# Problem with Base.push! in 0.7.0-alpha (?)

**URL:** <https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921>\
**Category:** General Usage\
**Created:** [June 25, 2018, 6:13am UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921 "2018-06-25T06:13:49Z")\
**Posts on this page:** 15\
**Page:** 1

<div class="post-metadata">

**Author:** ![f-fathurrahman](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/f-fathurrahman/32/8847_2.png) [@f-fathurrahman](https://discourse.julialang.org/u/f-fathurrahman)\
**Post date:** [June 25, 2018, 6:13am UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/1 "2018-06-25T06:13:49Z")

</div>

Dear all,

I am a computational physicist and a novice Julia programmer.I have written several simple codes using Julia, although mostly they still look like Fortran 😅.

With the release of Julia 0.7.0-alpha, I have been trying to update my code.  
So far so good until I came to this serious problem (IMHO) which make me to hard restart my laptop several times.

I am sorry because I could not present the minimal code that reproduce the problem I have faced because I could not risk to do any more hard restart again on my laptop.

I will just give the link to github of the problematic code below.

[https://github.com/f-fathurrahman/ffr-ElectronicStructure.jl/blob/master/LO\_Gaussian/test\_BasisSet.jl](https://github.com/f-fathurrahman/ffr-ElectronicStructure.jl/blob/master/LO_Gaussian/test_BasisSet.jl)

The code is my effort to refactor PyQuante.jl code of Rick Mueller.

Using Julia 0.6.3 the code runs fine. However, when I use 0.7.0-alpha, I got the following error:

```nohighlight
ERROR: LoadError: LoadError: error in method definition: function Base.push! must be explicitly imported to be extended
Stacktrace:
 [1] top-level scope
 [2] include at ./boot.jl:314 [inlined]
 [3] include_relative(::Module, ::String) at ./loading.jl:1071
 [4] include(::Module, ::String) at ./sysimg.jl:29
 [5] include(::String) at ./client.jl:393
 [6] top-level scope
 [7] include at ./boot.jl:314 [inlined]
 [8] include_relative(::Module, ::String) at ./loading.jl:1071
 [9] include(::Module, ::String) at ./sysimg.jl:29
 [10] exec_options(::Base.JLOptions) at ./client.jl:267
 [11] _start() at ./client.jl:427
in expression starting at /home/efefer/WORKS/my_github_repos/ElectronicStructure.jl/ffr-ElectronicStructure.jl/LO_Gaussian/CGBF.jl:44
in expression starting at /home/efefer/WORKS/my_github_repos/ElectronicStructure.jl/ffr-ElectronicStructure.jl/LO_Gaussian/test_BasisSet.jl:9

```

So, I try to import `Base.push!` in file CGBF.jl:

```julia
import Base.push!
# This should become the constructor along with center and power
function push!(cbf::CGBF,expn,coef)
    Base.push!(cbf.pgbfs, PGBF(expn, cbf.center, cbf.power))
    Base.push!(cbf.coefs, coef)
    normalize!(cbf)
end

```

When I do it like this the code run at some point before call to this function and then it hang up. I first thought that this is not a Julia problem and simply my laptop hangs (again because of unknown problem, which happened sometimes).  
However, I run into this problem again when running `julia-0.7.0-alpha test_BasisSet.jl`. After several hard restart, I tried to make sense of this problem and try to see what happened to my laptop when I run this. So, I open up `htop` and observed that memory usage of Julia jumps up to 55% and before my laptop hang up.

I have encountered the hang up problems when I used Julia before (mainly because I tried to construct sparse matrix using `kron`), but this problem is the most severe I have encountered so far.

This problem might be solved if I avoid using push and allocate memory beforehand which is the usual way I am handling this problem in Fortran. However, I might use push! somewhere and be aware of this problem.

Any help will be appreciated.  
Best regards,

Fadjar Fathurrahman

* * *

I am using Ubuntu 16.04, 64 bit

```julia
julia> Sys.total_memory()/2^20
3835.27734375

julia> Sys.cpu_
cpu_info cpu_summary
julia> Sys.cpu_info()
2-element Array{Base.Sys.CPUinfo,1}:
 Intel(R) Pentium(R) CPU B980 @ 2.40GHz: 
        speed user nice sys idle irq
      840 MHz 37364 s 141 s 7177 s 272661 s 0 s
 Intel(R) Pentium(R) CPU B980 @ 2.40GHz: 
        speed user nice sys idle irq
      971 MHz 40149 s 239 s 7743 s 268268 s 0 s

```

---

<div class="post-metadata">

**Author:** ![Tamas\_Papp](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tamas_papp/32/25949_2.png) [@Tamas\_Papp](https://discourse.julialang.org/u/Tamas_Papp)\
**Post date:** [June 25, 2018, 6:50am UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/2 "2018-06-25T06:50:28Z")

</div>

You are probably affected by this [language change](https://github.com/JuliaLang/julia/blob/master/NEWS.md):

> The syntax `using A.B` can now only be used when `A.B` is a module, and the syntax `using A: B` can only be used for adding single bindings

Use

```julia
import Base: push!

```

instead.

---

<div class="post-metadata">

**Author:** ![f-fathurrahman](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/f-fathurrahman/32/8847_2.png) [@f-fathurrahman](https://discourse.julialang.org/u/f-fathurrahman)\
**Post date:** [June 25, 2018, 7:47am UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/3 "2018-06-25T07:47:29Z")

</div>

Thank you very much for quick reply.

I have tried your proposed solution however I still get the problem (I have to hard restart again).

By the way, I have used the syntax `import Base.println` without any problem in my code.

---

<div class="post-metadata">

**Author:** ![f-fathurrahman](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/f-fathurrahman/32/8847_2.png) [@f-fathurrahman](https://discourse.julialang.org/u/f-fathurrahman)\
**Post date:** [June 25, 2018, 7:47am UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/4 "2018-06-25T07:47:31Z")

</div>

By the way, is it possible to upload zip file of the code ?  
(In case it is annoying to download the code one-by-one or you don’t want to download the entire git repo).

---

<div class="post-metadata">

**Author:** ![Tamas\_Papp](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tamas_papp/32/25949_2.png) [@Tamas\_Papp](https://discourse.julialang.org/u/Tamas_Papp)\
**Post date:** [June 25, 2018, 7:58am UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/5 "2018-06-25T07:58:47Z")

</div>

It is best to make a minimal working example. You learn about the problem in the process (and may even solve it), and reviewing smaller files makes it easier to help you.

---

<div class="post-metadata">

**Author:** ![f-fathurrahman](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/f-fathurrahman/32/8847_2.png) [@f-fathurrahman](https://discourse.julialang.org/u/f-fathurrahman)\
**Post date:** [June 27, 2018, 8:30am UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/6 "2018-06-27T08:30:50Z")

</div>

Sorry I was panicked at that time.

Here is some code I put in `COMMON.jl`:

```julia
const Tuple3F64 = Tuple{Float64,Float64,Float64}
const Tuple3I64 = Tuple{Int64,Int64,Int64}

struct PGBF
    center::Tuple3F64
    power::Tuple3I64
    expn::Float64
    NORM::Float64
end

function PGBF( expn::Float64, center::Tuple3F64, power::Tuple3I64 )
    NORM = 1.0
    p = PGBF( center, power, expn, NORM )
    return p
end

function PGBF( expn::Float64, center::Tuple3F64 )
    power = (0,0,0)
    NORM = 1.0
    p = PGBF( center, power, expn, NORM )
    return p
end

function PGBF( expn::Float64 )
    center = (0.0,0.0,0.0)
    power = (0,0,0)
    NORM = 1.0
    p = PGBF( center, power, expn, NORM )
    return p
end

mutable struct CGBF
    center::Tuple3F64
    power::Tuple3I64
    pgbfs::Array{PGBF,1}
    coefs::Array{Float64,1}
    NORM::Float64
end

function init_CGBF( center::Tuple3F64, power::Tuple3I64 )
    return CGBF( center, power, PGBF[], Float64[], 1.0 )
end

init_CGBF(x=0,y=0,z=0,I=0,J=0,K=0) = CGBF( (x,y,z), (I,J,K), PGBF[], Float64[], 1.0 )

#import Base: push! # The problem is here
function push!(cbf::CGBF,expn,coef)
    Base.push!(cbf.pgbfs, PGBF(expn, cbf.center, cbf.power))
    Base.push!(cbf.coefs, coef)
end

const ZATOMS = Dict(
    "H" => 1,
    "He" => 2,
    "Li" => 3 )

    const sto3g = Any[
      # H
      [("S",
        [(3.4252509099999999, 0.15432897000000001),
         (0.62391373000000006, 0.53532813999999995),
         (0.16885539999999999, 0.44463454000000002)])],
      # He
      [("S",
        [(6.3624213899999997, 0.15432897000000001),
         (1.1589229999999999, 0.53532813999999995),
         (0.31364978999999998, 0.44463454000000002)])],
    ]
    const basis_set_data = Dict{Any,Any}("sto3g" => sto3g);

const BasisSet = Array{CGBF,1}

function push!(basis::BasisSet,cbf::CGBF)
    Base.push!(basis,cbf)
end

function build_basis( Natoms::Int64, atsymbs::Array{String,1},
                      positions::Array{Float64,2}; name="sto3g" )
    data = basis_set_data[name]
    basis = BasisSet()

    for ia = 1:Natoms

        atno = ZATOMS[atsymbs[ia]]
        x = positions[1,ia]
        y = positions[2,ia]
        z = positions[3,ia]

        for btuple in data[atno]
            sym,primlist = btuple
            for (I,J,K) in sym2power[sym]
                cbf = init_CGBF( (x,y,z), (I,J,K) )
                push!(basis,cbf)
                for (expn,coef) in primlist
                    push!(cbf,expn,coef)
                end
            end
        end

    end

    return basis
end

const sym2power = Dict{Any,Any}(
  "S" => [(0,0,0)],
  "P" => [(1,0,0),(0,1,0),(0,0,1)],
  "D" => [(2,0,0),(0,2,0),(0,0,2),(1,1,0),(1,0,1),(0,1,1)]
  )

```

Now, in the calling function:

```julia
if VERSION > v"0.6.3"
    using Printf
end

include("COMMON.jl")

function test_main()
    Natoms = 1
    positions = zeros(Float64,3,Natoms)
    basis = build_basis(1, ["H"], positions)
    println(basis)
end

test_main()

```

Using julia-0.6.3:

```nohighlight
julia test_BasisSet.jl 
CGBF[CGBF((0.0, 0.0, 0.0), (0, 0, 0), PGBF[PGBF((0.0, 0.0, 0.0), (0, 0, 0), 3.42525, 1.0), PGBF((0.0, 0.0, 0.0), (0, 0, 0), 0.623914, 1.0), PGBF((0.0, 0.0, 0.0), (0, 0, 0), 0.168855, 1.0)], [0.154329, 0.535328, 0.444635], 1.0)]

```

Julia 0.7.0-alpha will complain:

```nohighlight
julia-0.7.0-alpha test_BasisSet.jl 
ERROR: LoadError: LoadError: error in method definition: function Base.push! must be explicitly imported to be extended
Stacktrace:
 [1] top-level scope
 [2] include at ./boot.jl:314 [inlined]
 [3] include_relative(::Module, ::String) at ./loading.jl:1071
 [4] include(::Module, ::String) at ./sysimg.jl:29
 [5] include(::String) at ./client.jl:393
 [6] top-level scope
 [7] include at ./boot.jl:314 [inlined]
 [8] include_relative(::Module, ::String) at ./loading.jl:1071
 [9] include(::Module, ::String) at ./sysimg.jl:29
 [10] exec_options(::Base.JLOptions) at ./client.jl:267
 [11] _start() at ./client.jl:427
in expression starting at /home/efefer/WORKS/JULIA/LO_gaussian_2_MWE/COMMON.jl:47
in expression starting at /home/efefer/WORKS/JULIA/LO_gaussian_2_MWE/test_BasisSet.jl:5

```

Last time I tried, adding Base.push! will hang up.

Reversing the lines:

```julia
                cbf = init_CGBF( (x,y,z), (I,J,K) )
                push!(basis,cbf)
                for (expn,coef) in primlist
                    push!(cbf,expn,coef)
                end

```

to:

```julia
                cbf = init_CGBF( (x,y,z), (I,J,K) )
                for (expn,coef) in primlist
                    push!(cbf,expn,coef)
                end
                push!(basis,cbf)

```

might solve the problem.

---

<div class="post-metadata">

**Author:** ![fredrikekre](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/fredrikekre/32/1688_2.png) [@fredrikekre](https://discourse.julialang.org/u/fredrikekre)\
**Post date:** [June 27, 2018, 9:38am UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/7 "2018-06-27T09:38:08Z")

</div>

Instead of

```julia
function push!(cbf::CGBF,expn,coef)
    Base.push!(cbf.pgbfs, PGBF(expn, cbf.center, cbf.power))
    Base.push!(cbf.coefs, coef)
end

```

Did you try

```julia
import Base: push!
function push!(cbf::CGBF,expn,coef)
    push!(cbf.pgbfs, PGBF(expn, cbf.center, cbf.power))
    push!(cbf.coefs, coef)
end

```

alternatively

```julia
function Base.push!(cbf::CGBF,expn,coef)
    push!(cbf.pgbfs, PGBF(expn, cbf.center, cbf.power))
    push!(cbf.coefs, coef)
end

```

---

<div class="post-metadata">

**Author:** ![f-fathurrahman](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/f-fathurrahman/32/8847_2.png) [@f-fathurrahman](https://discourse.julialang.org/u/f-fathurrahman)\
**Post date:** [June 27, 2018, 9:56am UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/8 "2018-06-27T09:56:15Z")

</div>

Thank you very much for your response.

I believed that I have tried:

```julia
# ...
import Base: push!
function push!(cbf::CGBF,expn,coef)
    push!(cbf.pgbfs, PGBF(expn, cbf.center, cbf.power))
    push!(cbf.coefs, coef)
end
# ...

```

along with the following lines in function `build_basis`:

```julia
                cbf = init_CGBF( (x,y,z), (I,J,K) )
                push!(basis,cbf)
                for (expn,coef) in primlist
                    push!(cbf,expn,coef)
                end

```

which caused my laptop to hang.  
I’m sorry if I was mistaken, but currently I could not risk trying this on my laptop to make sure. I will report back soon as I can get access to my work PC.

---

<div class="post-metadata">

**Author:** ![Tamas\_Papp](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tamas_papp/32/25949_2.png) [@Tamas\_Papp](https://discourse.julialang.org/u/Tamas_Papp)\
**Post date:** [June 27, 2018, 10:07am UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/9 "2018-06-27T10:07:11Z")

</div>

> [@f-fathurrahman](#):
>
> which caused my laptop to hang.  
> I’m sorry if I was mistaken, but currently I could not risk trying this on my laptop to make sure

Are you sure it wasn’t something unrelated? Julia _is_ powerful, but merely running code as a non-root user should not be able to affect the system.

---

<div class="post-metadata">

**Author:** ![f-fathurrahman](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/f-fathurrahman/32/8847_2.png) [@f-fathurrahman](https://discourse.julialang.org/u/f-fathurrahman)\
**Post date:** [June 27, 2018, 10:16am UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/10 "2018-06-27T10:16:14Z")

</div>

Yes this is not related to root or non root.

What I mean is that I have encountered several hang-up after running that script (probably because of memory-related problem?) which caused me to hard restart my laptop.

Actually, I can only reproduce the problem on Linux systems: my laptop and and my work PC, which both running Linux 16.04.

When I tried to ‘overload’ `Base.push!`:

```julia
import Base: push! 
function push!(cbf::CGBF,expn,coef)
    Base.push!(cbf.pgbfs, PGBF(expn, cbf.center, cbf.power))
    Base.push!(cbf.coefs, coef)
end

```

and running the file `test_BasisSet.jl`

```julia
if VERSION > v"0.6.3"
    using Printf
end

include("COMMON.jl")

function test_main()
    Natoms = 1
    positions = zeros(Float64,3,Natoms)
    basis = build_basis(1, ["H"], positions)
    println(basis)
end

test_main()

```

I got my laptop hang up.

I’m sorry if I am not clear in the problem statement.

---

<div class="post-metadata">

**Author:** ![f-fathurrahman](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/f-fathurrahman/32/8847_2.png) [@f-fathurrahman](https://discourse.julialang.org/u/f-fathurrahman)\
**Post date:** [June 27, 2018, 12:56pm UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/11 "2018-06-27T12:56:03Z")

</div>

**UPDATE**

I got stackoverflow error when running on Juliabox.

 ![stackoverflow_v1](https://global.discourse-cdn.com/julialang/original/3X/c/e/ce02d5485495e1220c6b22fa40fe0a3e7f1247aa.png)

---

<div class="post-metadata">

**Author:** ![Tamas\_Papp](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tamas_papp/32/25949_2.png) [@Tamas\_Papp](https://discourse.julialang.org/u/Tamas_Papp)\
**Post date:** [June 27, 2018, 12:59pm UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/12 "2018-06-27T12:59:10Z")

</div>

Again, having a **minimal** working example would make it so much easier to help you.

---

<div class="post-metadata">

**Author:** ![f-fathurrahman](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/f-fathurrahman/32/8847_2.png) [@f-fathurrahman](https://discourse.julialang.org/u/f-fathurrahman)\
**Post date:** [June 27, 2018, 1:47pm UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/13 "2018-06-27T13:47:23Z")

</div>

I am sorry with the ugly code. The truth is I am still learning the original code which is written by R.P Muller ([https://github.com/rpmuller/pyquante2/tree/master/julia](https://github.com/rpmuller/pyquante2/tree/master/julia)).

In the mean time I think I have solved the problem of hang up laptop and reproduced stackoverflow error on my laptop.

In my `.bashrc`, I used to add the statement `ulimit -s unlimited` because this is required by code generated by Intel Fortran compiler. It seems that this is no longer required and I have removed that line from my bashrc. My work PC also have this statement in its `.bashrc`.

@Tamas_Papp I think you are right about the problem. Julia is not wrong here, it is simply my setting which is not safe. Also thank you for pointing out the `import Base: push!` syntax, I got no deprecation messages about this.

I will come back again if I can isolate the real problem here.

---

<div class="post-metadata">

**Author:** ![kristoffer.carlsson](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kristoffer.carlsson/32/22_2.png) [@kristoffer.carlsson](https://discourse.julialang.org/u/kristoffer.carlsson)\
**Post date:** [June 27, 2018, 1:49pm UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/14 "2018-06-27T13:49:50Z")

</div>

I think the problem is quite simple. You have managed to define a method that calls itself over and over (and that is what the stacktrace in JuliaBox is showing) giving you an infinite recursion until stackoverflow.

---

<div class="post-metadata">

**Author:** ![f-fathurrahman](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/f-fathurrahman/32/8847_2.png) [@f-fathurrahman](https://discourse.julialang.org/u/f-fathurrahman)\
**Post date:** [June 27, 2018, 1:55pm UTC](https://discourse.julialang.org/t/problem-with-base-push-in-0-7-0-alpha/11921/15 "2018-06-27T13:55:58Z")

</div>

Ups, I think it is 😓. The problem vanish when I comment

```julia
const BasisSet = Array{CGBF,1}

#function push!(basis::BasisSet,cbf::CGBF)
# Base.push!(basis,cbf)
#end

```

I guess I have panicked because my laptop hang up due to statement `ulimit -s unlimited` in my `.bashrc`.