Protection stack too large
Posted on
Ryan
Joined: 02/08/2014
Forums
Dear all,
Did anyone have a warning like:
"Warning message:
In runHelper(model, frontendStart, intervals, silent, suppressWarnings, :
Protection stack too large; report this problem to the OpenMx forum"
Does anyone know how we can handle this?
Other information:
- The version of OpenMx: 2.0.0-4004 MASS_7.3-35
- The version of R: 3.1.2
- The operating system and architecture: x86_64, Apple OSX 10.8.5.
- R syntax that brings this warning is a command in "metaSEM": --tssem1--
Thanks!
protection stack
It should be easy to fix. Can you share the model that provokes this error?
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In reply to protection stack by jpritikin
protection stack
Thanks Josh!
The model is pretty simple. Its R code is:
#####
entry <- readLowTriMat(file="116-16entry.txt", no.var=16, na.strings="NA")
samplesize <- read.table("116samplesize.txt")
random1 <- tssem1(entry, samplesize, method="REM", RE.type="Diag")
######
The last line provokes the error.
The dataset has 116 matrices and 16 variables per matrix.
This error never occurred before OpenMx 2.0. With OpenMx 1.4, I even run 118 matrices with 22 variables per matrix.
By the way, I increased my computer's stack size by -- ulimit -s --, but this didn't help me go through this problem.
I probably have to go back to OpenMx 1.4.
Best,
Ryan
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In reply to protection stack by Ryan
how to reproduce
Can you attach the 2 data files to your forum post?
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In reply to how to reproduce by jpritikin
Data files for reproducing
Dear Joshua,
Here come the data files and the syntax.
Details about - tssem1 - are available at: http://courses.nus.edu.sg/course/psycwlm/Internet/metaSEM/.
Thanks in advance!
Ryan
p.s., Running the same syntax with OpenMx1.4 does not evoke this error.
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In reply to Data files for reproducing by Ryan
can't reproduce, so far
Ah, thanks for the data. I am running your script now. It is taking a long time.
Can you build OpenMx from subversion? If you can build SVN 4161 then you can enable some diagnostics,
mxOption(NULL, "Debug Protect Stack", 1)
I will let your script keep running. Maybe I will get some results soon.
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In reply to can't reproduce, so far by jpritikin
How to build SVN4161?
Thanks Joshua!
Sorry, I don't know how to "build OpenMx from subversion". I only find this "http://openmx.psyc.virginia.edu/wiki/howto-build-openmx-source-repository". Is this what you mean?
Also, I can't find relevant information about "SVN4161".
Without SVN4161, the -- mxOption(NULL,"maxStackDepth", 25000) -- increases stack a bit, because the syntax seems to start working, but reports errors finally.
Best,
Ryan
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In reply to How to build SVN4161? by Ryan
build from source
> Sorry, I don't know how to "build OpenMx from subversion". I only find this "http://openmx.psyc.virginia.edu/wiki/howto-build-openmx-source-repository". Is this what you mean?
Yes. Or if you can wait a little bit then we're scheduled to release 2.0.1 soon.
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In reply to build from source by jpritikin
2.0.1 released, can you try again?
I was able to run your model without error. Can you try again with 2.0.1?
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In reply to 2.0.1 released, can you try again? by jpritikin
2.0.1 worked it out
The dataset and syntax can go through with 2.0.1.
Thank you very much!
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In reply to can't reproduce, so far by jpritikin
fixed?
I let your script run overnight and it finally finished without error. Maybe the problem you noticed has been fixed in subversion trunk.
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