I want to run several jobs with Condor, my executable take as an argument b such that: b1=50+ $(($(Process)/41)), where $(())stands for the quotient of $(Process) divided by 41. b is defined in quotient.sh. Here is my submit file:
# Unix submit description file
include : PATH/quotient.sh
executable = PATH/script_test.sh
arguments = $(b) $(Process)
log = fit_it_data_$INT(b)_$(Process).log
output = outfile_fit_$INT(b)_$(Process).txt
error = errors_fit_$INT(b)_$(Process).txt
transfer_input_files = PATH
should_transfer_files = Yes
when_to_transfer_output = ON_EXIT
queue 81
However I am getting the error Submitting job(s)ERROR at Queue statement on Line 13: $INT() macro: 50+ $((0/41)) does not evaluate to an integer!. I don't understand why it complains that is does not evaluate to an integer, since b should be equal to 50 here...
Any idea how to fix that issue?
b1=50+ $(($(Process)/41))
I think you have an extra "$" in there. Try this:
b1=50+ ($(Process)/41)
Related
Issue
Following is a minimal, contrived example:
read :: FilePath -> Aff String
read f = do
log ("File: " <> f) -- (1)
readTextFile UTF8 f -- (2)
I would like to do some debug logging in (1), before a potential error on (2) occurs. Executing following code in Spago REPL works for success cases so far:
$ spago repl
> launchAff_ $ read "test/data/tree/root.txt"
File: test/data/tree/root.txt
unit
Problem: If there is an error with (2) - file is directory here - , (1) seems to be not executed at all:
$ spago repl
> launchAff_ $ read "test/data/tree"
~/purescript-book/exercises/chapter9/.psci_modules/node_modules/Effect.Aff/foreign.js:532
throw util.fromLeft(step);
^
[Error: EISDIR: illegal operation on a directory, read] {
errno: -21,
code: 'EISDIR',
syscall: 'read'
}
The original problem is more complex including several layers of recursions (see E-Book exercise 3), where I need logging to debug above error.
Questions
How can I properly log regardless upcoming errors here?
(Optional) Is there a more sophisticated, well-established debugging alternative - purescript-debugger? A decicated VS Code debug extension/functionality would be the cherry on the cake.
First of all, the symptoms you observe do not mean that the first line doesn't execute. It does always execute, you're just not seeing output from it due to how console works in the PureScript REPL. The output gets swallowed. Not the only problem with REPL, sadly.
You can verify that the first line is always executed by replacing log with throwError and observing that the error always gets thrown. Or, alternatively, you can make the first line modify a mutable cell instead of writing to the console, and then examine the cell's contents.
Finally, this only happens in REPL. If you put that launchAff_ call inside main and run the program, you will always get the console output.
Now to the actual question at hand: how to debug trace.
Logging to console is fine if you can afford it, but there is a more elegant way: Debug.trace.
This function has a hidden effect - i.e. its type says it's pure, but it really produces an effect when called. This little lie lets you use trace in a pure setting and thus debug pure code. No need for Effect! This is ok as long as used for debugging only, but don't put it in production code.
The way it works is that it takes two parameters: the first one gets printed to console and the second one is a function to be called after printing, and the result of the whole thing is whatever that function returns. For example:
calculateSomething :: Int -> Int -> Int
calculateSomething x y =
trace ("x = " <> show x) \_ ->
x + y
main :: Effect Unit
main =
log $ show $ calculateSomething 37 5
> npx spago run
'x = 37'
42
The first parameter can be anything at all, not just a string. This lets you easily print a lot of stuff:
calculateSomething :: Int -> Int -> Int
calculateSomething x y =
trace { x, y } \_ ->
x + y
> npx spago run
{ x: 37, y: 5 }
42
Or, applying this to your code:
read :: FilePath -> Aff String
read f = trace ("File: " <> f) \_ -> do
readTextFile UTF8 f
But here's a subtle detail: this tracing happens as soon as you call read, even if the resulting Aff will never be actually executed. If you need tracing to happen on effectful execution, you'll need to make the trace call part of the action, and be careful not to make it the very first action in the sequence:
read :: FilePath -> Aff String
read f = do
pure unit
trace ("File: " <> f) \_ -> pure unit
readTextFile UTF8 f
It is, of course, a bit inconvenient to do this every time you need to trace in an effectful context, so there is a special function that does it for you - it's called traceM:
read :: FilePath -> Aff String
read f = do
traceM ("File: " <> f)
readTextFile UTF8 f
If you look at its source code, you'll see that it does exactly what I did in the example above.
The sad part is that trace won't help you in REPL when an exception happens, because it's still printing to console, so it'll still get swallowed for the same reasons.
But even when it doesn't get swallowed, the output is a bit garbled, because trace actually outputs in color (to help you make it out among other output), and PureScript REPL has a complicated relationship with color:
> calculateSomething 37 5
←[32m'x = 37'←[39m
42
In addition to Fyodor Soikin's great answer, I found a variant using VS Code debug view.
1.) Make sure to build with sourcemaps:
spago build --purs-args "-g sourcemaps"
2.) Add debug configuration to VS Code launch.json:
{
"version": "0.2.0",
"configurations": [
{
"type": "pwa-node",
"request": "launch",
"name": "Launch Program",
"skipFiles": ["<node_internals>/**"],
"runtimeArgs": ["-e", "require('./output/Main/index.js').main()"],
"smartStep": true // skips files without (valid) source map
}
]
}
Replace "./output/Main/index.js" / .main() with the compiled .js file / function to be debugged.
3.) Set break points and step through the .purs file via sourcemap support.
In Julia, I want to use addprocs and pmap inside a function that is defined inside a module. Here's a silly example:
module test
using Distributions
export g, f
function g(a, b)
a + rand(Normal(0, b))
end
function f(A, b)
close = false
if length(procs()) == 1 # If there are already extra workers,
addprocs() # use them, otherwise, create your own.
close = true
end
W = pmap(x -> g(x, b), A)
if close == true
rmprocs(workers()) # Remove the workers you created.
end
return W
end
end
test.f(randn(5), 1)
This returns a very long error
WARNING: Module test not defined on process 4
WARNING: Module test not defined on process 3
fatal error on fatal error on WARNING: Module test not defined on process 2
43: : WARNING: Module test not defined on process 5
fatal error on fatal error on 5: 2: ERROR: UndefVarError: test not defined
in deserialize at serialize.jl:504
in handle_deserialize at serialize.jl:477
in deserialize at serialize.jl:696
...
in message_handler_loop at multi.jl:878
in process_tcp_streams at multi.jl:867
in anonymous at task.jl:63
Worker 3 terminated.
Worker 2 terminated.ERROR (unhandled task failure): EOFError: read end of file
WARNING: rmprocs: process 1 not removed
Worker 5 terminated.ERROR (unhandled task failure): EOFError: read end of file
4-element Array{Any,1}:Worker 4 terminated.ERROR (unhandled task failure): EOFError: read end of file
ERROR (unhandled task failure): EOFError: read end of file
ProcessExitedException()
ProcessExitedException()
ProcessExitedException()
ProcessExitedException()
What I'm trying to do is write a package that contains functions that perform operations that can be optionally parallelized at the user's discretion. So a function like f might take an argument par::Bool that does something like I've shown above if the user calls f with par = true and loops otherwise. So from within the definition of f (and within the definition of the module test), I want to create workers and broadcast the Distributions package and the function g to them.
What's wrong with using #everywhere in your function? The following, for example, works fine on my computer.
function f(A, b)
close = false
if length(procs()) == 1 # If there are already extra workers,
addprocs() # use them, otherwise, create your own.
#everywhere begin
using Distributions
function g(a, b)
a + rand(Normal(0, b))
end
end
close = true
end
W = pmap(x -> g(x, b), A)
if close == true
rmprocs(workers()) # Remove the workers you created.
end
return W
end
f(randn(5), 1)
Note: when I first ran this, I needed to recompile the Distributions package since it had been updated since I had last used it. When I first tried the above script right after the recompiling, it failed. But, I then quit Julia and reopened it and it worked fine. Perhaps that was what is causing your error?
Suppose there is a script A that calls function B, both in Julia.
There are some errors in function B, which cause the script to be stopped at runtime.
Is there a neat way to find out which line is causing the error?
It does not make any sense, to have to put messages like println manually in each line to find out upto which line the code survives, and in which line error happens.
Edit: I am using Linux Red Hat 4.1.2 and Julia version 0.3.6. directly. With no IDE.
Reading the backtrace:
juser#juliabox:~$ cat foo.jl
# line 1 empty comment
foo() = error("This is line 2")
foo() # line 3
juser#juliabox:~$ julia foo.jl
ERROR: This is line 2
in foo at /home/juser/foo.jl:2
in include at ./boot.jl:245
in include_from_node1 at loading.jl:128
in process_options at ./client.jl:285
in _start at ./client.jl:354
while loading /home/juser/foo.jl, in expression starting on line 3
This lines in foo at /home/juser/foo.jl:2 ... while loading /home/juser/foo.jl, in expression starting on line 3 reads as: "there was an error at line 2 in /home/juser/foo.jl file ... while loading /home/juser/foo.jl, in expression starting on line 3"
Looks pretty clear to me!
Edit: /home/juser/foo.jl:2 means; file: /home/juser/foo.jl, line number: 2.
Also you could use #show macro instead of println function for debugging purposes:
julia> println(1 < 5 < 10)
true
julia> #show 1 < 5 < 10
(1<5<10) => true
true
I am try to learn Erlang. I've installed a runtime but cannot get it working. The following code:
X = 3.
works, but none of the following statements work:
f(X)->X.
F() ->0.
F([])->[].
I get back 1: syntax error before: '->'. I tried the word_count from this tutorial. And I get the same error.
What is wrong here?
In REPL you have to use fun(...) -> ... end:
1> F = fun(X) -> X end.
#Fun<erl_eval.6.80484245>
2> F(42).
42
If you have code in file use c command:
1> c(word_count).
{ok,word_count}
2> word_count:word_count([]).
0
There is difference in sytax when writing functions in Erlang module and Erlang shell (REPL). As P_A mentioned you need to call as F = fun(X) -> X end, F("Echo").
Also note that function names are atoms so has to start with lowercase when you are writing in Erlang module. If you are serious about learning Erlang I would suggest you go through this.
You mentioned that you worked on F#. The basic difference between F# and Erlang in this case is that expression
let Lilo = [|5; 3; -3; 0; 0.5|];; Can be written directly in the file and executed. In Erlang it can only be done in Erlang shell and not inside a file.
So the expression you are trying should be inside a function inside a module with the same name as file. Consider test.erl file. Any function you export can be called from outside (shell).
-module(test).
-export([test/0]).
test() ->
Lilo = [5, 3, -3, 0, 0.5],
[X*2 || X <-Lilo].
I have a bash script that creates a csv file and an R file that creates graphs from that.
At the end of the bash script I call Rscript Graphs.R 10
The response I get is as follows:
Error in is.vector(X) : subscript out of bounds
Calls: print ... <Anonymous> -> lapply -> FUN -> lapply -> is.vector
Execution halted
The first few lines of my Graphs.R are:
#!/bin/Rscript
args <- commandArgs(TRUE)
CorrAns = args[1]
No idea what I am doing wrong? The advice on the net appears to me to say that this should work. Its very hard to make sense of commandArgs
With the following in args.R
print(commandArgs(TRUE)[1])
and the following in args.sh
Rscript args.R 10
I get the following output from bash args.sh
[1] "10"
and no error. If necessary, convert to a numberic type using as.numeric(commandArgs(TRUE)[1]).
Just a guess, perhaps you need to convert CorrAns from character to numeric, since Value section of ?CommandArgs says:
A character vector containing the name
of the executable and the
user-supplied command line arguments.
UPDATE: It could be as easy as:
#!/bin/Rscript
args <- commandArgs(TRUE)
(CorrAns = args[1])
(CorrAns = as.numeric(args[1]))
Reading the docs, it seems you might need to remove the TRUE from the call to commandArgs() as you don't call the script with --args. Either that, or you need to call Rscript Graphs.R --args 10.
Usage
commandArgs(trailingOnly = FALSE)
Arguments
trailingOnly logical. Should only
arguments after --args be returned?
Rscript args.R 10 where 10 is the numeric value we want to pass to the R script.
print(as.numeric(commandArgs(TRUE)[1]) prints out the value which can then be assigned to a variable.