Build failed to get libcoinblas #38

blegat · 2018-09-17T16:14:03Z

When building on Julia v1.0 and Arch Linux I get

ERROR: LoadError: LoadError: LibraryProduct(nothing, ["libcoinblas"], Symbol(""), "Prefix(/home/blegat/.julia/dev/Clp/deps/usr)") is not satisfied, cannot generate deps.jl!
Stacktrace:
 [1] #write_deps_file#134(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /home/blegat/.julia/packages/BinaryProvider/UTYxu/src/Products.jl:409
 [2] write_deps_file(::String, ::Array{LibraryProduct,1}) at /home/blegat/.julia/packages/BinaryProvider/UTYxu/src/Products.jl:396
 [3] top-level scope at none:0
 [4] include at ./sysimg.jl:29 [inlined]
 [5] include(::String) at ./loading.jl:1073
 [6] top-level scope at none:0
in expression starting at /home/blegat/.julia/dev/Clp/deps/build_COINBLASBuilder.v1.4.6.jl:45
in expression starting at /home/blegat/.julia/dev/Clp/deps/build.jl:46

However, I get

$ ls -R usr
usr:
downloads  lib  logs  manifests

usr/downloads:
COINBLASBuilder.v1.4.6.x86_64-linux-gnu.tar.gz  COINBLASBuilder.v1.4.6.x86_64-linux-gnu.tar.gz.sha256

usr/lib:
libcoinblas.a  libcoinblas.la  libcoinblas.so  libcoinblas.so.1  libcoinblas.so.1.4.6  pkgconfig

usr/lib/pkgconfig:
coinblas.pc

usr/logs:
COINBLASBuilder.log

usr/manifests:
COINBLASBuilder.v1.4.6.x86_64-linux-gnu.list

The text was updated successfully, but these errors were encountered:

mlubin · 2018-09-18T11:40:49Z

@juan-pablo-vielma

mlubin · 2018-09-18T11:41:40Z

@blegat how was Julia installed? AFAIK BinaryBuilder binaries don't work with Julia source builds.

blegat · 2018-09-18T13:46:48Z

Through pacman

juan-pablo-vielma · 2018-09-18T15:40:07Z

Can you please post the output of ldd libcoinblas.so and ls -la on julia-1.0.0/lib/julia

juan-pablo-vielma · 2018-09-18T15:56:38Z

actually I see pacman uses the systems gcc (there is no libgfortran in usr/lib/julia/) so the important info is the version of libgfortran installed by that version of gcc. Looks like it would be gcc v8 which comes with libgfortran v5, while
libcoinblas.so requires libgfortran v4 which would explain the problem. If this is indeed the case, adding libgfortran.so.4 (e.g. from GCC v7) to the LD_LIBRARY_PATH should fix it (or copying it to Clp's usr/lib directory).

blegat · 2018-09-18T17:00:45Z

Indeed, it seems to be the missing libgfortran.so.4

$ ldd libcoinblas.so
	linux-vdso.so.1 (0x00007ffc97dca000)
	libgfortran.so.4 => not found
	libm.so.6 => /usr/lib/libm.so.6 (0x00007f38ca445000)
	libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007f38ca42b000)
	libquadmath.so.0 => /usr/lib/libquadmath.so.0 (0x00007f38ca3e8000)
	libc.so.6 => /usr/lib/libc.so.6 (0x00007f38ca224000)
	/usr/lib64/ld-linux-x86-64.so.2 (0x00007f38ca849000)
$ cd /usr/lib/julia 
$ julia ls -a
.                      libgit2.so          libpcre2-8.so
..                     libgmp.so           libpcre2-8.so.0
libamd.so              libmpfr.so          libpcre2-8.so.0.6.0
libcamd.so             libmpfr.so.6        libspqr.so
libccalltest.so        libmpfr.so.6.0.1    libsuitesparseconfig.so
libccalltest.so.debug  libopenblas.so      libsuitesparse_wrapper.so
libccolamd.so          libopenblas.so.0    libumfpack.so
libcholmod.so          libopenlibm.so      sys.so
libcolamd.so           libopenlibm.so.2
libdSFMT.so            libopenlibm.so.2.5

juan-pablo-vielma · 2018-09-18T22:44:51Z

I just thought of inelegant, but simple solution. Copy the libgfortran.so.4 from the Julia pre-build binaries to somewhere BP can find 🙂

ianfiske · 2018-09-19T20:58:19Z

Sounds similar to the workaround being implemented by users of Arpack.jl: JuliaLinearAlgebra/Arpack.jl#5 (comment), needed by folks to get Gadfly working, as noted in https://discourse.julialang.org/t/julia-1-0-support-just-landed-on-gadfly-master/14978/16.

juan-pablo-vielma · 2018-09-19T21:02:20Z

Linking this BB issue that should eventually resolve everything
JuliaPackaging/BinaryBuilder.jl/issues/253

jzazo · 2018-10-09T02:25:47Z

Hi! It seems the previous issue was recently closed. I however cannot use Clp in Julia v0.7 or v1 because of the following build error:

Error: Error building `Clp`:
│   % Total    % Received % Xferd  Average Speed   Time    Time     TimeCurrent
│                                  Dload  Upload   Total   Spent    LeftSpeed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--100   172    0   172    0     0   1508      0 --:--:-- --:--:-- --:--:--1508
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--100   622    0   622    0     0   3417      0 --:--:-- --:--:-- --:--:--607k
│ curl: (6) Could not resolve host: github-production-release-asset-2e65be.s3.amazonaws.com
│ ┌ Warning: platform_key() is deprecated, use platform_key_abi() from now on
│ │   caller = ip:0x0
│ └ @ Core :-1
│ ERROR: LoadError: failed process: Process(`curl -g -L -f -o build_COINBLASBuilder.v1.4.6.jl https://github.com/juan-pablo-vielma/COINBLASBuilder/releases/download/v1.4.6-beta2/build_COINBLASBuilder.v1.4.6.jl`, ProcessExited(6)) [6]

Can a fix be released now that BB has been updated?
I assume the error I get is related, but maybe is a different issue. Thanks.

juan-pablo-vielma · 2018-10-09T16:34:49Z

Can you send me more info on your system, it could be unrelated.

jzazo · 2018-10-09T16:55:44Z

It seems it was unrelated. I am on Ubuntu 18.04. Yesterday I installed gfortran-7 but I didn't reboot. Today I tried again and it was building, maybe that was it. I will report if I encounter the problem again, but it looks fine at the moment. Thank you.

blegat · 2018-10-09T17:07:34Z

I also encountered this problem on Travis, then I restarted the build and it succeeded

yakir12 · 2018-11-29T11:22:04Z

Same problem here:

   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.0.2 (2018-11-08)
 _/ |\__'_|_|_|\__'_|  |  
|__/                   |

(v1.0) pkg> build Clp
  Building Clp → `~/.julia/packages/Clp/9Gz64/deps/build.log`
┌ Error: Error building `Clp`: 
│   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
│                                  Dload  Upload   Total   Spent    Left  Speed
100   172    0   172    0     0     39      0 --:--:--  0:00:04 --:--:--    39
100   622    0   622    0     0    117      0 --:--:--  0:00:05 --:--:--     0
100  3355  100  3355    0     0    394      0  0:00:08  0:00:08 --:--:--  1430
│ ┌ Warning: platform_key() is deprecated, use platform_key_abi() from now on
│ │   caller = ip:0x0
│ └ @ Core :-1
│ ERROR: LoadError: LoadError: LibraryProduct(nothing, ["libcoinblas"], Symbol(""), "Prefix(/home/yakir/.julia/packages/Clp/9Gz64/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] #write_deps_file#152(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /home/yakir/.julia/packages/BinaryProvider/4F5Hq/src/Products.jl:414
│  [2] write_deps_file(::String, ::Array{LibraryProduct,1}) at /home/yakir/.julia/packages/BinaryProvider/4F5Hq/src/Products.jl:395
│  [3] top-level scope at none:0
│  [4] include at ./sysimg.jl:29 [inlined]
│  [5] include(::String) at ./loading.jl:1079
│  [6] top-level scope at none:0
│ in expression starting at /home/yakir/.julia/packages/Clp/9Gz64/deps/build_COINBLASBuilder.v1.4.6.jl:45
│ in expression starting at /home/yakir/.julia/packages/Clp/9Gz64/deps/build.jl:38
└ @ Pkg.Operations /build/julia/src/julia/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1097

I'm on Manjaro.

juan-pablo-vielma · 2018-11-29T17:33:50Z

what version of BinaryProvider is installed? (e.g. ] st -m)

yakir12 · 2018-11-29T21:22:53Z

[b99e7846] BinaryProvider v0.5.3

juan-pablo-vielma · 2018-11-29T21:49:58Z

Can you please try
] add https://github.com/juan-pablo-vielma/Clp.jl.git
and see if that builds ok?

yakir12 · 2018-11-30T05:37:47Z

That worked! Thanks!!!

blegat · 2018-11-30T10:39:10Z

@juan-pablo-vielma I am impressed, how did you make it work ? Is is https://github.com/JuliaOpt/COINBLASBuilder that creates a blas library that is with the 64_ suffix that is installed for ArchLinux ?

juan-pablo-vielma · 2018-11-30T23:48:14Z

Just used the new multi-gcc version of BB/BP that figures the right version of libgfortran available to Julia. COINBLASBuilder then provides a version of blas that uses that version of libgfortran. So it is still not using ArchLinux's (or Julia's) blas library. I still need to double check that this "COIN" version of blas plays nice with (at least) Julia's version when they are both used at the same time. It looks like the error in jump-dev/Cbc.jl#56 was because there were two incompatible versions of the Osi libraries that were loaded at the same time (the BB version from Clp and the old one from Cbc).

Any pointers on how to test this are welcome.

sbromberger · 2018-12-20T00:00:44Z

Just as an aside, this also resolved the build problems on a source-built Julia 1.0.3 on OSX. (I haven't tested functionality yet, but using works without issue.)

blegat mentioned this issue Oct 18, 2018

WARNING: Clp had build errors #43

Closed

juan-pablo-vielma mentioned this issue Dec 30, 2018

Multi-GCC BinaryBuilder Binary Dependencies for Julia v1.0 #48

Merged

mlubin closed this as completed in #48 Jan 4, 2019

gtollefson mentioned this issue Apr 3, 2019

compiled binary files compbiocore/VariantVisualization.jl#41

Closed

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Build failed to get libcoinblas #38

Build failed to get libcoinblas #38

blegat commented Sep 17, 2018

mlubin commented Sep 18, 2018

mlubin commented Sep 18, 2018

blegat commented Sep 18, 2018

juan-pablo-vielma commented Sep 18, 2018

juan-pablo-vielma commented Sep 18, 2018

blegat commented Sep 18, 2018 •

edited

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juan-pablo-vielma commented Sep 18, 2018

ianfiske commented Sep 19, 2018

juan-pablo-vielma commented Sep 19, 2018

jzazo commented Oct 9, 2018

juan-pablo-vielma commented Oct 9, 2018

jzazo commented Oct 9, 2018

blegat commented Oct 9, 2018

yakir12 commented Nov 29, 2018

juan-pablo-vielma commented Nov 29, 2018

yakir12 commented Nov 29, 2018

juan-pablo-vielma commented Nov 29, 2018

yakir12 commented Nov 30, 2018

blegat commented Nov 30, 2018

juan-pablo-vielma commented Nov 30, 2018

sbromberger commented Dec 20, 2018

Build failed to get libcoinblas #38

Build failed to get libcoinblas #38

Comments

blegat commented Sep 17, 2018

mlubin commented Sep 18, 2018

mlubin commented Sep 18, 2018

blegat commented Sep 18, 2018

juan-pablo-vielma commented Sep 18, 2018

juan-pablo-vielma commented Sep 18, 2018

blegat commented Sep 18, 2018 • edited Loading

juan-pablo-vielma commented Sep 18, 2018

ianfiske commented Sep 19, 2018

juan-pablo-vielma commented Sep 19, 2018

jzazo commented Oct 9, 2018

juan-pablo-vielma commented Oct 9, 2018

jzazo commented Oct 9, 2018

blegat commented Oct 9, 2018

yakir12 commented Nov 29, 2018

juan-pablo-vielma commented Nov 29, 2018

yakir12 commented Nov 29, 2018

juan-pablo-vielma commented Nov 29, 2018

yakir12 commented Nov 30, 2018

blegat commented Nov 30, 2018

juan-pablo-vielma commented Nov 30, 2018

sbromberger commented Dec 20, 2018

blegat commented Sep 18, 2018 •

edited

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