casperwberg
commented
3 years ago HI Jason,
Very recently we fixed an issue in the DATRAS package (it was not working properly with newer R versions). Could you please try to re-install DATRAS and see if this fixes the problem?
Wrt. openBLAS, actually an even better (and easier) option may be to install Microsoft R open (this includes optimized BLAS libraries as well). This works on both Windows and Linux. I would highly recommend this both for the GAMs and VAST as it gives quite drastic speed-ups.
Kind regards, Casper
Den lør. 14. nov. 2020 kl. 00.26 skrev Jason Conner < notifications@github.com>:
Hi @casperwberg https://github.com/casperwberg ,
I am running your gam.R code without BLAS (R version 4.02, SurveyIndex 1.09, DATRAS 1.01), and when fitting the model, I get this error:
6: stop("Error occured for age ", a, ".\n", "Try reducing the number of age groups or decrease the basis dimension of the smooths, k\n") 5: FUN(X[[i]], ...) 4: lapply(X, FUN, ...) 3: parallel::mclapply(1:noAges, do.one.a, mc.cores = mc.cores) 2: getSurveyIdx(ds[[SPECIES]], 1, myids = NULL, predD = allpd, cutOff = 0, fam = "Tweedie", modelP = fm, gamma = 1, control = list(trace = TRUE, maxit = 20)) 1: system.time(models[[SPECIES]] <- getSurveyIdx(ds[[SPECIES]], 1, myids = NULL, predD = allpd, cutOff = 0, fam = "Tweedie", modelP = fm, gamma = 1, control = list(trace = TRUE, maxit = 20)))
Have you run into this and do you have suggestions? I installed RhpcBLASctl, but I don't know how to install openBLAS, and I believe the code should work in serial.
Thank you
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Hi @casperwberg ,
I am running your gam.R code without BLAS (R version 4.02, SurveyIndex 1.09, DATRAS 1.01), and when fitting the model, I get this error:
6: stop("Error occured for age ", a, ".\n", "Try reducing the number of age groups or decrease the basis dimension of the smooths, k\n") 5: FUN(X[[i]], ...) 4: lapply(X, FUN, ...) 3: parallel::mclapply(1:noAges, do.one.a, mc.cores = mc.cores) 2: getSurveyIdx(ds[[SPECIES]], 1, myids = NULL, predD = allpd, cutOff = 0, fam = "Tweedie", modelP = fm, gamma = 1, control = list(trace = TRUE, maxit = 20)) 1: system.time(models[[SPECIES]] <- getSurveyIdx(ds[[SPECIES]], 1, myids = NULL, predD = allpd, cutOff = 0, fam = "Tweedie", modelP = fm, gamma = 1, control = list(trace = TRUE, maxit = 20)))
Have you run into this and do you have suggestions? I installed RhpcBLASctl, but I don't know how to install openBLAS, and I believe the code should work in serial.
Thank you