Build error on 0.3.3 about specialfunctions.jl

[ararslan]

What's your versioninfo()?

[marius311]

Julia Version 0.6.0
Commit 9036443 (2017-06-19 13:05 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Xeon(R) CPU           E5472  @ 3.00GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Penryn)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.9.1 (ORCJIT, penryn)

[ararslan]

Hm. Okay, can you do these things and let me know what happens?

1. cd ~/.julia/v0.6/SpecialFunctions, git clean -fdx, then back to Julia and Pkg.build("SpecialFunctions")
2. using BinDeps; BinDeps.debug("SpecialFunctions")

[marius311]

Thanks for the help, here's what I see:

mmillea@ln05:~/.julia/v0.6/SpecialFunctions$ git clean -fdx
Removing deps/downloads/
Removing deps/usr/
mmillea@ln05:~/.julia/v0.6/SpecialFunctions$ cd
mmillea@ln05:~$ julia 
               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: https://docs.julialang.org
   _ _   _| |_  __ _   |  Type "?help" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.6.0 (2017-06-19 13:05 UTC)
 _/ |\__'_|_|_|\__'_|  |  Official http://julialang.org/ release
|__/                   |  x86_64-pc-linux-gnu

julia> Pkg.build("SpecialFunctions")
INFO: Building SpecialFunctions
INFO: Attempting to Create directory /wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/downloads
INFO: Downloading file https://github.com/ararslan/openspecfun-builder/releases/download/v0.5.3/libopenspecfun-0.5.3-linux-x86_64.tar.gz
--08:56:54--  https://github.com/ararslan/openspecfun-builder/releases/download/v0.5.3/libopenspecfun-0.5.3-linux-x86_64.tar.gz
           => `/wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/downloads/libopenspecfun-0.5.3-linux-x86_64.tar.gz'
Resolving github.com... 192.30.253.113, 192.30.253.112
Connecting to github.com|192.30.253.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/102292870/84e1e9ba-93fa-11e7-8839-b655b0c63939?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20170922%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20170922T065655Z&X-Amz-Expires=300&X-Amz-Signature=44b8babc963c25e823089957e7d937fc0d0c9cf3a13373f234533a8e5bec5fc9&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dlibopenspecfun-0.5.3-linux-x86_64.tar.gz&response-content-type=application%2Foctet-stream [following]
--08:56:55--  https://github-production-release-asset-2e65be.s3.amazonaws.com/102292870/84e1e9ba-93fa-11e7-8839-b655b0c63939?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20170922%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20170922T065655Z&X-Amz-Expires=300&X-Amz-Signature=44b8babc963c25e823089957e7d937fc0d0c9cf3a13373f234533a8e5bec5fc9&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dlibopenspecfun-0.5.3-linux-x86_64.tar.gz&response-content-type=application%2Foctet-stream
           => `/wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/downloads/libopenspecfun-0.5.3-linux-x86_64.tar.gz'
Resolving github-production-release-asset-2e65be.s3.amazonaws.com... 54.231.32.107
Connecting to github-production-release-asset-2e65be.s3.amazonaws.com|54.231.32.107|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2,638,794 (2.5M) [application/octet-stream]

100%[========================================================================================>] 2,638,794      2.83M/s             

08:56:56 (2.82 MB/s) - `/wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/downloads/libopenspecfun-0.5.3-linux-x86_64.tar.gz' saved [2638794/2638794]

INFO: Done downloading file https://github.com/ararslan/openspecfun-builder/releases/download/v0.5.3/libopenspecfun-0.5.3-linux-x86_64.tar.gz
INFO: Attempting to Create directory /wrk/mmillea/.julia/v0.6/SpecialFunctions
INFO: Directory /wrk/mmillea/.julia/v0.6/SpecialFunctions already created
====================================================[ ERROR: SpecialFunctions ]=====================================================

LoadError: Provider BinDeps.Binaries failed to satisfy dependency libopenspecfun
while loading /wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/build.jl, in expression starting on line 43

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

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

WARNING: SpecialFunctions had build errors.

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

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

julia> using BinDeps

julia> BinDeps.debug("SpecialFunctions")
INFO: Reading build script...
The package declares 1 dependencies.
 - Library "libopenspecfun"
    - Providers:
      - Binaries

julia> 

[ararslan]

If you have tree or similar installed on your system, can you tree ~/.julia/v0.6/SpecialFunctions/deps?

[marius311]

mmillea@ln03:~/.julia/v0.6/SpecialFunctions$ tree .
.
|-- LICENSE
|-- README.md
|-- REQUIRE
|-- appveyor.yml
|-- deps
|   |-- build.jl
|   |-- downloads
|   |   `-- libopenspecfun-0.5.3-linux-x86_64.tar.gz
|   |-- scratch.jl
|   `-- usr
|       `-- lib
|           |-- libgcc_s.so.1
|           |-- libgfortran.so.4
|           |-- libopenlibm.so -> libopenlibm.so.2.3
|           |-- libopenlibm.so.2 -> libopenlibm.so.2.3
|           |-- libopenlibm.so.2.3
|           |-- libopenspecfun.a
|           |-- libopenspecfun.so -> libopenspecfun.so.1.3
|           |-- libopenspecfun.so.1 -> libopenspecfun.so.1.3
|           |-- libopenspecfun.so.1.3
|           `-- libquadmath.so.0
|-- docs
|   |-- make.jl
|   `-- src
|       |-- index.md
|       `-- special.md
|-- src
|   |-- SpecialFunctions.jl
|   |-- bessel.jl
|   |-- deprecated.jl
|   |-- erf.jl
|   |-- gamma.jl
|   `-- sincosint.jl
`-- test
    `-- runtests.jl

8 directories, 27 files

[ararslan]

Hmm. Now how about ldd ./usr/lib/libopenspecfun.so?

[marius311]

mmillea@ln04:~/.julia/v0.6/SpecialFunctions/deps$ ldd ./usr/lib/libopenspecfun.so
./usr/lib/libopenspecfun.so: /lib64/libc.so.6: version `GLIBC_2.6' not found (required by /wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/./usr/lib/libgfortran.so.4)
./usr/lib/libopenspecfun.so: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/./usr/lib/libgfortran.so.4)
./usr/lib/libopenspecfun.so: /lib64/libc.so.6: version `GLIBC_2.10' not found (required by /wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/./usr/lib/libquadmath.so.0)
	linux-vdso.so.1 =>  (0x00007fffb8368000)
	libopenlibm.so.2 => /wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/./usr/lib/libopenlibm.so.2 (0x00002b45e8460000)
	libgfortran.so.4 => /wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/./usr/lib/libgfortran.so.4 (0x00002b45e8691000)
	libm.so.6 => /lib64/libm.so.6 (0x00002b45e8a63000)
	libgcc_s.so.1 => /wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/./usr/lib/libgcc_s.so.1 (0x00002b45e8bb8000)
	libquadmath.so.0 => /wrk/mmillea/.julia/v0.6/SpecialFunctions/deps/./usr/lib/libquadmath.so.0 (0x00002b45e8dd0000)
	libc.so.6 => /lib64/libc.so.6 (0x00002b45e900f000)
	/lib64/ld-linux-x86-64.so.2 (0x0000555555554000)

Fyi, my glibc version on the system:

mmillea@ln04:~/.julia/v0.6/SpecialFunctions/deps$ /lib/libc.so.6
GNU C Library stable release version 2.4 (20130516), by Roland McGrath et al.
Copyright (C) 2006 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.
Configured for i686-suse-linux.
Compiled by GNU CC version 4.1.2 20070115 (SUSE Linux).
Compiled on a Linux 2.6.16 system on 2013-05-16.
Available extensions:
	crypt add-on version 2.1 by Michael Glad and others
	GNU Libidn by Simon Josefsson
	GNU libio by Per Bothner
	NIS(YP)/NIS+ NSS modules 0.19 by Thorsten Kukuk
	NoVersion patch for broken glibc 2.0 binaries
	Native POSIX Threads Library by Ulrich Drepper et al
	BIND-8.2.3-T5B
Thread-local storage support included.
For bug reporting instructions, please see:
<http://www.gnu.org/software/libc/bugs.html>.

[ararslan]

Is the libc that's in /lib64 different from the one in /lib?

[marius311]

mmillea@ln04:~/.julia/v0.6/SpecialFunctions/deps$ /lib64/libc.so.6 
GNU C Library stable release version 2.4 (20130516), by Roland McGrath et al.
Copyright (C) 2006 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.
Configured for x86_64-suse-linux.
Compiled by GNU CC version 4.1.2 20070115 (SUSE Linux).
Compiled on a Linux 2.6.16 system on 2013-05-16.
Available extensions:
	crypt add-on version 2.1 by Michael Glad and others
	GNU Libidn by Simon Josefsson
	GNU libio by Per Bothner
	NIS(YP)/NIS+ NSS modules 0.19 by Thorsten Kukuk
	Native POSIX Threads Library by Ulrich Drepper et al
	BIND-8.2.3-T5B
Thread-local storage support included.
For bug reporting instructions, please see:
<http://www.gnu.org/software/libc/bugs.html>.

[ararslan]

Okay, so I guess your glibc is too old to be used by the openspecfun binaries I built? Odd though, since they were build on CentOS 6.9, which should have a pretty old glibc IIUC.

[staticfloat]

@marius311 what Linux distro are you using that has such an old glibc?

[marius311]

Its SUSE Linux Enterprise Server 10 SP4, fairly ancient as its on an old cluster which I do not manage, but which by virtue of ancientness is nice and undersubscribed :)

Downgrading to 0.3.1 was a fine solution for now, but it'd be nice to know if there's a way to force manual compilation or some maintainable solution like that.

[ararslan]

It should be doable to introduce an option to compile from source. I did something along those lines recently in FFTW.

[staticfloat]

Yes, that would be nice. We use CentOS 6.9 (the oldest, supported CentOS version) for our build infrastructure, which has a glibc version of 2.12. Our older buildbots (which are what built Julia 0.5.2 and 0.6.0) were running on CentOS 5.11 (with a glibc version of 2.5), although that distro is now unsupported so we won't be using it anymore. Did you compile Julia from source?