bug#30282: package julia build error

bug#30282: package julia build error

[Marco van Hulten]

Hi—

Building julia ends like badly:


$ guix package -i julia
[...]
base64 (2)                |    0.41  |  0.00  |  0.0 |  2.10      | 1559.96
serialize (2)             |    7.05  |  0.29  |  4.1 | 80.75      | 1559.96
WARNING: readuntil(IO,AbstractString) will perform poorly with a long string
WARNING: readuntil(IO,AbstractString) will perform poorly with a long string
WARNING: readuntil(IO,AbstractString) will perform poorly with a long string
Warning: threaded loop executed in order
threads (3)               |   12.18  |  1.90  | 15.6 | 93.54      | 1708.66
enums (3)                 |   12.64  |  0.41  |  3.2 | 147.02     | 1708.66
i18n (3)                  |    0.06  |  0.00  |  0.0 |  0.07      | 1708.66
workspace (3)             |    6.38  |  0.00  |  0.0 |  4.33      | 1708.66
sh: /sbin/ldconfig: No such file or directory
libdl (3)                 |    2.77  |  0.00  |  0.0 | 10.04      | 1708.66
int (3)                   |    9.51  |  0.19  |  2.0 | 29.06      | 1708.66
misc (2)                  |   68.30  |  9.99  | 14.6 | 1734.26    | 1654.81
intset (2)                |    4.31  |  0.14  |  3.3 | 29.06      | 1654.81
checked (3)               |    9.04  |  0.14  |  1.6 | 51.62      | 1708.66
floatfuncs (2)            |   12.98  |  0.34  |  2.6 | 117.90     | 1654.81
inline (2)                |   10.71  |  0.13  |  1.2 | 40.40      | 1654.81
boundscheck (2)           |   24.83  |  0.00  |  0.0 |  8.59      | 1654.81
error (2)                 |    7.12  |  2.34  | 32.9 |  7.45      | 1654.81
cartesian (2)             |    0.07  |  0.00  |  0.0 |  0.05      | 1654.81
asmvariant (2)            |    0.29  |  0.00  |  0.0 |  0.54      | 1654.81
osutils (2)               |    0.10  |  0.00  |  0.0 |  0.25      | 1654.81
channels (2)              |   32.41  | 12.07  | 37.2 | 456.26     | 1654.81
iostream (2)              |    1.04  |  0.00  |  0.0 |  2.89      | 1654.81
WARNING: Method definition f(Tuple{Vararg{Int64, N}}, AbstractArray{T, N}) in module Test51Main_specificity at /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/specificity.jl:87 overwritten at /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/specificity.jl:93.
specificity (2)           |    0.29  |  0.00  |  0.0 |  0.84      | 1654.81
fft (2)                   |   61.87  |  1.68  |  2.7 | 541.40     | 1654.81
dsp (2)                   |   19.35  |  0.99  |  5.1 | 245.84     | 1654.81
EOFError()CapturedExceptionEOFError(()CapturedException(EOFError()CapturedException(EOFError(EOFError()), EOFError(), , Any[Any[(Any[(((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(33) - Unknown remote, closing connection.
(::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})(::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(29) - Unknown remote, closing connection.
() at event.jl:73, 1)])
Process(31) - Unknown remote, closing connection.
EOFError()CapturedException(EOFError()EOFError()CapturedException(EOFErrorCapturedException((), EOFErrorEOFError(()), , Any[AnyAny[[(EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(31) - Unknown remote, closing connection.
EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(33) - Unknown remote, closing connection.
(((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, (::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})1)])
Process(34) - Unknown remote, closing connection.
(::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(30) - Unknown remote, closing connection.
() at event.jl:73, 1)])
Process(32) - Unknown remote, closing connection.
EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(32) - Unknown remote, closing connection.
EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(34) - Unknown remote, closing connection.
EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(33) - Unknown remote, closing connection.
EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(34) - Unknown remote, closing connection.
distributed (3)           |  190.79  |  0.00  |  0.0 |  1.01      | 1708.66
examples (2)              |   31.02  |  1.51  |  4.9 | 617.02     | 1654.81
ERROR: LoadError: rmprocs: pids [3] not terminated after 30 seconds.
Stacktrace:
 [1] _rmprocs(::Array{Int64,1}, ::Int64) at ./distributed/cluster.jl:807
 [2] #rmprocs#70(::Int64, ::Function, ::Array{Int64,1}, ::Vararg{Array{Int64,1},N} where N) at ./distributed/cluster.jl:775
 [3] (::##40#46)() at /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/runtests.jl:93
 [4] cd(::##40#46, ::String) at ./file.jl:70
while loading /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/runtests.jl, in expression starting on line 29
make[1]: *** [Makefile:18: all] Error 1
make: *** [Makefile:558: test] Error 2
phase `check' failed after 2266.9 seconds
builder for `/gnu/store/zkx3jjnqg043yd3k2kl3lgw57rx39vmy-julia-0.6.0.drv' failed with exit code 1
guix package: error: build failed: build of
`/gnu/store/zkx3jjnqg043yd3k2kl3lgw57rx39vmy-julia-0.6.0.drv' failed


One issue seems that /sbin/ldconfig does not exist; this is provided
differently in GuixSD compared to most GNU distros.  The critical
problem appears to be at event.jl:73.

—Marco

bug#30282: package julia build error

[Ludovic Courtès]

Hi,

Marco van Hulten <marco@hulten.org> skribis:

> $ guix package -i julia
> [...]

[...]

> EOFError()CapturedExceptionEOFError(()CapturedException(EOFError()CapturedException(EOFError(EOFError()), EOFError(), , Any[Any[(Any[(((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
> Process(33) - Unknown remote, closing connection.
> (::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})(::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
> Process(29) - Unknown remote, closing connection.
> () at event.jl:73, 1)])
> Process(31) - Unknown remote, closing connection.
> EOFError()CapturedException(EOFError()EOFError()CapturedException(EOFErrorCapturedException((), EOFErrorEOFError(()), , Any[AnyAny[[(EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
> Process(31) - Unknown remote, closing connection.
> EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
> Process(33) - Unknown remote, closing connection.
> (((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, (::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})1)])
> Process(34) - Unknown remote, closing connection.
> (::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
> Process(30) - Unknown remote, closing connection.
> () at event.jl:73, 1)])
> Process(32) - Unknown remote, closing connection.
> EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
> Process(32) - Unknown remote, closing connection.
> EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
> Process(34) - Unknown remote, closing connection.
> EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
> Process(33) - Unknown remote, closing connection.
> EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
> Process(34) - Unknown remote, closing connection.
> distributed (3)           |  190.79  |  0.00  |  0.0 |  1.01      | 1708.66
> examples (2)              |   31.02  |  1.51  |  4.9 | 617.02     | 1654.81
> ERROR: LoadError: rmprocs: pids [3] not terminated after 30 seconds.
> Stacktrace:
>  [1] _rmprocs(::Array{Int64,1}, ::Int64) at ./distributed/cluster.jl:807
>  [2] #rmprocs#70(::Int64, ::Function, ::Array{Int64,1}, ::Vararg{Array{Int64,1},N} where N) at ./distributed/cluster.jl:775
>  [3] (::##40#46)() at /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/runtests.jl:93
>  [4] cd(::##40#46, ::String) at ./file.jl:70
> while loading /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/runtests.jl, in expression starting on line 29
> make[1]: *** [Makefile:18: all] Error 1

The test failures I have with current master are different:

--8<---------------cut here---------------start------------->8---
Error in testset distributed:
Error During Test
  Got an exception of type LoadError outside of a @test
  LoadError: Distributed test failed, cmd : `/tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/usr/bin/julia --check-bounds=yes --startup-file=no --depwarn=error distributed_exec.jl`
  while loading /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/distributed.jl, in expression starting on line 9
Error in testset libgit2:
Test Failed
  Expression: startswith(sprint(show, e), "GitError(Code:ENOTFOUND, Class:OS, Failed to resolve path")
Error in testset libgit2:
Test Failed
  Expression: err.msg == "Invalid Content-Type: text/plain"
   Evaluated: "invalid Content-Type: text/plain" == "Invalid Content-Type: text/plain"
ERROR: LoadError: Test run finished with errors
while loading /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/runtests.jl, in expression starting on line 29
make[1]: *** [Makefile:18: all] Error 1
make: *** [Makefile:558: test] Error 2
phase `check' failed after 1300.8 seconds
--8<---------------cut here---------------end--------------->8---

I fixed the libgit2 errors and got rid of the ldconfig warnings we had:

  9805ad6f8 * gnu: julia: Don't invoke /sbin/ldconfig.
  d40b5684c * gnu: julia: Adjust libgit2 tests.

However I now get another test failure:

--8<---------------cut here---------------start------------->8---
Error in testset linalg/arnoldi:
Test Failed
  Expression: sort((eigs(A, B, nev=k, sigma=1.0))[1]) ≈ sort((eigvals(A, B))[1:k])
   Evaluated: [0.022743, 0.165356, 2.892] ≈ [0.022743, 2.892, 1.0574e15]
ERROR: LoadError: Test run finished with errors
while loading /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/runtests.jl, in expression starting on line 29
make[1]: *** [Makefile:18: all] Error 1
--8<---------------cut here---------------end--------------->8---

Thoughts?  :-)

Ludo’.

bug#30282: package julia build error

[Andreas Enge]

Hello,

just for reference, I locally updated julia to 0.6.2, and the tests still fail,
but not in the same way:

Error in testset linalg/arnoldi:
Test Failed
  Expression: sort((eigs(A, B, nev=k, sigma=1.0))[1]) ≈ sort((eigvals(A, B))[1:k])
   Evaluated: [0.022743, 0.165356, 2.892] ≈ [0.022743, 2.892, 1.0574e15]
Error in testset misc:
Error During Test
  Got an exception of type LoadError outside of a @test
  LoadError: Deprecation test failed, cmd : `/tmp/guix-build-julia-0.6.2.drv-0/julia-0.6.2/usr/bin/julia --check-bounds=yes --startup-file=no deprecation_exec.jl`
  while loading /tmp/guix-build-julia-0.6.2.drv-0/julia-0.6.2/test/misc.jl, in expression starting on line 717
ERROR: LoadError: Test run finished with errors
while loading /tmp/guix-build-julia-0.6.2.drv-0/julia-0.6.2/test/runtests.jl, in expression starting on line 29

Andreas

bug#30282: package julia build error

[Ludovic Courtès]

Hello,

ludo@gnu.org (Ludovic Courtès) skribis:

> Error in testset linalg/arnoldi:
> Test Failed
>   Expression: sort((eigs(A, B, nev=k, sigma=1.0))[1]) ≈ sort((eigvals(A, B))[1:k])
>    Evaluated: [0.022743, 0.165356, 2.892] ≈ [0.022743, 2.892, 1.0574e15]
> ERROR: LoadError: Test run finished with errors
> while loading /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/runtests.jl, in expression starting on line 29
> make[1]: *** [Makefile:18: all] Error 1

Commit c0edb5b5430a5278a3ebc9aeea9d3c8ae9a2e1f1 fixes this one.

Now for other test failures:

--8<---------------cut here---------------start------------->8---
Error in testset distributed:
Error During Test
  Got an exception of type LoadError outside of a @test
  LoadError: Distributed test failed, cmd : `/tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/usr/bin/julia --check-bounds=yes --startup-file=no --depwarn=error distributed_exec.jl`
  while loading /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/distributed.jl, in expression starting on line 9
ERROR: LoadError: Test run finished with errors
while loading /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/runtests.jl, in expression starting on line 29
make[1]: *** [Makefile:18: all] Error 1
--8<---------------cut here---------------end--------------->8---

Help welcome!

Ludo’.

bug#30282: package julia build error

[Pjotr Prins]

> Help welcome!

I'll take a look.

Pj.
-- 

bug#30282: package julia build error

[Pjotr Prins]

One immediate problem is that Julia comes with patches for LLVM 3.9
only:

  https://github.com/JuliaLang/julia#llvm

it downloads, patches and compiles a specific LLVM. We actually need
this even though the failing tests are possibly not related (I suspect
the math libraries are not showing the same results as the built-in
ones).

I think we need to follow the recommended build steps for Julia first.
Then the tests should pass. Next perhaps link out components and send
bug reports upstream.

Pj.

bug#30282: package julia build error

[Ludovic Courtès]

[-- Attachment #1: Type: text/plain, Size: 970 bytes --]

Hi Pjotr,

Pjotr Prins <pjotr.public12@thebird.nl> skribis:

> One immediate problem is that Julia comes with patches for LLVM 3.9
> only:
>
>   https://github.com/JuliaLang/julia#llvm
>
> it downloads, patches and compiles a specific LLVM. We actually need
> this even though the failing tests are possibly not related (I suspect
> the math libraries are not showing the same results as the built-in
> ones).

Oh, indeed.

For arpack-ng using the right version did help.  It might be similar for
other dependencies.

I tried the patch below (README.md in Julia 0.6.0 says that plain LLVM
3.9 without patches is OK), but that didn’t solve the
distributed.jl-related test failures.

> I think we need to follow the recommended build steps for Julia first.
> Then the tests should pass. Next perhaps link out components and send
> bug reports upstream.

Yeah, though we’d rather extract these bundled pieces somehow.

Thanks,
Ludo’.


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: Type: text/x-patch, Size: 440 bytes --]

diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index 41bbc66dd..8e5e81314 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -314,7 +314,7 @@
         "USE_SYSTEM_LIBGIT2=1"
         "USE_SYSTEM_OPENSPECFUN=1")))
     (inputs
-     `(("llvm" ,llvm)
+     `(("llvm" ,llvm-3.9.1)
        ("arpack-ng" ,arpack-ng)
        ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
        ("lapack" ,lapack)

bug#30282: package julia build error

[Andreas Enge]

Hello,

On Tue, Mar 13, 2018 at 06:02:07PM +0100, Ludovic Courtès wrote:
> I tried the patch below (README.md in Julia 0.6.0 says that plain LLVM
> 3.9 without patches is OK), but that didn’t solve the
> distributed.jl-related test failures.

there is a 0.6.2 version already. I do not expect it to solve test failures,
but it might make sense to try an update first.

Andreas

bug#30282: package julia build error

[Pjotr Prins]

On Tue, Mar 13, 2018 at 06:54:18PM +0100, Andreas Enge wrote:
> Hello,
> 
> On Tue, Mar 13, 2018 at 06:02:07PM +0100, Ludovic Courtès wrote:
> > I tried the patch below (README.md in Julia 0.6.0 says that plain LLVM
> > 3.9 without patches is OK), but that didn’t solve the
> > distributed.jl-related test failures.
> 
> there is a 0.6.2 version already. I do not expect it to solve test failures,
> but it might make sense to try an update first.

I am on 0.6.2. Not sure where it will end. Starting to appreciate
Julia a little (as a language, not as a deployment). It is a fast LISP
with Ruby syntax ;)

Pj.
-- 

bug#30282: package julia build error

[Pjotr Prins]

After some investigation I have found Julia's build system to be a
challenge. The problem is that, to 'control' the environment, the
developers have chosen to fixate all dependencies by pulling them in
and patching them (including LLVM). The only time I got a successful
build outside Guix was by using the exact gcc/g++/gfortran-4.7
compilers (no earlier and no later versions) and letting Julia have
its way downloading and building openblas, etc. All Julia tests pass
if it is done this way.

I tried to build Julia in a Guix environment - adding dependencies one
by one - and this failed spectularly too. Turns out that Julia is very
specific about the compilers and dependencies it uses, which is OK,
but it downloads dependencies from source and patches them, which is
not great. Worst, the whole build system is based on defaults - so if
you change anything things start failing.

I.e., you try to change anything, such as using the system openblas
libs, and the Julia build system gets confused. It should work,
according to the docs, but I can't even get it to a compiled stage
this way. These are the things Julia 0.6.0 downloads and builds:

ls deps/scratch/ 

    arpack-ng-3.3.0
    cmake-3.7.1-Linux-x86_64
    curl-7.53.1
    dsfmt-2.2.3
    fftw-3.3.6-pl1-double
    fftw-3.3.6-pl1-single
    gmp-6.1.2
    libgit2-2fcb8705e584ca61f6c4657525c9d2713f6a39d2
    libssh2-30e9c1347e3b8baa2951db612f05e6d87fc8e2f2
    libunwind-1.1-julia2
    libuv-52d72a52cc7ccd570929990f010ed16e2ec604c8
    llvm-3.9.1
    mbedtls-2.3.0-gpl
    mpfr-3.1.5
    openblas-85636ff1a015d04d3a8f960bc644b85ee5157135
    openlibm-1581174c85f7b645b15ba1ac1c3a98fb601f0fe7
    openspecfun-39699a1c1824bf88410cabb8a7438af91ea98f4c
    patchelf-0.9
    pcre2-10.23
    SuiteSparse-4.4.5
    utf8proc-40e605959eb5cb90b2587fa88e3b661558fbc55a

ls deps/patches/

    arpack-tests-blasint.patch         llvm-3.7.1.patch                        llvm-D28759-loopclearance.patch
    compiler-rt-3.7.1.patch            llvm-3.7.1_symlinks.patch               llvm-D28786-callclearance.patch
    dSFMT.c.patch                      llvm-3.8.0_bindir.patch                 llvm-D9168_argument_alignment.patch
    dSFMT.h.patch                      llvm-3.8.0_ppc64_SUBFC8.patch           llvm-nodllalias.patch
    gmp-exception.patch                llvm-3.8.0_threads.patch                llvm-PR22923.patch
    instcombine-llvm-3.3.patch         llvm-3.8.0_winshlib.patch               llvm-PR26180.patch
    int128-vector.llvm-3.3.patch       llvm-3.8.1-version.patch                llvm-PR27046.patch
    libgit2-agent-nonfatal.patch       llvm-3.9.0_cygwin.patch                 llvm-PR276266.patch
    libgit2-free-config.patch          llvm-3.9.0_D27296-libssp.patch          llvm-PR277939.patch
    libgit2-gitconfig-symlink.patch    llvm-3.9.0_threads.patch                llvm-PR278088.patch
    libgit2-mbedtls.patch              llvm-3.9.0_win64-reloc-dwarf.patch      llvm-PR278321.patch
    libgit2-mbedtls-verify.patch       llvm-arm-fix-prel31.patch               llvm-PR278923.patch
    libgit2-mbedtls-writer-fix.patch   llvm-D14260.patch                       llvm-PR29010-i386-xmm.patch
    libgit2-remote-push-NULL.patch     llvm-D17165-D18583.patch                llvm-r282182.patch
    libgit2-ssh.patch                  llvm-D17326_unpack_load.patch           llvm-rL279933-ppc-atomicrmw-lowering.patch
    libssh2-encryptedpem.patch         llvm-D17712.patch                       llvm-rL293230-icc17-cmake.patch
    libssh2-netinet-in.patch           llvm-D21271-instcombine-tbaa-3.7.patch  llvm-win64-reloc-dwarf.patch
    libunwind-arm-dyn.patch            llvm-D21271-instcombine-tbaa-3.8.patch  mbedtls-ssl.h.patch
    libunwind-arm-pc-offset.patch      llvm-D23597_sdag_names.patch            openblas-clangasmbug.patch
    libunwind-dwarf-ver.patch          llvm-D24300_ptx_intrinsics.patch        openblas-cross-compile.patch
    libunwind-freebsd-mapper.patch     llvm-D25865-cmakeshlib.patch            openblas-freebsd.patch
    libunwind-prefer-extbl.patch       llvm-D27389.patch                       openblas-power-assembly-fixes.patch
    lldb-3.7.1.patch                   llvm-D27397.patch                       osx-10.10.llvm-3.3.patch
    llvm-3.3.patch                     llvm-D27609-AArch64-UABS_G3.patch       pcre-mingw.patch
    llvm-3.7.0.patch                   llvm-D27629-AArch64-large_model.patch   SuiteSparse-winclang.patch
    llvm-3.7.1_2.patch                 llvm-D28009.patch                       win64-int128.llvm-3.3.patch
    llvm-3.7.1_3.patch                 llvm-D28215_FreeBSD_shlib.patch
    llvm-3.7.1_destsharedlibdir.patch  llvm-D28221-avx512.patch

I mean, seriously!

As I wrote before, the test of the current Guix build probably fails due to the
openblas linkage Guix uses (openblas output does change and depends on build
choices). Not sure which switch is causing it, but it should be fixable. There
are more tests failing, however, that need fixing. 

For version 7 Julia promises no longer to patch LLVM, see 

  https://discourse.julialang.org/t/why-is-source-build-julia-required-to-use-gpu-packages/9747/2

So, unless someone feels incensed to fix things, I propose to hold out until
Julia7 and maybe have another go again. 

Pj.

bug#30282: package julia build error

[Ludovic Courtès]

Hey Pjotr,

Pjotr Prins <pjotr.public12@thebird.nl> skribis:

> ls deps/scratch/ 
>
>     arpack-ng-3.3.0
>     cmake-3.7.1-Linux-x86_64
>     curl-7.53.1
>     dsfmt-2.2.3
>     fftw-3.3.6-pl1-double
>     fftw-3.3.6-pl1-single
>     gmp-6.1.2
>     libgit2-2fcb8705e584ca61f6c4657525c9d2713f6a39d2
>     libssh2-30e9c1347e3b8baa2951db612f05e6d87fc8e2f2
>     libunwind-1.1-julia2
>     libuv-52d72a52cc7ccd570929990f010ed16e2ec604c8
>     llvm-3.9.1
>     mbedtls-2.3.0-gpl
>     mpfr-3.1.5
>     openblas-85636ff1a015d04d3a8f960bc644b85ee5157135
>     openlibm-1581174c85f7b645b15ba1ac1c3a98fb601f0fe7
>     openspecfun-39699a1c1824bf88410cabb8a7438af91ea98f4c
>     patchelf-0.9
>     pcre2-10.23
>     SuiteSparse-4.4.5
>     utf8proc-40e605959eb5cb90b2587fa88e3b661558fbc55a
>
> ls deps/patches/
>
>     arpack-tests-blasint.patch         llvm-3.7.1.patch                        llvm-D28759-loopclearance.patch
>     compiler-rt-3.7.1.patch            llvm-3.7.1_symlinks.patch               llvm-D28786-callclearance.patch
>     dSFMT.c.patch                      llvm-3.8.0_bindir.patch                 llvm-D9168_argument_alignment.patch
>     dSFMT.h.patch                      llvm-3.8.0_ppc64_SUBFC8.patch           llvm-nodllalias.patch
>     gmp-exception.patch                llvm-3.8.0_threads.patch                llvm-PR22923.patch
>     instcombine-llvm-3.3.patch         llvm-3.8.0_winshlib.patch               llvm-PR26180.patch
>     int128-vector.llvm-3.3.patch       llvm-3.8.1-version.patch                llvm-PR27046.patch
>     libgit2-agent-nonfatal.patch       llvm-3.9.0_cygwin.patch                 llvm-PR276266.patch
>     libgit2-free-config.patch          llvm-3.9.0_D27296-libssp.patch          llvm-PR277939.patch
>     libgit2-gitconfig-symlink.patch    llvm-3.9.0_threads.patch                llvm-PR278088.patch
>     libgit2-mbedtls.patch              llvm-3.9.0_win64-reloc-dwarf.patch      llvm-PR278321.patch
>     libgit2-mbedtls-verify.patch       llvm-arm-fix-prel31.patch               llvm-PR278923.patch
>     libgit2-mbedtls-writer-fix.patch   llvm-D14260.patch                       llvm-PR29010-i386-xmm.patch
>     libgit2-remote-push-NULL.patch     llvm-D17165-D18583.patch                llvm-r282182.patch
>     libgit2-ssh.patch                  llvm-D17326_unpack_load.patch           llvm-rL279933-ppc-atomicrmw-lowering.patch
>     libssh2-encryptedpem.patch         llvm-D17712.patch                       llvm-rL293230-icc17-cmake.patch
>     libssh2-netinet-in.patch           llvm-D21271-instcombine-tbaa-3.7.patch  llvm-win64-reloc-dwarf.patch
>     libunwind-arm-dyn.patch            llvm-D21271-instcombine-tbaa-3.8.patch  mbedtls-ssl.h.patch
>     libunwind-arm-pc-offset.patch      llvm-D23597_sdag_names.patch            openblas-clangasmbug.patch
>     libunwind-dwarf-ver.patch          llvm-D24300_ptx_intrinsics.patch        openblas-cross-compile.patch
>     libunwind-freebsd-mapper.patch     llvm-D25865-cmakeshlib.patch            openblas-freebsd.patch
>     libunwind-prefer-extbl.patch       llvm-D27389.patch                       openblas-power-assembly-fixes.patch
>     lldb-3.7.1.patch                   llvm-D27397.patch                       osx-10.10.llvm-3.3.patch
>     llvm-3.3.patch                     llvm-D27609-AArch64-UABS_G3.patch       pcre-mingw.patch
>     llvm-3.7.0.patch                   llvm-D27629-AArch64-large_model.patch   SuiteSparse-winclang.patch
>     llvm-3.7.1_2.patch                 llvm-D28009.patch                       win64-int128.llvm-3.3.patch
>     llvm-3.7.1_3.patch                 llvm-D28215_FreeBSD_shlib.patch
>     llvm-3.7.1_destsharedlibdir.patch  llvm-D28221-avx512.patch
>
> I mean, seriously!

Yeah.  :-/

> As I wrote before, the test of the current Guix build probably fails due to the
> openblas linkage Guix uses (openblas output does change and depends on build
> choices). Not sure which switch is causing it, but it should be fixable. There
> are more tests failing, however, that need fixing. 

Indeed there’s always the possibility that test failures are due to a
missing patch.

> For version 7 Julia promises no longer to patch LLVM, see 
>
>   https://discourse.julialang.org/t/why-is-source-build-julia-required-to-use-gpu-packages/9747/2
>
> So, unless someone feels incensed to fix things, I propose to hold out until
> Julia7 and maybe have another go again. 

That sounds reasonable.

It’s a bit weird that 0.6.0 tests passed at some point in Guix, and
eventually started failing.  Not sure what happened.

Ludo’.

bug#30282: package julia build error

[Pjotr Prins]

On Sat, Mar 17, 2018 at 07:39:28PM +0100, Ludovic Courtès wrote:
> It’s a bit weird that 0.6.0 tests passed at some point in Guix, and
> eventually started failing.  Not sure what happened.

Probably an openblas or LLVM update. Unfortunately hydra no longer has
the logs.

Pj.
-- 

bug#30282: package julia build error

[zimoun]

Dear,

On Sun, 28 Jan 2018 at 23:43, Marco van Hulten <marco@hulten.org> wrote:

> Building julia ends like badly:

[...]


> `/gnu/store/zkx3jjnqg043yd3k2kl3lgw57rx39vmy-julia-0.6.0.drv' failed

Does this more-than-2-years-old bug report still make sense?  Because
now, Julia v1.4.1 is included in Guix.

I am in favor to close it.  WDYT?


All the best,
simon

bug#30282: package julia build error

[Ludovic Courtès]

Hi,

zimoun <zimon.toutoune@gmail.com> skribis:

> On Sun, 28 Jan 2018 at 23:43, Marco van Hulten <marco@hulten.org> wrote:
>
>> Building julia ends like badly:
>
> [...]
>
>
>> `/gnu/store/zkx3jjnqg043yd3k2kl3lgw57rx39vmy-julia-0.6.0.drv' failed
>
> Does this more-than-2-years-old bug report still make sense?  Because
> now, Julia v1.4.1 is included in Guix.
>
> I am in favor to close it.  WDYT?

Agreed.  Closing!

Ludo’.