file(::String, ::Array{LibraryProduct,1}) at /home/user/.julia/packages/BinaryProvider/cVlaj/src/Products.jl:395
│  [3] top-level scope at none:0
│  [4] include(::String) at ./client.jl:388
│  [5] top-level scope at none:0
│ in expression starting at /home/user/.julia/packages/Arpack/WP3ru/deps/build.jl:40
└ @ Pkg.Operations /build/julia/src/julia/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1069
ghost commented 6 years ago

@eli-schwartz can you add any detail regarding your symlink suggestion? I tried the shell command ln -s /usr/local/lib/libarpack.so /home/my-user-name/.julia/packages/Arpack/UiiMc/deps/usr/libarpack then Pkg.build("Arpack") back in the Julia REPL. My output was no different than what @mindbound was getting. I also tried to build after editing the build.jl to look in /usr/local/lib/ directly...same error message.

blegat commented 6 years ago

For ArchLinux, you can do the following hack: First download Julia v1.0.1 and unpack it to a dir unpacked_dir and then, do

$ sudo ln -s unpacked_dir/lib/julia/libopenblas64_.so* /usr/lib
$ julia
] build Arpack
damiendr commented 6 years ago

On MacOS 10.12.6 with Julia 1.1-dev#367aab3 and today's Arpack#master, the cause of failure is this:

Libdl.dlopen("/Users/username/.julia/dev/Arpack/deps/usr/lib/libarpack.2.0.0.dylib"; throw_error=true)
ERROR: could not load library "/Users/username/.julia/dev/Arpack/deps/usr/lib/libarpack.2.0.0.dylib"
dlopen(/Users/username/.julia/dev/Arpack/deps/usr/lib/libarpack.2.0.0.dylib, 1):
  Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: /Users/username/.julia/dev/Arpack/deps/usr/lib/libarpack.2.0.0.dylib
  Reason: image not found
staticfloat commented 6 years ago

@damiendr are you running your julia out of the build tree? E.g. you ran make and then ran ./julia without running make install? If so, running make install will bundle Julia together into a directory (named something like julia-367aab3) and if you run Julia out of that directory it should work, as it will have collected all the necessary dependent libraries (such as libgfortran) already. I have a PR open to do this earlier (e.g. during build time, not just during make install time) but it unfortunately has not been merged yet.

damiendr commented 6 years ago

@staticfloat correct, thanks for pointing this out! I've just run make install but this did not fix the problem, and indeed there is no libgfortran in julia-367aab3dc1/lib/julia. Compared to the 1.0 official binary, that lib dir is missing libgcc, libgfortran and libquadmath. But I realise I'm running an untagged dev version, maybe I should wait for the next tagged release and try again.

staticfloat commented 6 years ago

I'm terribly sorry, it's not make install its make binary-dist; that will generate a .tar.gz that contains everything bundled up and ready for distribution. You can then unpack that anywhere you want. It's not a perfect workaround, but it should solve the issue for you.

damiendr commented 6 years ago

@staticfloat that fixed it, thanks a lot! Arpack now builds & passes tests.

platawiec commented 6 years ago

I've been following this issue and #7, and from what I gather this only fixes the build issue when Julia is built from source with OpenBLAS. If so, is there any way for Arpack to build from MKL with the current master? Or will this be addressed in a future PR?

eli-schwartz commented 6 years ago

@platawiec

It is much simpler for everyone if the binaries are built once, and simply distributed to users in the format they were going to compile down to anyway.

The maintainers of this software have engaged in significant, nontrivial effort to provide prebuilt libarpack.so binaries for a wide variety of possible from-source build permutations, completely ignoring the underlying issue which is that from-source builds already come with ecosystem libarpack.so that works. They're plainly uninterested in any sort of fallback mode that helps downstream choice at the expense of highly theoretical compilation woes.

Your only hope, apparently, is to add another 6 or 7 prebuilt artifacts to a giant case statement and release a new version of the software, then repeat this every time something on your system changes.

x-ji commented 6 years ago

@blegat That didn't seem to work though... I still got the same errors and eventually I had to uninstall Julia and use the binary download version on Arch Linux. Using Arpack#master didn't help either.

blakejohnson commented 6 years ago

It's still the case for me that the only thing that works on the Mac is to run julia as: DYLD_LIBRARY_PATH=/usr/local/opt/gcc@8/lib/gcc/8 ./julia

I've tried symlinking libgfortran.5.dylib into the Arpack deps/usr/lib folder and that did not fix the problem.

andreasnoack commented 6 years ago

@blakejohnson Did you try to build julia with make binary-dist?

blakejohnson commented 6 years ago

@andreasnoack I was running julia from the repo directory (i.e. just make and then ./julia)

heroxbd commented 6 years ago

It is quite unfortunate to know the Julia does not support compiling from source. I am surprised because arpack is such a central package for many high-level libraries.

arnonerba commented 5 years ago

To clarify, does this bug mean that it is currently impossible to install Arpack.jl when Julia is built from source with Intel MKL, or is there a workaround? If there is no workaround, are there any plans to support Julia + MKL?

chriselrod commented 5 years ago 
(v1.0) pkg> test Arpack
   Testing Arpack
 Resolving package versions...
    Status `/tmp/tmpLoS05i/Manifest.toml`
  [7d9fca2a] Arpack v0.3.0+ [`~/.julia/dev/Arpack`]
  [b99e7846] BinaryProvider v0.5.2
  [2a0f44e3] Base64  [`@stdlib/Base64`]
  [ade2ca70] Dates  [`@stdlib/Dates`]
  [8ba89e20] Distributed  [`@stdlib/Distributed`]
  [b77e0a4c] InteractiveUtils  [`@stdlib/InteractiveUtils`]
  [76f85450] LibGit2  [`@stdlib/LibGit2`]
  [8f399da3] Libdl  [`@stdlib/Libdl`]
  [37e2e46d] LinearAlgebra  [`@stdlib/LinearAlgebra`]
  [56ddb016] Logging  [`@stdlib/Logging`]
  [d6f4376e] Markdown  [`@stdlib/Markdown`]
  [44cfe95a] Pkg  [`@stdlib/Pkg`]
  [de0858da] Printf  [`@stdlib/Printf`]
  [3fa0cd96] REPL  [`@stdlib/REPL`]
  [9a3f8284] Random  [`@stdlib/Random`]
  [ea8e919c] SHA  [`@stdlib/SHA`]
  [9e88b42a] Serialization  [`@stdlib/Serialization`]
  [6462fe0b] Sockets  [`@stdlib/Sockets`]
  [2f01184e] SparseArrays  [`@stdlib/SparseArrays`]
  [8dfed614] Test  [`@stdlib/Test`]
  [cf7118a7] UUIDs  [`@stdlib/UUIDs`]
  [4ec0a83e] Unicode  [`@stdlib/Unicode`]
Test Summary: | Pass  Total
eigs          |   56     56
Test Summary: | Pass  Total
real svds     |  189    189
Test Summary: | Pass  Total
complex svds  |    7      7
Test Summary: | Pass  Total
promotion     |    3      3
Test Summary:               | Pass  Total
svds for non-AbstractMatrix |    1      1
   Testing Arpack tests passed 

julia> using LinearAlgebra

julia> BLAS.vendor()
:mkl

I think my workaround was simply to have Julia built with OpenBLAS installed and use that to install Arpack. Seems that lets me call it just fine from Julia + MKL.

rjkat commented 5 years ago

Can confirm @chriselrod's workaround. Maybe Arpack.jl should just go and download Julia itself :upside_down_face:

platawiec commented 5 years ago

I can confirm as well! To get it to work, I simply had to make sure that the Julia built with OpenBLAS was installing Arpack in the environment I wanted to use it in for the MKL version.

carstenbauer commented 5 years ago

Maybe I don't understand but the "fix" doesn't work for me. If I install and build Arpack with Julia + OpenBLAS (binaries) and then use my compiled Julia + MKL to use it I get:

julia> using Arpack
[ Info: Recompiling stale cache file /gpfs/homea/hku27/hku273/.julia-mkl/compiled/v1.0/Arpack/X5VZL.ji for Arpack [7d9fca2a-8960-54d3-9f78-7d1dccf2cb97]

julia> eigs(rand(100,100))
ERROR: error compiling aupd_wrapper: error compiling naupd: could not load library "/gpfs/homea/hku27/hku273/.julia-mkl/packages/Arpack/0oGDs/deps/usr/lib/libarpack.so"
libopenblas64_.so.0: cannot open shared object file: No such file or directory
Stacktrace:
 [1] #_eigs#17(::Int64, ::Int64, ::Symbol, ::Float64, ::Int64, ::Nothing, ::Array{Float64,1}, ::Bool, ::typeof(Arpack._eigs), ::Array{Float64,2}, ::LinearAlgebra.UniformScaling{Bool}) at /gpfs/homea/hku27/hku273/.julia-mkl/packages/Arpack/0oGDs/src/Arpack.jl:120
 [2] _eigs at /gpfs/homea/hku27/hku273/.julia-mkl/packages/Arpack/0oGDs/src/Arpack.jl:88 [inlined]
 [3] #eigs#10 at /gpfs/homea/hku27/hku273/.julia-mkl/packages/Arpack/0oGDs/src/Arpack.jl:63 [inlined]
 [4] eigs at /gpfs/homea/hku27/hku273/.julia-mkl/packages/Arpack/0oGDs/src/Arpack.jl:63 [inlined]
 [5] #eigs#9 at /gpfs/homea/hku27/hku273/.julia-mkl/packages/Arpack/0oGDs/src/Arpack.jl:62 [inlined]
 [6] eigs(::Array{Float64,2}) at /gpfs/homea/hku27/hku273/.julia-mkl/packages/Arpack/0oGDs/src/Arpack.jl:62
 [7] top-level scope at none:0

Do have to use a self-compiled Julia + OpenBLAS?

carstenbauer commented 5 years ago

Note that I also can't use Distributions.jl because of this (as it seems to depend on Arpack).

dlfivefifty commented 5 years ago

Deleting and reinstalling Homebrew fixed the issue with Arpack for me.

riccardosven commented 5 years ago

The problem seems to be that libarpack is linked to libopenblas64_.so as shown in 

$ ldd ~/.julia/packages/Arpack/UiiMc/deps/usr/liblibarpack.so
    linux-vdso.so.1 (0x00007fff363c5000)
    libopenblas64_.so.0 => not found
    libgfortran.so.5 => /usr/lib/libgfortran.so.5 (0x00007f67481fe000)
    libm.so.6 => /usr/lib/libm.so.6 (0x00007f6748079000)
    libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007f674805f000)
    libquadmath.so.0 => /usr/lib/libquadmath.so.0 (0x00007f674801c000)
    libc.so.6 => /usr/lib/libc.so.6 (0x00007f6747e58000)
    libz.so.1 => /usr/lib/../lib/libz.so.1 (0x00007f6747c3f000)
    /usr/lib64/ld-linux-x86-64.so.2 (0x00007f6748709000)

On Archlinux with community LibOpenblas, a symbolic link to libopenblas.so fixes the issue:

# ln -s /usr/lib/libopenblas.so /usr/lib/libopenblas64_.so.0

and Arpack builds fine. (@crstnbr, this also fixes the problem with Distributions.jl).

Why is the "64_" added to the library filename?

carstenbauer commented 5 years ago

@rsrsl Unfortunately, I don't have write access to /usr/lib. I'm on a university cluster.

Also, for me the ouput is

$ ldd packages/Arpack/UiiMc/deps/usr/lib/libarpack.so
        linux-vdso.so.1 =>  (0x00007ffda671f000)
        libopenblas64_.so.0 => not found
        libgfortran.so.5 => not found
        libm.so.6 => /lib64/libm.so.6 (0x00002b1702652000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b17028d6000)
        libquadmath.so.0 => not found
        libc.so.6 => /lib64/libc.so.6 (0x00002b1702aed000)
        /lib64/ld-linux-x86-64.so.2 (0x0000003801600000)

so apparently more than just libopenblas64_.so.0 can't be found.

Regarding the 64_ suffix, maybe this has something to do with the comment here:

Binaries designed to be compatible with Julia are regularly provided in https://github.com/staticfloat/OpenBLASBuilder/releases . Note that their 64bit builds with INTERFACE64=1 have _64 appended to the function symbol names, so your code needs to refer to e.g. gemm64 rather than gemm_

aytekinar commented 5 years ago

@crstnbr, you have libgfortran missing on the cluster. Both libgfortran and libquadmath are provided in that package.

@rsrsl Unfortunately, I don't have write access to /usr/lib. I'm on a university cluster.

Maybe you can try

mkdir -p $HOME/usr/lib
ln -fis /usr/lib/libopenblas.so $HOME/usr/lib/libopenblas64_.so.0
LD_LIBRARY_PATH=$HOME/usr/lib julia

to set the symbolic link in your home folder, configure your LD_LIBRARY_PATH environment variable accordingly and fire up julia. Then, ]build Arpack should work.

IMHO the line that forces Julia's preference on the so naming convention of OpenBLAS is the problem. It would be better if ArpackBuilder downloaded OpenBLAS from source and built it, and then built Arpack using cmake's CMAKE_PREFIX_PATH variable to point to $prefix to link against the OpenBLAS built from source. This way, the tarballs would be self-contained.

In principle, I think that the prebuilt binaries should (re-)distribute their dependencies without assuming how the target system is configured. But I am no expert, either :(

andreasnoack commented 5 years ago

Why is the "64_" added to the library filename?

Because we build OpenBLAS with 64 bit integers. I think most Linux distros build with 32 bit integers.