OpenMDAO v1.x: output of sub Group in ParallelGroup does not exist - parallel-processing

When running in parallel I am unable to connect unknowns of subgroups in a ParallelGroup() even though I can connect to the subgroups' params. The code causing the problem (with names changed for clarity) is below. This code is within a group of a larger structure, but is the only place where MPI is being used:
for i in range(0, nTasks):
self.connect('comp_a.output%i' % i, 'parallel_group.sub_group%i.param_a' % i)
self.connect('input_param%i' % i, 'parallel_group.sub_group%i.param_b' % i)
self.connect('parallel_group.sub_group%i.output' % i, 'comp_b.input%i' % i)
The first two connections seem to work fine, but the last one throws an error:
NameError: Source 'parallel_group.sub_group0.output' cannot be connected to target 'comb_b.input0': 'parallel_group.sub_group0.output' does not exist.
Also, if I comment out the offending line, then first line in the loop fails for the second process with the same error message:
NameError: Source 'comp_a.output1' cannot be connected to target 'parallel_group.sub_group1.param_a': 'parallel_group.sub_group1.param_a' does not exist.
All the connections work fine with our serial version of the code. The serial version is the same except that the sub_groups are added directly to the group this code is in rather than being wrapped in parallel_group.
I have tried to look over the tutorials and examples but have not been able to figure what might be wrong. I would really appreciate any suggestions of what to check or what may be wrong. Sorry to not post a complete code sample.

its a little unclear, but it sounds like you've added a new group in the parallel version of the code, named "parallel_group". When you did this, did you promote anything (or everything) from that group? If so, then you shouldn't add the parallel group into the variable name path for the connection.
That seems like the only thing likely to trip you up. I could try to debug a bit more if you can come up with a sample code you can post up here that would show the problem.

Related

PyQGIS - wrapped C/C++ object of type QgsVectorLayer has been deleted when editing the layer

I'm currently developing a QGIS plug-in.
When i start editing a layer either with with edit(QgsVectorLayer) or with QgsVectorLayer.startediting() this RuneTimeError happens the majority of runs: RuntimeError: wrapped C/C++ object of type QgsVectorLayer has been deleted. I can run 10 times the script and have no error and then run it another 10 times and get 10 times in a row the error. It feels completely random.
As i understood by reading post such as Understanding the "underlying C/C++ object has been deleted" error it might be a garbage collector problem C++ side. But none of the post i saw was about QgsVectorLayer so i'm not really sure it applies.
It really annoys me to the point where i start creating empty layers to store modified features instead of editing.
I tried to move start editing before the loop as i was thinking to continually start editing and commit changes for each feature might cause the issue but the error still appears.
Then i thought it might be the use of break at the end but removing it doesn't resolve the error.
As it is the first time i really use PyQGIS i spent sometimes reading the developer cookbook or searching online (Anita Graser - creating and editing a new vector layer) but i could not find any solutions.
I tried with different version, LTR or not. With another computer by despair but the issue is still here.
I also read somewhere that the progress bar was the issue, so i removed the feedback in my script also without success.
Here are some code example :
nodesLayer = self.parameterAsVectorLayer(parameters, self.INPUT_NODE, context)
arcsLayer = self.parameterAsVectorLayer(parameters, self.INPUT_LINE, context)
# Fill node Id_line_x
# Create spatial index
index = QgsSpatialIndex(nodesLayer.getFeatures())
for line in arcsLayer.getFeatures():
# Construct a geometry engine to speed up spatial relationship
engine = QgsGeometry.createGeometryEngine(line.geometry().constGet())
engine.prepareGeometry()
# Get potential neighbour
candidateIds = index.intersects(line.geometry().boundingBox())
request = QgsFeatureRequest().setFilterFids(candidateIds)
for node in nodesLayer.getFeatures(request):
# Get real neighbour
if engine.intersects(node.geometry().constGet()):
# Fill the Id_line fields for the number of neighbour
for fld in range(1, node["Nb_seg"] + 1):
if node["fk_Id_line_%d" %fld] == NULL:
with edit(nodesLayer):
node["fk_Id_line_%d" %fld] = line["Id_line"]
nodesLayer.updateFeature(node)
break
And the exact error :
Traceback (most recent call last):
File "/some/path/to/a/file.py", line 331, in processAlgorithm
nodesLayer.updateFeature(node)
RuntimeError: wrapped C/C++ object of type QgsVectorLayer has been deleted
Hope the example is enough. The goal of the code is for the nodes to be aware of their surroundings without going through the lines. it's just for treatment and those fields would be removed in the final output.

Logging and asserting the number of previously-unknown DOM elements

I'ts my first tme using Cypress and I almost finalized my first test. But to do so I need to assert against a unknown number. Let me explain:
When the test starts, a random number of elements is generated and I shouldn't have control on such a number (is a requirement). So, I'm trying to get such number in this way:
var previousElems = cy.get('.list-group-item').its('length');
I'm not really sure if I'm getting the right data, since I can not log it (the "cypress console" shows me "[Object]" when I print it). But let's say such line returns (5) to exemplify.
During the test, I simulate a user creating extra elements (2) and removing an (1) element. Let's say the user just creates one single extra element.
So, at the end os the test, I need to check if the number of eements with the same class are equals to (5+2-1) = (6) elements. I'm doing it in this way:
cy.get('.list-group-item').its('length').should('eq', (previousTasks + 1));
But I get the following message:
CypressError: Timed out retrying: expected 10 to equal '[object Object]1'
So, how can I log and assert this?
Thanks in advance,
PD: I also tryed:
var previousTasks = (Cypress.$("ul").children)? Cypress.$("ul").children.length : 0;
But it always returns a fixed number (2), even if I put a wait before to make sure all the items are fully loaded.
I also tryed the same with childNodes but it always return 0.
Your problem stems from the fact that Cypress test code is run all at once before the test starts. Commands are queued to be run later, and so storing variables as in your example will not work. This is why you keep getting objects instead of numbers; the object you're getting is called a chainer, and is used to allow you to chain commands off other commands, like so: cy.get('#someSelector').should('...');
Cypress has a way to get around this though; if you need to operate on some data directly, you can provide a lambda function using .then() that will be run in order with the rest of your commands. Here's a basic example that should work in your scenario:
cy.get('.list-group-item').its('length').then(previousCount => {
// Add two elements and remove one...
cy.get('.list-group-item').its('.length').should('eq', previousCount + 1);
});
If you haven't already, I strongly suggest reading the fantastic introduction to Cypress in the docs. This page on variables and aliases should also be useful in this case.

How to put 7 events in one eventset in PAPI

In PAPI Im trying to put 7 events in one eventset so I can read 7 results in one operation but I always get return -1 ,can anyone help me?my code like this:
int events1[] = {
PAPI_L1_TCM,
PAPI_L2_TCM,
PAPI_L3_TCM,
PAPI_MEM_WCY,
PAPI_RES_STL,
PAPI_TLB_DM,
PAPI_TLB_IM};
PAPI_library_init(PAPI_VER_CURRENT);
i = PAPI_start_counters(events1,7);
where i appears to be -1 which means PAPI_EINVAL.
I tried change the value PAPI_NUM_TLS but it didn't work.
I have the same problem now. But as I have found, the trouble comes from 5th and 6th counters. Here: https://icl.cs.utk.edu/projects/papi/wiki/PAPI3:PAPI_add_event.3
at IBM POWER6 NOTES there is mentioned that these two counters are specific and as I understand should count concrete events. I have not found the solution yet. For 5th one, I added PAPI_TOT_INS and seems to work but for 6th one PAPI_TOT_CYC gives PAPI_ECNFLCT error as they say.

Report Builder Expressions

Im new to Report Builder and having issues with some expressions that Im trying to implement in a report. I got the standard ones to work however as soon as I try any distinctions, I get error messages. Over the last couple weeks, Ive tried many combinations, read the expression help, google and looking at other questions at internet sites. To reduce my frustrations, I even would jump to other expressions and walk away hoping I would have different insight coming back.
Its probably something simple or something I dont know about writing expressions.
Im hoping that someone can help with these expressions; they are the versions I get the least errors with(usually just expression expected) and show what Im trying to accomplish.
=IIF((Fields!RECORDFLAG.Value)='D',COUNTDISTINCT(Fields!TICKETNUM.Value),0)
=IIF((Fields!TRANSTYPE.Value)='1' and (Fields!RECORDFLAG.VALUE)='A' or
'B',SUM(Fields!DOLLARS.Value),0)
=IIF((Fields!TRANSTYPE.Value)='1' and
(Fields!RECORDFLAG.VALUE)='P',SUM(Fields!DOLLARS.Value),0)
=Sum([DOLLARS] case when [RECORDFLAG]='P' then -1*[DOLLARS])
Thank You.
=IIF((Fields!RECORDFLAG.Value)=”D”,COUNTDISTINCT(Fields!TICK‌​ETNUM.Value))
The error message gives you the answer here - no false part of the iif() has been specified. Use =IIF((Fields!RECORDFLAG.Value)=”D”,COUNTDISTINCT(Fields!TICK‌​ETNUM.Value), 0)
=IIF((Fields!TRANSTYPE.Value)="1" and (Fields!RECORDFLAG.VALUE)="A" or "B",SUM(Fields!DOLLARS.Value),0)
This is not how an OR works in SSRS. Use:
=IIF((Fields!TRANSTYPE.Value)="1" and (Fields!RECORDFLAG.VALUE="A" or Fields!RECORDFLAG.Value = "B"),SUM(Fields!DOLLARS.Value),0)
The 0s are returned due to your report design. countdistinct() is an aggregate function - it's meant to be used on a set of data. However, your iif() is only testing on a per row basis - you're basically saying "if the current row is thing, count all the distinct values" which doesn't make sense. There are a couple of ways forward:
You can count the number of times a certain value occurs in a given condition using a sum(). This is not the same as the countdistinct(), but if you use =sum(iif(Fields!RECORDFLAG.Value = "D", 1, 0)) then you will get the number of times RECORDFLAG is D in that set. Note: this requires the data to be aggregated (so in SSRS, grouped in a tablix).
You can use custom code to count distinct values in a set. See https://itsalocke.com/aggregate-on-a-lookup-in-ssrs/. You can apply this even if you have only one dataset - just reference the same one twice.
You can change the way your report works. You can group on Fields!RECORDFLAG.Value and filter the group to where Fields!RECORDFLAG.Value = "D". Then in your textbox, use =countdistinct(Fields!TICKETNUM.Value) to get the distinct values for TICKETNUM when RECORDFLAG is D.

What is your favorite R debugging trick? [duplicate]

I get an error when using an R function that I wrote:
Warning messages:
1: glm.fit: algorithm did not converge
2: glm.fit: algorithm did not converge
What I have done:
Step through the function
Adding print to find out at what line the error occurs suggests two functions that should not use glm.fit. They are window() and save().
My general approaches include adding print and stop commands, and stepping through a function line by line until I can locate the exception.
However, it is not clear to me using those techniques where this error comes from in the code. I am not even certain which functions within the code depend on glm.fit. How do I go about diagnosing this problem?
I'd say that debugging is an art form, so there's no clear silver bullet. There are good strategies for debugging in any language, and they apply here too (e.g. read this nice article). For instance, the first thing is to reproduce the problem...if you can't do that, then you need to get more information (e.g. with logging). Once you can reproduce it, you need to reduce it down to the source.
Rather than a "trick", I would say that I have a favorite debugging routine:
When an error occurs, the first thing that I usually do is look at the stack trace by calling traceback(): that shows you where the error occurred, which is especially useful if you have several nested functions.
Next I will set options(error=recover); this immediately switches into browser mode where the error occurs, so you can browse the workspace from there.
If I still don't have enough information, I usually use the debug() function and step through the script line by line.
The best new trick in R 2.10 (when working with script files) is to use the findLineNum() and setBreakpoint() functions.
As a final comment: depending upon the error, it is also very helpful to set try() or tryCatch() statements around external function calls (especially when dealing with S4 classes). That will sometimes provide even more information, and it also gives you more control over how errors are handled at run time.
These related questions have a lot of suggestions:
Debugging tools for the R language
Debugging lapply/sapply calls
Getting the state of variables after an error occurs in R
R script line numbers at error?
The best walkthrough I've seen so far is:
http://www.biostat.jhsph.edu/%7Erpeng/docs/R-debug-tools.pdf
Anybody agree/disagree?
As was pointed out to me in another question, Rprof() and summaryRprof() are nice tools to find slow parts of your program that might benefit from speeding up or moving to a C/C++ implementation. This probably applies more if you're doing simulation work or other compute- or data-intensive activities. The profr package can help visualizing the results.
I'm on a bit of a learn-about-debugging kick, so another suggestion from another thread:
Set options(warn=2) to treat warnings like errors
You can also use options to drop you right into the heat of the action when an error or warning occurs, using your favorite debugging function of choice. For instance:
Set options(error=recover) to run recover() when an error occurs, as Shane noted (and as is documented in the R debugging guide. Or any other handy function you would find useful to have run.
And another two methods from one of #Shane's links:
Wrap an inner function call with try() to return more information on it.
For *apply functions, use .inform=TRUE (from the plyr package) as an option to the apply command
#JoshuaUlrich also pointed out a neat way of using the conditional abilities of the classic browser() command to turn on/off debugging:
Put inside the function you might want to debug browser(expr=isTRUE(getOption("myDebug")))
And set the global option by options(myDebug=TRUE)
You could even wrap the browser call: myBrowse <- browser(expr=isTRUE(getOption("myDebug"))) and then call with myBrowse() since it uses globals.
Then there are the new functions available in R 2.10:
findLineNum() takes a source file name and line number and returns the function and environment. This seems to be helpful when you source() a .R file and it returns an error at line #n, but you need to know what function is located at line #n.
setBreakpoint() takes a source file name and line number and sets a breakpoint there
The codetools package, and particularly its checkUsage function can be particularly helpful in quickly picking up syntax and stylistic errors that a compiler would typically report (unused locals, undefined global functions and variables, partial argument matching, and so forth).
setBreakpoint() is a more user-friendly front-end to trace(). Details on the internals of how this works are available in a recent R Journal article.
If you are trying to debug someone else's package, once you have located the problem you can over-write their functions with fixInNamespace and assignInNamespace, but do not use this in production code.
None of this should preclude the tried-and-true standard R debugging tools, some of which are above and others of which are not. In particular, the post-mortem debugging tools are handy when you have a time-consuming bunch of code that you'd rather not re-run.
Finally, for tricky problems which don't seem to throw an error message, you can use options(error=dump.frames) as detailed in this question:
Error without an error being thrown
At some point, glm.fit is being called. That means one of the functions you call or one of the functions called by those functions is using either glm, glm.fit.
Also, as I mention in my comment above, that is a warning not an error, which makes a big difference. You can't trigger any of R's debugging tools from a warning (with default options before someone tells me I am wrong ;-).
If we change the options to turn warnings into errors then we can start to use R's debugging tools. From ?options we have:
‘warn’: sets the handling of warning messages. If ‘warn’ is
negative all warnings are ignored. If ‘warn’ is zero (the
default) warnings are stored until the top-level function
returns. If fewer than 10 warnings were signalled they will
be printed otherwise a message saying how many (max 50) were
signalled. An object called ‘last.warning’ is created and
can be printed through the function ‘warnings’. If ‘warn’ is
one, warnings are printed as they occur. If ‘warn’ is two or
larger all warnings are turned into errors.
So if you run
options(warn = 2)
then run your code, R will throw an error. At which point, you could run
traceback()
to see the call stack. Here is an example.
> options(warn = 2)
> foo <- function(x) bar(x + 2)
> bar <- function(y) warning("don't want to use 'y'!")
> foo(1)
Error in bar(x + 2) : (converted from warning) don't want to use 'y'!
> traceback()
7: doWithOneRestart(return(expr), restart)
6: withOneRestart(expr, restarts[[1L]])
5: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg,
call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
4: .signalSimpleWarning("don't want to use 'y'!", quote(bar(x +
2)))
3: warning("don't want to use 'y'!")
2: bar(x + 2)
1: foo(1)
Here you can ignore the frames marked 4: and higher. We see that foo called bar and that bar generated the warning. That should show you which functions were calling glm.fit.
If you now want to debug this, we can turn to another option to tell R to enter the debugger when it encounters an error, and as we have made warnings errors we will get a debugger when the original warning is triggered. For that you should run:
options(error = recover)
Here is an example:
> options(error = recover)
> foo(1)
Error in bar(x + 2) : (converted from warning) don't want to use 'y'!
Enter a frame number, or 0 to exit
1: foo(1)
2: bar(x + 2)
3: warning("don't want to use 'y'!")
4: .signalSimpleWarning("don't want to use 'y'!", quote(bar(x + 2)))
5: withRestarts({
6: withOneRestart(expr, restarts[[1]])
7: doWithOneRestart(return(expr), restart)
Selection:
You can then step into any of those frames to see what was happening when the warning was thrown.
To reset the above options to their default, enter
options(error = NULL, warn = 0)
As for the specific warning you quote, it is highly likely that you need to allow more iterations in the code. Once you've found out what is calling glm.fit, work out how to pass it the control argument using glm.control - see ?glm.control.
So browser(), traceback() and debug() walk into a bar, but trace() waits outside and keeps the motor running.
By inserting browser somewhere in your function, the execution will halt and wait for your input. You can move forward using n (or Enter), run the entire chunk (iteration) with c, finish the current loop/function with f, or quit with Q; see ?browser.
With debug, you get the same effect as with browser, but this stops the execution of a function at its beginning. Same shortcuts apply. This function will be in a "debug" mode until you turn it off using undebug (that is, after debug(foo), running the function foo will enter "debug" mode every time until you run undebug(foo)).
A more transient alternative is debugonce, which will remove the "debug" mode from the function after the next time it's evaluated.
traceback will give you the flow of execution of functions all the way up to where something went wrong (an actual error).
You can insert code bits (i.e. custom functions) in functions using trace, for example browser. This is useful for functions from packages and you're too lazy to get the nicely folded source code.
My general strategy looks like:
Run traceback() to see look for obvious issues
Set options(warn=2) to treat warnings like errors
Set options(error=recover) to step into the call stack on error
After going through all the steps suggested here I just learned that setting .verbose = TRUE in foreach() also gives me tons of useful information. In particular foreach(.verbose=TRUE) shows exactly where an error occurs inside the foreach loop, while traceback() does not look inside the foreach loop.
Mark Bravington's debugger which is available as the package debug on CRAN is very good and pretty straight forward.
library(debug);
mtrace(myfunction);
myfunction(a,b);
#... debugging, can query objects, step, skip, run, breakpoints etc..
qqq(); # quit the debugger only
mtrace.off(); # turn off debugging
The code pops up in a highlighted Tk window so you can see what's going on and, of course you can call another mtrace() while in a different function.
HTH
I like Gavin's answer: I did not know about options(error = recover). I also like to use the 'debug' package that gives a visual way to step through your code.
require(debug)
mtrace(foo)
foo(1)
At this point it opens up a separate debug window showing your function, with a yellow line showing where you are in the code. In the main window the code enters debug mode, and you can keep hitting enter to step through the code (and there are other commands as well), and examine variable values, etc. The yellow line in the debug window keeps moving to show where you are in the code. When done with debugging, you can turn off tracing with:
mtrace.off()
Based on the answer I received here, you should definitely check out the options(error=recover) setting. When this is set, upon encountering an error, you'll see text on the console similar to the following (traceback output):
> source(<my filename>)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
Enter a frame number, or 0 to exit
1: source(<my filename>)
2: eval.with.vis(ei, envir)
3: eval.with.vis(expr, envir, enclos)
4: LinearParamSearch(data = dataset, y = data.frame(LGD = dataset$LGD10), data.names = data
5: LinearParamSearch.R#66: plot(x = x, y = y.data, xlab = names(y), ylab = data.names[i])
6: LinearParamSearch.R#66: plot.default(x = x, y = y.data, xlab = names(y), ylab = data.nam
7: LinearParamSearch.R#66: localWindow(xlim, ylim, log, asp, ...)
8: LinearParamSearch.R#66: plot.window(...)
Selection:
At which point you can choose which "frame" to enter. When you make a selection, you'll be placed into browser() mode:
Selection: 4
Called from: stop(gettextf("replacement has %d rows, data has %d", N, n),
domain = NA)
Browse[1]>
And you can examine the environment as it was at the time of the error. When you're done, type c to bring you back to the frame selection menu. When you're done, as it tells you, type 0 to exit.
I gave this answer to a more recent question, but am adding it here for completeness.
Personally I tend not to use functions to debug. I often find that this causes as much trouble as it solves. Also, coming from a Matlab background I like being able to do this in an integrated development environment (IDE) rather than doing this in the code. Using an IDE keeps your code clean and simple.
For R, I use an IDE called "RStudio" (http://www.rstudio.com), which is available for windows, mac, and linux and is pretty easy to use.
Versions of Rstudio since about October 2013 (0.98ish?) have the capability to add breakpoints in scripts and functions: to do this, just click on the left margin of the file to add a breakpoint. You can set a breakpoint and then step through from that point on. You also have access to all of the data in that environment, so you can try out commands.
See http://www.rstudio.com/ide/docs/debugging/overview for details. If you already have Rstudio installed, you may need to upgrade - this is a relatively new (late 2013) feature.
You may also find other IDEs that have similar functionality.
Admittedly, if it's a built-in function you may have to resort to some of the suggestions made by other people in this discussion. But, if it's your own code that needs fixing, an IDE-based solution might be just what you need.
To debug Reference Class methods without instance reference
ClassName$trace(methodName, browser)
I am beginning to think that not printing error line number - a most basic requirement - BY DEFAILT- is some kind of a joke in R/Rstudio. The only reliable method I have found to find where an error occurred is to make the additional effort of calloing traceback() and see the top line.

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