hrue
commented
2 months ago I guess you need to download another linux build, chose one from
inla.binary.install()
On Thu, 2024-06-20 at 17:21 -0700, Fernando Mayer wrote:
After placing a new licence of the Pardiso library in ~/panua.lic, I got the following error in inla.pardiso.check(): library(INLA) Loading required package: Matrix Loading required package: sp This is INLA_24.06.19 built 2024-06-19 13:30:03 UTC. - See www.r-inla.org/contact-us for how to get help. - List available models/likelihoods/etc with inla.list.models() - Use inla.doc(
) to access documentation inla.pardiso.check() sh: symbol lookup error: sh: undefined symbol: rl_trim_arg_from_keyseq sh: symbol lookup error: sh: undefined symbol: rl_trim_arg_from_keyseq [1] "[Panua] Internal error 0x3c" attr(,"status") [1] 60 Warning message: In system(paste(shQuote(inla.call.no.remote()), "-m pardiso"), intern = TRUE) : running command ''/home/mayer/R/library/INLA/bin/linux/64bit/inla.mkl.run' - m pardiso' had status 60 By ignoring this warning and running a simple example (from the R-INLA webpage), I also got this error and INLA fails: n = 100; a = 1; b = 1; tau = 100 z = rnorm(n) eta = a + bz scale = exp(rnorm(n)) prec = scaletau y = rnorm(n, mean = eta, sd = 1/sqrt(prec)) data = list(y=y, z=z) formula = y ~ 1+z result = inla(formula, family = "gaussian", data = data, verbose = TRUE) sh: symbol lookup error: sh: undefined symbol: rl_trim_arg_from_keyseq sh: symbol lookup error: sh: undefined symbol: rl_trim_arg_from_keyseq [Panua] Internal error 0x3c inla.core.safe: The inla program failed, but will rerun in case better initial values may help. try=1/1 sh: symbol lookup error: sh: undefined symbol: rl_trim_arg_from_keyseq sh: symbol lookup error: sh: undefined symbol: rl_trim_arg_from_keyseq [Panua] Internal error 0x3c Error in inla.core.safe(formula = formula, family = family, contrasts = contrasts, : The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully. If this does not help, please contact the developers at @.>. The inla program failed and the maximum number of tries has been reached. Searching around, I found out that the sh: symbol lookup error: sh: undefined symbol: rl_trim_arg_from_keyseq problem could be related with the libreadline version "shipped" with INLA, and the one on my system. As per this (unrelated with INLA) issue, the symbol rl_trim_arg_from_keyseq appears on my system nm -D /usr/lib/libreadline.so.8 | grep rl_trim_arg_from_keyseq 00000000000252e0 T rl_trim_arg_from_keyseq But it does not on the version from INLA nm -D ~/R/library/INLA/bin/linux/64bit/libreadline.so.8 | grep rl_trim_arg_from_keyseq I was able to solve this by linking my version of libreadline in INLA rm ~/R/library/INLA/bin/linux/64bit/libreadline.so.8 ln -s /usr/lib/libreadline.so.8 ~/R/library/INLA/bin/linux/64bit/libreadline.so.8 Now I get the message that Pardiso os working library(INLA) inla.pardiso.check() [1] "SUCCESS: PARDISO IS INSTALLED AND WORKING" However it appears another error and INLA fails anyway n = 100; a = 1; b = 1; tau = 100 z = rnorm(n) eta = a + bz scale = exp(rnorm(n)) prec = scaletau y = rnorm(n, mean = eta, sd = 1/sqrt(prec)) data = list(y=y, z=z) formula = y ~ 1+z result = inla(formula, family = "gaussian", data = data, verbose = TRUE) malloc(): invalid size (unsorted)
inla.core.safe: The inla program failed, but will rerun in case better initial values may help. try=1/1 malloc(): invalid size (unsorted) munmap_chunk(): invalid pointer Error in inla.core.safe(formula = formula, family = family, contrasts = contrasts, : The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully. If this does not help, please contact the developers at @.>. The inla program failed and the maximum number of tries has been reached. The full log of verbose is too long, so I pasted it here. Even with the sym-linked libreadline, if I remove ~/panua.lic, the example code runs with no errors. Can you please let me know if this is a problem specific to my system, or could it be something on the INLA side. I wonder it's not related to INLA because I couldn't find any other issues related to this. If that's the case, would you know any workaround to make possible to use Pardiso? This is my R info: sessionInfo() R version 4.4.1 (2024-06-14) Platform: x86_64-pc-linux-gnu Running under: Arch Linux
Matrix products: default BLAS/LAPACK: /opt/intel/oneapi/mkl/2024.1/lib/libmkl_gf_lp64.so.2; LAPACK version 3.11.0
locale: [1] LC_CTYPE=en_IE.UTF-8 LC_NUMERIC=C LC_TIME=en_IE.UTF-8 [4] LC_COLLATE=en_IE.UTF-8 LC_MONETARY=en_IE.UTF-8
LC_MESSAGES=en_IE.UTF-8 [7] LC_PAPER=en_IE.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=Ctime zone: America/Sao_Paulo tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] INLA_24.06.19 sp_2.1-4 Matrix_1.7-0
loaded via a namespace (and not attached): [1] fmesher_0.1.6.9003 lattice_0.22-6 magrittr_2.0.3 e1071_1.7-14 [5] splines_4.4.1 KernSmooth_2.23-24 parallel_4.4.1 lifecycle_1.0.4 [9] classInt_0.4-10 sf_1.0-16 cli_3.6.2 fortunes_1.5-4 [13] grid_4.4.1 DBI_1.2.3 withr_3.0.0 proxy_0.4-27 [17] class_7.3-22 compiler_4.4.1 tools_4.4.1 Rcpp_1.0.12 [21] rlang_1.1.4 units_0.8-5 MatrixModels_0.5-3 This is my system info: OS: Arch Linux x86_64 Host: XPS 9320 Kernel: 6.6.34-1-lts Shell: bash 5.2.26 CPU: 12th Gen Intel i7-1260P (16) @ 4.700GHz GPU: Intel Alder Lake-P GT2 [Iris Xe Graphics] Memory: 6745MiB / 31706MiB — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>
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fernandomayer
After placing a new licence of the Pardiso library in
~/panua.lic, I got the following error ininla.pardiso.check():By ignoring this warning and running a simple example (from the R-INLA webpage), I also got this error and INLA fails:
Searching around, I found out that the
problem could be related with the
libreadlineversion "shipped" with INLA, and the one on my system. As per this (unrelated with INLA) issue, the symbolrl_trim_arg_from_keyseqappears on my systemBut it does not on the version from INLA
I was able to solve this by linking my version of
libreadlinein INLANow I get the message that Pardiso is working
However it appears another error and INLA fails anyway
The full log of
verboseis too long, so I pasted it here.Even with the sym-linked
libreadline, if I remove~/panua.lic, the example code runs with no errors.Can you please let me know if this is a problem specific to my system, or could it be something on the INLA side. I wonder it's not related to INLA because I couldn't find any other issues related to this. If that's the case, would you know any workaround to make possible to use Pardiso?
This is my R info:
This is my system info:
This is my
libreadlineversion: