Error building ZMQ.jl v0.6.0 on CentOS 7 #176

felipenoris · 2018-04-20T18:27:19Z

When building on CentOS 7:

LoadError: BinaryProvider.LibraryProduct("/rhome/FNORO/.julia/v0.6/ZMQ/deps/usr/lib", String["libzmq"], :libzmq, "Prefix(/rhome/FNORO/.julia/v0.
6/ZMQ/deps/usr)") is not satisfied, cannot generate deps.jl!                                                                                    
while loading /rhome/FNORO/.julia/v0.6/ZMQ/deps/build.jl, in expression starting on line 40

If I revert to v0.5.1 using Pkg.pin("ZMQ", v"0.5.1") , then Pkg.build("ZMQ") works fine.

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

jebej · 2018-04-20T21:22:39Z

same here, on CentOS 7

stevengj · 2018-04-21T19:02:02Z

Sounds a lot like JuliaIO/Blosc.jl#50. Analogous to there, perhaps the error is fixed by rm(Pkg.dir("ZMQ", "deps", "usr"), recursive=true) followed by Pkg.build("ZMQ")?

felipenoris · 2018-04-21T21:22:03Z

@stevengj No.. it doesn't fix it. I'm installing ZMQ inside a docker container with a fresh Julia installation.
I'll try to dig into this problem to check what's going on.

Looks like something specific to CentOS 7. I had no trouble with macOS and Ubuntu.

stevengj · 2018-04-21T21:32:10Z

See my comment about verbose info: JuliaIO/Blosc.jl#50 (comment)

felipenoris · 2018-04-21T21:41:52Z

Nothing...

julia> ARGS
1-element Array{String,1}:
 "--verbose"

julia> Pkg.build("ZMQ")
INFO: Building ZMQ
===================================================================================================[ ERROR: ZMQ ]===================================================================================================

LoadError: BinaryProvider.LibraryProduct("/usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib", String["libzmq"], :libzmq, "Prefix(/usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr)") is not satisfied, cannot generate deps.jl!
while loading /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/build.jl, in expression starting on line 40

====================================================================================================================================================================================================================

==================================================================================================[ BUILD ERRORS ]==================================================================================================

WARNING: ZMQ had build errors.

 - packages with build errors remain installed in /usr/local/julia/share/julia/site/v0.6
 - build the package(s) and all dependencies with `Pkg.build("ZMQ")`
 - build a single package by running its `deps/build.jl` script

felipenoris · 2018-04-21T21:54:28Z

I manually edited build.jl and got some output:

julia> Pkg.build("ZMQ")
INFO: Building ZMQ
Checking satisfaction...
Info: Found a valid dl path libzmq.so while looking for libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so matches our search criteria of libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so cannot be dlopen'ed
Info: Found a valid dl path libzmq.so.5 while looking for libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5 matches our search criteria of libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5 cannot be dlopen'ed
Info: Found a valid dl path libzmq.so.5.1.5 while looking for libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5.1.5 matches our search criteria of libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5.1.5 cannot be dlopen'ed
Info: Could not locate libzmq inside /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib
BinaryProvider.LibraryProduct("/usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib", String["libzmq"], :libzmq, "Prefix(/usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr)") satisfied? : false
Info: Found a valid dl path libzmq.so while looking for libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so matches our search criteria of libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so cannot be dlopen'ed
Info: Found a valid dl path libzmq.so.5 while looking for libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5 matches our search criteria of libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5 cannot be dlopen'ed
Info: Found a valid dl path libzmq.so.5.1.5 while looking for libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5.1.5 matches our search criteria of libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5.1.5 cannot be dlopen'ed
Info: Could not locate libzmq inside /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib
My platform key is BinaryProvider.Linux(:x86_64, :glibc, :blank_abi)
platform key in download_info? true
Info: Destination file /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/downloads/ZMQ.x86_64-linux-gnu.tar.gz already exists, verifying...
Info: Hash cache is consistent, returning true
Info: Installing /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/downloads/ZMQ.x86_64-linux-gnu.tar.gz into /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr
Info: Removing files installed by manifests/ZMQ.x86_64-linux-gnu.list
Info:   include/zmq.h removed
Info:   include/zmq_utils.h removed
Info:   Culling empty directory include
Info:   logs/ZMQ.log removed
Info:   Culling empty directory logs
Info:   lib/pkgconfig/libzmq.pc removed
Info:   Culling empty directory lib/pkgconfig
Info:   lib/libzmq.la removed
Info:   lib/libzmq.so.5.1.5 removed
Info:   lib/libzmq.so removed
Info:   lib/libzmq.so.5 removed
Info:   lib/libzmq.a removed
Info:   Culling empty directory lib
Info:   manifests/ZMQ.x86_64-linux-gnu.list removed
ran install for url=https://github.com/JuliaInterop/ZMQBuilder/releases/download/v4.2.5+2/ZMQ.x86_64-linux-gnu.tar.gz and it WORKED!
Will write deps file

felipenoris · 2018-04-21T21:59:22Z

verbose argument is not passed to write_deps_file by build.jl .
I also edited that, and this is the output of write_deps_file execution with verbose=true, which is the last line in build.jl.

Info: Found a valid dl path libzmq.so while looking for libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so matches our search criteria of libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so cannot be dlopen'ed
Info: Found a valid dl path libzmq.so.5 while looking for libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5 matches our search criteria of libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5 cannot be dlopen'ed
Info: Found a valid dl path libzmq.so.5.1.5 while looking for libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5.1.5 matches our search criteria of libzmq
Info: /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib/libzmq.so.5.1.5 cannot be dlopen'ed
Info: Could not locate libzmq inside /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib
===================================================================================================[ ERROR: ZMQ ]===================================================================================================

LoadError: BinaryProvider.LibraryProduct("/usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr/lib", String["libzmq"], :libzmq, "Prefix(/usr/local/julia/share/julia/site/v0.6/ZMQ/deps/usr)") is not satisfied, cannot generate deps.jl!
while loading /usr/local/julia/share/julia/site/v0.6/ZMQ/deps/build.jl, in expression starting on line 54

stevengj · 2018-04-21T23:06:04Z

What happens if you manually call dlopen on the libzmq.so in deps/usr?

jebej · 2018-04-22T14:48:15Z

The problem seems to be that the "BinaryBuilder" binaries are not compatible with the "unofficial" CentOS julia package. If I use the generic linux binaries it works.

felipenoris · 2018-04-22T15:12:41Z

smells like ABI madness

oschulz · 2018-04-25T14:10:04Z

I also ran into this problem. A manual dlopen, as suggested by @stevengj, results in

julia> Libdl.dlopen("/some/path/.julia/v0.6/ZMQ/deps/usr/lib/libzmq.so")
ERROR: could not load library "/some/path/.julia/v0.6/ZMQ/deps/usr/lib/libzmq.so"
/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /some/path/.julia/v0.6/ZMQ/deps/usr/lib/libzmq.so)

oschulz · 2018-04-25T14:20:06Z

Would it be possible for ZMQBuilder to use an older GCC version, to provide more backward-compatibility? CentOS-7 will still be with us for a while ...

stevengj · 2018-04-25T16:26:39Z

That depends on the BinaryBuilder setup: filed JuliaPackaging/BinaryBuilder.jl#230

stevengj · 2018-04-25T16:30:47Z

See also https://stackoverflow.com/questions/44205687/glibcxx-3-4-21-not-found-on-centos-7 — it looks like the library might be there on CentOS 7, but there is a problem with the paths.

stevengj · 2018-04-25T20:32:37Z

As commented in the BinaryBuilder thread, this problem arises if you build Julia from source with old libstdc++ library. A workaround would be to use the official Linux julia binaries from https://julialang.org/downloads/

oschulz · 2018-04-26T08:53:31Z

this problem arises if you build Julia from source with old libstdc++ library

Sure - but of course, it's sometimes necessary to build Julia from source (enabling AVX-2, using BUILD_LLVM_CLANG=1, etc.).

Could we just have ZMQ.jl build the library from source if the default binary is not suitable for the current system?

stevengj · 2018-04-26T14:43:56Z

Could we just have ZMQ.jl build the library from source if the default binary is not suitable for the current system?

Yes, that would be possible. A PR would be welcome.

oschulz · 2018-04-26T15:11:11Z

Turns out that I need to override libstdc++ for the current Anaconda matplotlib anyhow, on CentOS-7. And that probably won't be the last thing that's usually supplied in binary form and needs a more recent one, so ...

mmikhasenko · 2018-05-02T09:58:20Z

Same problem with my CentOS

this problem arises if you build Julia from source with old libstdc++ library

The version from the yum repository has the same ZMQ, BinaryProvider error.
Indeed, taking built version gives the way around.

felipenoris · 2018-05-07T11:01:18Z

GR.jl has interesting code for detecting Redhat, on GR.jl/deps/build.jl file.

if Sys.KERNEL == :NT
    os = :Windows
  else
    os = Sys.KERNEL
  end
  const arch = Sys.ARCH
  if os == :Linux && arch == :x86_64
    if isfile("/etc/redhat-release")
      rel = String(read(pipeline(`cat /etc/redhat-release`, `sed s/.\*release\ //`, `sed s/\ .\*//`)))[1:end-1]
      if rel > "7.0"
        os = "Redhat"
      end

ChrisRackauckas · 2018-05-12T15:08:01Z

@nalimilan just so he's aware.

stevengj · 2018-05-17T18:52:23Z

Can someone on CentOS confirm that this is fixed in the latest master?

Pkg.add("CMakeWrapper")
Pkg.checkout("ZMQ")
Pkg.build("ZMQ")

ChrisRackauckas · 2018-05-17T23:51:55Z

Works great.

oschulz · 2018-05-18T07:06:07Z

Thanks, @stevengj!

felipenoris changed the title ~~Error building ZMQ.jl for Release v0.6.0~~ Error building ZMQ.jl for Release v0.6.0 on CentOS 7 Apr 21, 2018

felipenoris changed the title ~~Error building ZMQ.jl for Release v0.6.0 on CentOS 7~~ Error building ZMQ.jl v0.6.0 on CentOS 7 Apr 21, 2018

stevengj mentioned this issue Apr 25, 2018

Support older glibcxx versions on Linux? JuliaPackaging/BinaryBuilder.jl#230

Closed

stevengj mentioned this issue May 8, 2018

Blosc: v0.3.0 => v0.4.1 failed at CentOS JuliaIO/Blosc.jl#50

Closed

stevengj mentioned this issue May 17, 2018

add build fallback that compiles from source #178

Merged

stevengj closed this as completed in #178 May 17, 2018

stevengj mentioned this issue Jan 24, 2019

Pkg + BinaryProvider JuliaLang/Pkg.jl#841

Closed

stevengj mentioned this issue Jan 16, 2020

build failure on CentOS 7 #199

Closed

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Error building ZMQ.jl v0.6.0 on CentOS 7 #176

Error building ZMQ.jl v0.6.0 on CentOS 7 #176

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Error building ZMQ.jl v0.6.0 on CentOS 7 #176

Error building ZMQ.jl v0.6.0 on CentOS 7 #176

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