Hi, Still trying to make this work. I think the problem is that the task is packaged with one file (data/data1.csv for instance), and so the other two datafiles don't exist in the CARE archive. I've been trying to use the hostFiles option as explained here http://www.openmole.org/Documentation_Language_Tasks_Native.html#Usinglocalresources but no success. Is this option still valid in openmole? Is the argument the path of the file ("data/data1.csv"), or the path to the repo containing the file ("data/")?
Any help much appreciated! Thanks, Hélène 2017-06-29 17:35 GMT+02:00 Hélène Arduin <[email protected]>: > Hi Jonathan, > > Thank you for your answer. > > When input is specified as data.csv it runs fine, but it's not doing > what's expected (i.e sampling over the three input files in the data repo). > > So I modified the CARETask as explained before, and also the R script to > read the second argument > n <- as.character(args[2]) > use it as the data file name > data <- read.csv(n, header=T, sep=",") > and repackaged with care. > > But I get an error (see attached file) when I try to run it on openmole. > > Hélène > > 2017-06-29 16:57 GMT+02:00 Jonathan Passerat-Palmbach < > [email protected]>: > >> Hi Helene, >> >> In this case it seems the csv file is hardcoded in the R script: >> >> https://github.com/openmole/openmole-market/blob/7-dev/R-hello/test.R >> >> it's always reading from "data.csv" regardless of the second command line >> argument >> >> you can either update the R script and repackage or make sure `input` get >> written as "data.csv" in the CARETask >> >> ... >> >> inputFiles += (input, "data.csv"), >> >> ... >> >> >> Cheers >> >> J >> >> On 29/06/17 14:51, Hélène Arduin wrote: >> >> Hi, >> >> I've been trying to run the Hello World in R >> <http://www.openmole.org/Documentation_Market%20Place_R.html> example, >> since I think it's supposed to do what I want my own code to do, but it's >> not working well. >> >> First I had to repackage the R code to produce a .tgz.bin archive, the >> .bin doesn't work even when I try to repackage it (seg fault). >> >> With the .tgz.bin archive, the RFiles.oms is executed and I get result >> files. >> From what I understand, the R code should be run with each of the >> three data files of the "data" repo as input, however it is always run with >> the data.csv input. Only the names of the three data files are used to name >> the result files (data1_1.csv ; data1_2.csv ; data2_1.csv etc), but not the >> actual data inside. >> Is this the expected behavior? >> >> I've tried to modify the RFiles.oms (see below) in order to vary the >> input files and read each of the three files from the "data" repo but it's >> not a success... >> >> // R task >> val rTask = >> CARETask(workDirectory / "care.tgz.bin", "R --slave -f test.R --args >> ${i} *${n}*") set ( >> i := 42, >> (inputs, outputs) += (i, n), >> inputFiles += (input, "*${n}*"), >> outputFiles += ("results.csv", output) >> ) >> >> (I've also modified accordingly the test.R file and repackaged >> care.tgz.bin.) >> >> Does anyone have an idea of how to read different input files on each >> iteration of the model? >> >> Thanks! >> >> Hélène >> >> >> _______________________________________________ >> OpenMOLE-users mailing >> [email protected]http://fedex.iscpif.fr/mailman/listinfo/openmole-users >> >> >> -- >> Jonathan Passerat-Palmbach, PhD >> Research Associate >> Department of Computing >> Imperial College London >> >> South Kensington Campus >> Huxley Building - room 344 >> 180 Queen's Gate >> London SW7 2AZ >> https://jopasser.at >> >> >> _______________________________________________ >> OpenMOLE-users mailing list >> [email protected] >> http://fedex.iscpif.fr/mailman/listinfo/openmole-users >> >> >
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