GNU bug report logs - #30282
Julia 0.6.0 fails tests

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Package: guix; Reported by: Marco van Hulten <marco@HIDDEN>; dated Sun, 28 Jan 2018 23:44:01 UTC; Maintainer for guix is bug-guix@HIDDEN.

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From: Pjotr Prins <pjotr.public12@HIDDEN>
To: Andreas Enge <andreas@HIDDEN>
Subject: Re: bug#30282: package julia build error
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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.
-- 




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bug#30282; Package guix. Full text available.

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Date: Tue, 13 Mar 2018 18:54:18 +0100
From: Andreas Enge <andreas@HIDDEN>
To: Ludovic =?iso-8859-15?Q?Court=E8s?= <ludo@HIDDEN>
Subject: Re: bug#30282: package julia build error
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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





Information forwarded to bug-guix@HIDDEN:
bug#30282; Package guix. Full text available.

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From: ludo@HIDDEN (Ludovic =?utf-8?Q?Court=C3=A8s?=)
To: Pjotr Prins <pjotr.public12@HIDDEN>
Subject: Re: bug#30282: package julia build error
References: <20180128234305.03c958b0@HIDDEN>
 <87607a5ckn.fsf@HIDDEN> <87po49mis5.fsf@HIDDEN>
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--=-=-=
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Hi Pjotr,

Pjotr Prins <pjotr.public12@HIDDEN> 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=E2=80=99t 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=E2=80=99d rather extract these bundled pieces somehow.

Thanks,
Ludo=E2=80=99.


--=-=-=
Content-Type: text/x-patch
Content-Disposition: inline

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)

--=-=-=--




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To: Pjotr Prins <pjotr.public12@HIDDEN>
Subject: Re: bug#30282: package julia build error
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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.




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Subject: Re: bug#30282: package julia build error
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> Help welcome!

I'll take a look.

Pj.
-- 




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From: ludo@HIDDEN (Ludovic =?utf-8?Q?Court=C3=A8s?=)
To: Marco van Hulten <marco@HIDDEN>
Subject: Re: bug#30282: package julia build error
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Hello,

ludo@HIDDEN (Ludovic Court=C3=A8s) skribis:

> Error in testset linalg/arnoldi:
> Test Failed
>   Expression: sort((eigs(A, B, nev=3Dk, sigma=3D1.0))[1]) =E2=89=88 sort(=
(eigvals(A, B))[1:k])
>    Evaluated: [0.022743, 0.165356, 2.892] =E2=89=88 [0.022743, 2.892, 1.0=
574e15]
> 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.dr=
v-0/julia-0.6.0/usr/bin/julia --check-bounds=3Dyes --startup-file=3Dno --de=
pwarn=3Derror distributed_exec.jl`
  while loading /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/distribu=
ted.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.j=
l, in expression starting on line 29
make[1]: *** [Makefile:18: all] Error 1
--8<---------------cut here---------------end--------------->8---

Help welcome!

Ludo=E2=80=99.




Information forwarded to bug-guix@HIDDEN:
bug#30282; Package guix. Full text available.
Changed bug title to 'Julia 0.6.0 fails tests' from 'package julia build error' Request was from ludo@HIDDEN (Ludovic Courtès) to control <at> debbugs.gnu.org. Full text available.

Message received at 30282 <at> debbugs.gnu.org:


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Subject: Re: bug#30282: package julia build error
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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





Information forwarded to bug-guix@HIDDEN:
bug#30282; Package guix. Full text available.

Message received at 30282 <at> debbugs.gnu.org:


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From: ludo@HIDDEN (Ludovic =?utf-8?Q?Court=C3=A8s?=)
To: Marco van Hulten <marco@HIDDEN>
Subject: Re: bug#30282: package julia build error
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Date: Tue, 06 Feb 2018 17:04:40 +0100
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Hi,

Marco van Hulten <marco@HIDDEN> skribis:

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

[...]

> EOFError()CapturedExceptionEOFError(()CapturedException(EOFError()Capture=
dException(EOFError(EOFError()), EOFError(), , Any[Any[(Any[(((::Base.Distr=
ibuted.##99#100{TCPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
> Process(33) - Unknown remote, closing connection.
> (::Base.Distributed.##99#100{TCPSocket,TCPSocket,Bool})(::Base.Distribute=
d.##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(EOFErro=
rCapturedException((), EOFErrorEOFError(()), , Any[AnyAny[[(EOFError()Captu=
redException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSoc=
ket,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:7=
3, (::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{In=
t64,1},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.dr=
v-0/julia-0.6.0/usr/bin/julia --check-bounds=3Dyes --startup-file=3Dno --de=
pwarn=3Derror distributed_exec.jl`
  while loading /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/distribu=
ted.jl, in expression starting on line 9
Error in testset libgit2:
Test Failed
  Expression: startswith(sprint(show, e), "GitError(Code:ENOTFOUND, Class:O=
S, Failed to resolve path")
Error in testset libgit2:
Test Failed
  Expression: err.msg =3D=3D "Invalid Content-Type: text/plain"
   Evaluated: "invalid Content-Type: text/plain" =3D=3D "Invalid Content-Ty=
pe: 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.j=
l, 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=3Dk, sigma=3D1.0))[1]) =E2=89=88 sort((e=
igvals(A, B))[1:k])
   Evaluated: [0.022743, 0.165356, 2.892] =E2=89=88 [0.022743, 2.892, 1.057=
4e15]
ERROR: LoadError: Test run finished with errors
while loading /tmp/guix-build-julia-0.6.0.drv-0/julia-0.6.0/test/runtests.j=
l, in expression starting on line 29
make[1]: *** [Makefile:18: all] Error 1
--8<---------------cut here---------------end--------------->8---

Thoughts?  :-)

Ludo=E2=80=99.




Information forwarded to bug-guix@HIDDEN:
bug#30282; Package guix. Full text available.

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Hi=E2=80=94

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.dr=
v-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()CapturedE=
xception(EOFError(EOFError()), EOFError(), , Any[Any[(Any[(((::Base.Distrib=
uted.##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(EOFErrorC=
apturedException((), EOFErrorEOFError(()), , Any[AnyAny[[(EOFError()Capture=
dException(EOFError(), Any[((::Base.Distributed.##99#100{TCPSocket,TCPSocke=
t,Bool})() at event.jl:73, 1)])
Process(31) - Unknown remote, closing connection.
EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{T=
CPSocket,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{T=
CPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(32) - Unknown remote, closing connection.
EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{T=
CPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(34) - Unknown remote, closing connection.
EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{T=
CPSocket,TCPSocket,Bool})() at event.jl:73, 1)])
Process(33) - Unknown remote, closing connection.
EOFError()CapturedException(EOFError(), Any[((::Base.Distributed.##99#100{T=
CPSocket,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{Int6=
4,1},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/ru=
ntests.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.j=
l, 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' f=
ailed 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.

=E2=80=94Marco




Acknowledgement sent to Marco van Hulten <marco@HIDDEN>:
New bug report received and forwarded. Copy sent to bug-guix@HIDDEN. Full text available.
Report forwarded to bug-guix@HIDDEN:
bug#30282; Package guix. Full text available.
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