REPL print overshadow after sampling.

[justinjjlee]

Hi,

I am using the latest version of CmdStan.jl an Stan - 2.26.

Seems like wrapper is at work, but I am having some interface issue. After the first run, my julia REPL gets 'shadowed' by what it seems like an output. I can't really see anything after the run and I can't get it to disappear (tried print, read lines, escape, etc...). See the image below.

Any idea how I can troubleshoot this?

Thanks in advance.

[goedman]

Which terminal are you using? I'm guessing you are on Windows? Can you use the Powershell?

[justinjjlee]

I am using VScode and julia addon/interface.

[goedman]

@justinjoliver Are you asking for the stansummary output? That output also seems to contain these page make up characters. Is this VSCode running on Windows?

[justinjjlee]

That is what I am trying to see. but the bits of string is just covering the entire command prompt for julia. Regardless of what I am querying, I can't see anything (not even what I am typing).

Yes - I am running VSCode running on Windows.

[goedman]

Can you send me the script you are trying to run?

[goedman]

Just ran a simple script on VSCode, including a call to read_summary(), but no problems on my system (macOS). Recently I helped someone else who was able to switch to Powershell (from the github bash shell I believe), which resolved thsis issue.

I'll check a bit if that would be feasible in VSCode.

[goedman]

Ok, just installed PowerShell on my system and then installed it in VSCode. If I then run a Julia script, pwsh seems to turn into the Julia REPL. Guess that's the closest I can come to emulate Windows on my system.

I'm assuming you can start a Julia REPL and execute non-Cmdstan scripts in that REPL?

[goedman]

Above you write "That is what I am trying to see". You mean the output of stansummary by calling read_summary(model)?

[justinjjlee]

So, I can execute any operations. The issue is not related to the operation of Stan, but relates to what happens afterwards.

After I run the Stan model, my REPL is covered by the the text shown in the image - instead of command line starting with 'julia>'

FYI - I was running example bernoulli example.

[goedman]

Hi Justin,

Great, what I'm trying to find out is what step in executing a script causes the shell to go nuts. E.g. can you execute line by line below program, e.g. by copy-pasting into the REPL?

using CmdStan
bm = "
  data { 
    int<lower=1> N; 
    int<lower=0,upper=1> y[N];
  } 
  parameters {
    real<lower=0,upper=1> theta;
  } 
  model {
    theta ~ beta(1,1);
    y ~ bernoulli(theta);
  }
";
data = Dict("N" => 10, "y" => [0, 1, 0, 1, 0, 0, 0, 0, 0, 1])
sm = Stanmodel(name="bernoulli", model=bm, printsummary=false); 
data # Just to check if terminal is still ok
rc, samples, cnames = stan(sm, data, pwd(), CmdStanDir=CMDSTAN_HOME);
samples # Just checking again
if rc == 0
  sum_df = read_summary(stanmodel)
  draw_df = read_samples(
end
println()
sum_df

[justinjjlee]

Ah, got you. Hope I can be more helpful.

I have executed the program above. The phenomenon starts with the line,

rc, samples, cnames = stan(sm, data, pwd(), CmdStanDir=CMDSTAN_HOME);

As you can see from the image below.

Because the sample prints the long dataframe, I have cut the image and am showing the rest below,

Hope this helps, and thank you so much for the (very very timely) troubleshoot. I really appreciate it!

[goedman]

One more, hopefully quick test. Can you replace the lines after the data definition by:

...
data = Dict("N" => 10, "y" => [0, 1, 0, 1, 0, 0, 0, 0, 0, 1])

sm = Stanmodel(name="bernoulli", model=bm, printsummary=false)
sm |> display
rc, samples, cnames = stan(sm, data; summary=false, CmdStanDir=CMDSTAN_HOME);
nt = CmdStan.convert_a3d(samples, cnames, Val(:namedtuple))
mean(nt.theta, dims=1) |> display

[goedman]

In above test I have explicitly disabled running stansummary (under the covers, part of stan()).

Have you ever tried something like:

m = rand(3,4,5)
m |> display

If that works fine, we know for sure it is caused by something in CmdStan.jl because in the first run samples is a simple 3 dimensional array.

[justinjjlee]

So, your first test, the phenomenon persists,

For your second test - it seems like it is causing any issue.

[goedman]

In your terminal (where you see the above output) I have a control. which shows the shells being used, in my case

1. zsh
2. Julia REPL