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Build on MacOS Catalina #12

Closed
CHNPAT005 opened this issue Jan 5, 2020 · 8 comments
Closed

Build on MacOS Catalina #12

CHNPAT005 opened this issue Jan 5, 2020 · 8 comments

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@CHNPAT005
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Hi there, many thanks for the work. I am running Catalina with JuliaPro v1.2.0. I have followed the steps and have installed the relevant dependencies according to the instructions provided by flatironinstitute. The build seems to be successful, however when I try to run test FINUFFT I get this error:

Test Summary: | Error Total FINUFFT | 1 1 ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/test/runtests.jl:3 ERROR: Package FINUFFT errored during testing

The origin of this error seems to arise because it can't seem to load libfinufft:

ERROR: LoadError: LoadError: LoadError: Unable to load libfinufft (/Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/lib/libfinufft.dylib) Please re-run Pkg.build(package), and restart Julia.

A similar issue I have found JuliaLang/julia#29720 suggests creating a simlink. If this is the solution - do you know which paths I am supposed to link? Otherwise do you have any other suggestions on resolving the issue?

Below is the full error message when running test FINUFFT:

(v1.2) pkg> test FINUFFT
Testing FINUFFT
Resolving package versions...
Status /var/folders/r3/8h3wf5111v96y8vqd4y966l40000gp/T/jl_DX6vRx/Manifest.toml
[9e28174c] BinDeps v0.8.10
[34da2185] Compat v2.2.0
[8f4d0f93] Conda v1.3.0
[d8beea63] FINUFFT v0.4.2
[682c06a0] JSON v0.21.0
[69de0a69] Parsers v0.3.10
[30578b45] URIParser v0.4.0
[81def892] VersionParsing v1.2.0
[2a0f44e3] Base64 [@stdlib/Base64]
[b99e7846] BinaryProvider [@stdlib/BinaryProvider]
[864e158e] CredentialsHandler [@stdlib/CredentialsHandler]
[ade2ca70] Dates [@stdlib/Dates]
[8bb1440f] DelimitedFiles [@stdlib/DelimitedFiles]
[8ba89e20] Distributed [@stdlib/Distributed]
[cd3eb016] HTTP [@stdlib/HTTP]
[83e8ac13] IniFile [@stdlib/IniFile]
[b77e0a4c] InteractiveUtils [@stdlib/InteractiveUtils]
[76f85450] LibGit2 [@stdlib/LibGit2]
[8f399da3] Libdl [@stdlib/Libdl]
[37e2e46d] LinearAlgebra [@stdlib/LinearAlgebra]
[56ddb016] Logging [@stdlib/Logging]
[d6f4376e] Markdown [@stdlib/Markdown]
[739be429] MbedTLS [@stdlib/MbedTLS]
[a63ad114] Mmap [@stdlib/Mmap]
[44cfe95a] Pkg [@stdlib/Pkg]
[de0858da] Printf [@stdlib/Printf]
[3fa0cd96] REPL [@stdlib/REPL]
[9a3f8284] Random [@stdlib/Random]
[ea8e919c] SHA [@stdlib/SHA]
[9e88b42a] Serialization [@stdlib/Serialization]
[1a1011a3] SharedArrays [@stdlib/SharedArrays]
[6462fe0b] Sockets [@stdlib/Sockets]
[2f01184e] SparseArrays [@stdlib/SparseArrays]
[10745b16] Statistics [@stdlib/Statistics]
[9d418dce] TOML [@stdlib/TOML]
[8dfed614] Test [@stdlib/Test]
[cf7118a7] UUIDs [@stdlib/UUIDs]
[4ec0a83e] Unicode [@stdlib/Unicode]
ERROR: LoadError: LoadError: LoadError: Unable to load

libfinufft (/Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/lib/libfinufft.dylib)

Please re-run Pkg.build(package), and restart Julia.
Stacktrace:
[1] error(::String, ::String) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[2] @checked_lib(::LineNumberNode, ::Module, ::Any, ::Any) at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/deps.jl:11
[3] include_relative(::Module, ::String) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[4] include at ./Base.jl:31 [inlined]
[5] include(::String) at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/src/FINUFFT.jl:2
[6] top-level scope at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/src/FINUFFT.jl:22
[7] include_relative(::Module, ::String) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[8] include(::Module, ::String) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[9] top-level scope at none:2
[10] eval at ./boot.jl:330 [inlined]
[11] eval(::Expr) at ./client.jl:432
[12] top-level scope at ./none:3
in expression starting at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/deps.jl:26
in expression starting at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/deps.jl:26
in expression starting at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/src/FINUFFT.jl:21
FINUFFT: Error During Test at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/test/runtests.jl:3
Got exception outside of a @test
LoadError: Failed to precompile FINUFFT [d8beea63-0952-562e-9c6a-8e8ef7364055] to /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/compiled/v1.2/FINUFFT/WbG1O.ji.
Stacktrace:
[1] error(::String) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[2] compilecache(::Base.PkgId, ::String) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[3] _require(::Base.PkgId) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[4] require(::Base.PkgId) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:? (repeats 2 times)
[5] include_relative(::Module, ::String) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[6] include(::Module, ::String) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[7] include(::String) at ./client.jl:431
[8] top-level scope at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/test/runtests.jl:4
[9] top-level scope at /Users/vagrant/worker/juliapro-release-osx1011-0_6/build/tmp_julia/Julia-1.2.app/Contents/Resources/julia/share/julia/stdlib/v1.2/Test/src/Test.jl:1113
[10] top-level scope at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/test/runtests.jl:4
[11] include_relative(::Module, ::String) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[12] include(::Module, ::String) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[13] include(::String) at ./client.jl:431
[14] top-level scope at none:5
[15] eval(::Module, ::Any) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[16] exec_options(::Base.JLOptions) at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
[17] _start() at /Applications/JuliaPro-1.2.0-1.app/Contents/Resources/julia/Contents/Resources/julia/lib/julia/sys.dylib:?
in expression starting at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/test/test_error_handler.jl:1

Test Summary: | Error Total
FINUFFT | 1 1
ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/test/runtests.jl:3
ERROR: Package FINUFFT errored during testing
@ludvigak
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ludvigak commented Jan 9, 2020

Hi!
Sorry for replying late, let's see if we can get this working for you!

First thing to check is whether the build actually was successful.

  • Can you run build FINUFFT ?
  • Are any errors reported in deps/build.log ?
  • Is there a file called deps/usr/lib/libfinufft.* ?

I don't have access to a Mac myself, so setting up and debugging the build process is a bit tricky. It's currently hardwired to GCC 8, so you either need to have that or change the build script.

Also, I have no idea whether things might behave differently with JuliaPro. I would hope not, but I haven't tried it myself.

@CHNPAT005
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Hi, thank you for the response!

  • This is what I get from running `build FINUFFT':

build FINUFFT
Building Conda ──→ ~/.juliapro/JuliaPro_v1.2.0-1/packages/Conda/kLXeC/deps/build.log
Building FINUFFT → ~/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/build.log

  • Here is the output in deps/build.log:

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

==> WARNING: A newer version of conda exists. <==
current version: 4.8.0
latest version: 4.8.1

Please update conda by running

$ conda update -n base -c defaults conda

All requested packages already installed.

make: lib/libfinufft.so' is up to date. [ Info: Running conda install -y fftw` in /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr environment
[ Info: Attempting to create directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/downloads
[ Info: Directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/downloads already exists
[ Info: Downloading file https://github.com/flatironinstitute/finufft/archive/1.1.1.zip
[ Info: Done downloading file https://github.com/flatironinstitute/finufft/archive/1.1.1.zip
[ Info: Attempting to create directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src
[ Info: Directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src already exists
[ Info: Attempting to create directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps
[ Info: Directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps already exists
[ Info: Path /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1 already exists
[ Info: Changing directory to /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1
[ Info: Changing directory to /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1
[ Info: Attempting to create directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/lib
[ Info: Directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/lib already exists
[ Info: Changing directory to /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1
lib = BinDeps.libdir(fftw) = "/Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/lib"
inc = BinDeps.includedir(fftw) = "/Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/include"

  • There is currently no file called deps/usr/lib/libfinufft.* , there is only deps/usr/lib/libfinufft.dylib.

  • I did find that the error message:
    ERROR: LoadError: LoadError: LoadError: Unable to load libfinufft (/Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/lib/libfinufft.dylib) Please re-run Pkg.build(package), and restart Julia.
    Comes from an error message printed from the file deps/deps.jl

  • It seems that I am not running GCC 8, what do you think will be easier to change?

@ludvigak
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ludvigak commented Jan 9, 2020

Hmm, that is confusing, so are you saying that the file /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/lib/libfinufft.dylib exists?

@CHNPAT005
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CHNPAT005 commented Jan 9, 2020 •
edited

Yes it does

There previously wasn't

/Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/lib/libfinufft.a, but i added it recently as I noticed all the other files also had a .a version.

With or without the .a version - I get the same error as before.

@ludvigak
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ludvigak commented Jan 9, 2020

deps/deps.jl should have a line that starts with @checked_lib libfinufft , that points to the libfinufft library file created by the build process. If that file exists, then you shouldn't get that error.

Could you remove the folders deps/usr and deps/src, run build FINUFFT again, and re-post the contents of deps/build.log ?

@CHNPAT005
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I have changed it to GCC 8 and here is the new contents of deps/build.log:

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

Package Plan

environment location: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr

added / updated specs:
- fftw

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
fftw-3.3.8                 |       h1de35cc_3         2.0 MB
------------------------------------------------------------
                                       Total:         2.0 MB

The following NEW packages will be INSTALLED:

fftw pkgs/main/osx-64::fftw-3.3.8-h1de35cc_3

Downloading and Extracting Packages

fftw-3.3.8 | 2.0 MB | | 0%
fftw-3.3.8 | 2.0 MB | | 1%
fftw-3.3.8 | 2.0 MB | 1 | 2%
fftw-3.3.8 | 2.0 MB | 3 | 3%
fftw-3.3.8 | 2.0 MB | 5 | 5%
fftw-3.3.8 | 2.0 MB | 6 | 6%
fftw-3.3.8 | 2.0 MB | 8 | 9%
fftw-3.3.8 | 2.0 MB | # | 10%
fftw-3.3.8 | 2.0 MB | #1 | 12%
fftw-3.3.8 | 2.0 MB | #3 | 13%
fftw-3.3.8 | 2.0 MB | #4 | 15%
fftw-3.3.8 | 2.0 MB | #6 | 16%
fftw-3.3.8 | 2.0 MB | #7 | 18%
fftw-3.3.8 | 2.0 MB | #9 | 19%
fftw-3.3.8 | 2.0 MB | ## | 21%
fftw-3.3.8 | 2.0 MB | ##2 | 22%
fftw-3.3.8 | 2.0 MB | ##4 | 24%
fftw-3.3.8 | 2.0 MB | ##6 | 26%
fftw-3.3.8 | 2.0 MB | ##7 | 28%
fftw-3.3.8 | 2.0 MB | ###1 | 32%
fftw-3.3.8 | 2.0 MB | ###4 | 35%
fftw-3.3.8 | 2.0 MB | ###7 | 38%
fftw-3.3.8 | 2.0 MB | ####1 | 41%
fftw-3.3.8 | 2.0 MB | ####4 | 44%
fftw-3.3.8 | 2.0 MB | ####7 | 47%
fftw-3.3.8 | 2.0 MB | ####9 | 50%
fftw-3.3.8 | 2.0 MB | #####2 | 53%
fftw-3.3.8 | 2.0 MB | #####6 | 57%
fftw-3.3.8 | 2.0 MB | ###### | 60%
fftw-3.3.8 | 2.0 MB | ######4 | 64%
fftw-3.3.8 | 2.0 MB | ######8 | 69%
fftw-3.3.8 | 2.0 MB | #######2 | 73%
fftw-3.3.8 | 2.0 MB | #######8 | 78%
fftw-3.3.8 | 2.0 MB | ########2 | 83%
fftw-3.3.8 | 2.0 MB | ########7 | 88%
fftw-3.3.8 | 2.0 MB | #########2 | 92%
fftw-3.3.8 | 2.0 MB | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

==> WARNING: A newer version of conda exists. <==
current version: 4.8.0
latest version: 4.8.1

Please update conda by running

$ conda update -n base -c defaults conda

Archive: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/downloads/1.1.1.zip
abdee011c826ac95ff5e7069622bf87f2c18651e
creating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/CHANGELOG
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/LICENSE
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/README.md
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/TODO
creating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/contrib/
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/contrib/legendre_rule_fast.c
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/contrib/legendre_rule_fast.h
creating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/ESlocalpoly.m
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/eval_ker_expts.cpp
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/eval_ker_expts2.cpp
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/eval_ker_expts_ludvig.cpp
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/fig_speed_ker_ppval.m
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/gen_all_horner_C_code.m
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/gen_ker_horner_C_code.m
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/gen_ker_horner_loop_C_code.m
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/i7_1thr_ker_eval_speeds.png
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/ker_ppval_coeff_mat.m
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/test_ker_ppval.cpp
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/devel/time2d2interp.cpp
creating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/docs/
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/docs/Makefile
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inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/nuffttestnd.sh
creating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/README
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/check1d.sh.refout
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/check2d.sh.refout
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/check3d.sh.refout
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/dumbinputs.refout
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/gcc_vs_icc_xeon.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/nuffttestnd_results_i7_2-2-17.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/nuffttestnd_results_i7_3-16-17.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/nuffttestnd_results_i7_6-17-17.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/nuffttestnd_results_i7_gcc72_4-24-18.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/nuffttestnd_results_i7_gcc72_4-25-18.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/perftest_xeon-E5-2643v3.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/spreadtestnd_results_i7_2-2-17.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/spreadtestnd_results_i7_3-16-17.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/spreadtestnd_results_i7_6-17-17.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/spreadtestnd_results_i7_gcc72_4-24-18.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/spreadtestnd_results_i7_gcc72_4-25-18.txt
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/results/testutils.refout
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/spreadbenchmark.py
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/spreadtestnd.cpp
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/spreadtestnd.sh
inflating: /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1/test/testutils.cpp
g++-8 -c -fPIC -O3 -funroll-loops -march=native -fcx-limited-range -I src -fopenmp -DNEED_EXTERN_C -fopenmp src/spreadinterp.cpp -o src/spreadinterp.o
g++-8 -c -fPIC -O3 -funroll-loops -march=native -fcx-limited-range -I src -fopenmp -DNEED_EXTERN_C -fopenmp src/utils.cpp -o src/utils.o
g++-8 -fPIC -O3 -funroll-loops -march=native -fcx-limited-range -I src -fopenmp -DNEED_EXTERN_C -fopenmp -c -o src/finufft1d.o src/finufft1d.cpp
g++-8 -fPIC -O3 -funroll-loops -march=native -fcx-limited-range -I src -fopenmp -DNEED_EXTERN_C -fopenmp -c -o src/finufft2d.o src/finufft2d.cpp
g++-8 -fPIC -O3 -funroll-loops -march=native -fcx-limited-range -I src -fopenmp -DNEED_EXTERN_C -fopenmp -c -o src/finufft3d.o src/finufft3d.cpp
g++-8 -fPIC -O3 -funroll-loops -march=native -fcx-limited-range -I src -fopenmp -DNEED_EXTERN_C -fopenmp -c -o src/dirft1d.o src/dirft1d.cpp
g++-8 -fPIC -O3 -funroll-loops -march=native -fcx-limited-range -I src -fopenmp -DNEED_EXTERN_C -fopenmp -c -o src/dirft2d.o src/dirft2d.cpp
g++-8 -fPIC -O3 -funroll-loops -march=native -fcx-limited-range -I src -fopenmp -DNEED_EXTERN_C -fopenmp -c -o src/dirft3d.o src/dirft3d.cpp
g++-8 -c -fPIC -O3 -funroll-loops -march=native -fcx-limited-range -I src -fopenmp -DNEED_EXTERN_C -fopenmp src/common.cpp -o src/common.o
gcc-8 -c -fPIC -O3 -funroll-loops -march=native -fcx-limited-range -I src -fopenmp contrib/legendre_rule_fast.c -o contrib/legendre_rule_fast.o
g++-8 -c -fPIC -O3 -funroll-loops -march=native -fcx-limited-range -I src -fopenmp -DNEED_EXTERN_C -fopenmp fortran/finufft_f.cpp -o fortran/finufft_f.o
g++-8 -shared -fopenmp -lfftw3 -lm -lfftw3_threads src/spreadinterp.o src/utils.o src/finufft1d.o src/finufft2d.o src/finufft3d.o src/dirft1d.o src/dirft2d.o src/dirft3d.o src/common.o contrib/legendre_rule_fast.o fortran/finufft_f.o -o lib/libfinufft.so
[ Info: Running conda install -y fftw in /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr environment
[ Info: Attempting to create directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/downloads
[ Info: Directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/downloads already exists
[ Info: Downloading file https://github.com/flatironinstitute/finufft/archive/1.1.1.zip
[ Info: Done downloading file https://github.com/flatironinstitute/finufft/archive/1.1.1.zip
[ Info: Attempting to create directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src
[ Info: Attempting to create directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps
[ Info: Directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps already exists
[ Info: Changing directory to /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1
[ Info: Changing directory to /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1
[ Info: Attempting to create directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/lib
[ Info: Directory /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/lib already exists
[ Info: Changing directory to /Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/src/finufft-1.1.1
lib = BinDeps.libdir(fftw) = "/Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/lib"
inc = BinDeps.includedir(fftw) = "/Users/patrickchang/.juliapro/JuliaPro_v1.2.0-1/packages/FINUFFT/bgr7t/deps/usr/include"

I then ran test FINUFFT and it worked!!!

@CHNPAT005
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I am not sure what fixed the issue:

  • making sure I am using GCC8 or
  • deleting deps/usr and deps/src and rebuilding the package
    but it worked!

Thank you for your assistance in this matter and thank you for this work!

@ludvigak
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ludvigak commented Jan 9, 2020

Ok, that is good news! =)

@ludvigak ludvigak closed this as completed Jan 9, 2020
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@ludvigak @CHNPAT005