INLA install problem on HPC

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Radoslaw Panczak

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May 2, 2022, 4:35:05 AMMay 2
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Hi team,

I'm trying to set up INLA on our HPC infrastructure. 
Have access to R 4.1.0 on CentOS 7.9.2009.x86_64

I run 
    inla.binary.install()
after install 

Than simple example from the website gets me to an error


/storage/homefs/panczak/R/x86_64-pc-linux-gnu-library/4.1/INLA/bin/linux/64bit/inla.mkl: /storage/homefs/panczak/R/x86_64-pc-linux-gnu-library/4.1/INLA/bin/linux/64bit/first/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /software.el7/software/ICU/69.1-GCCcore-10.3.0/lib64/libicuuc.so.69)
/storage/homefs/panczak/R/x86_64-pc-linux-gnu-library/4.1/INLA/bin/linux/64bit/inla.mkl: /storage/homefs/panczak/R/x86_64-pc-linux-gnu-library/4.1/INLA/bin/linux/64bit/first/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /software.el7/software/ICU/69.1-GCCcore-10.3.0/lib64/libicui18n.so.69)
/storage/homefs/panczak/R/x86_64-pc-linux-gnu-library/4.1/INLA/bin/linux/64bit/inla.mkl: /storage/homefs/panczak/R/x86_64-pc-linux-gnu-library/4.1/INLA/bin/linux/64bit/first/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /software.el7/software/ICU/69.1-GCCcore-10.3.0/lib64/libicuuc.so.69)
/storage/homefs/panczak/R/x86_64-pc-linux-gnu-library/4.1/INLA/bin/linux/64bit/inla.mkl: /storage/homefs/panczak/R/x86_64-pc-linux-gnu-library/4.1/INLA/bin/linux/64bit/first/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /software.el7/software/ICU/69.1-GCCcore-10.3.0/lib64/libicui18n.so.69)
Error in inla.inlaprogram.has.crashed() :

Are there any issues with GCC? Is there a specific version needed?
Any pointers to what could be causing it and what could be tried to fix it?

Helpdesk

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May 2, 2022, 5:02:23 AMMay 2
to Radoslaw Panczak, R-inla discussion group

run

inla.binary.install()

and then chose the 'CentOS7' one ? (I cannot recall the number)


--
Håvard Rue
he...@r-inla.org

-----Original Message-----
From: Radoslaw Panczak <r.pa...@gmail.com>
To: R-inla discussion group <r-inla-disc...@googlegroups.com>
Subject: [r-inla] INLA install problem on HPC
Date: Mon, 2 May 2022 01:35:04 -0700 (PDT)

Hi team,
I'm trying to set up INLA on our HPC infrastructure. 
Have access to R 4.1.0 on CentOS 7.9.2009.x86_64

I run 
    inla.binary.install()
after install 

Than simple example from the website gets me to an error


/storage/homefs/panczak/R/x86_64-pc-linux-gnu-
library/4.1/INLA/bin/linux/64bit/inla.mkl:
/storage/homefs/panczak/R/x86_64-pc-linux-gnu-
library/4.1/INLA/bin/linux/64bit/first/libstdc++.so.6: version
`CXXABI_1.3.8' not found (required by /software.el7/software/ICU/69.1-
GCCcore-10.3.0/lib64/libicuuc.so.69)
/storage/homefs/panczak/R/x86_64-pc-linux-gnu-
library/4.1/INLA/bin/linux/64bit/inla.mkl:
/storage/homefs/panczak/R/x86_64-pc-linux-gnu-
library/4.1/INLA/bin/linux/64bit/first/libstdc++.so.6: version
`CXXABI_1.3.8' not found (required by /software.el7/software/ICU/69.1-
GCCcore-10.3.0/lib64/libicui18n.so.69)
/storage/homefs/panczak/R/x86_64-pc-linux-gnu-
library/4.1/INLA/bin/linux/64bit/inla.mkl:
/storage/homefs/panczak/R/x86_64-pc-linux-gnu-
library/4.1/INLA/bin/linux/64bit/first/libstdc++.so.6: version
`CXXABI_1.3.8' not found (required by /software.el7/software/ICU/69.1-
GCCcore-10.3.0/lib64/libicuuc.so.69)
/storage/homefs/panczak/R/x86_64-pc-linux-gnu-
library/4.1/INLA/bin/linux/64bit/inla.mkl:
/storage/homefs/panczak/R/x86_64-pc-linux-gnu-
library/4.1/INLA/bin/linux/64bit/first/libstdc++.so.6: version
`CXXABI_1.3.8' not found (required by /software.el7/software/ICU/69.1-
GCCcore-10.3.0/lib64/libicui18n.so.69)
Error in inla.inlaprogram.has.crashed() :

Are there any issues with GCC? Is there a specific version needed?
Any pointers to what could be causing it and what could be tried to fix
it?

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Radoslaw Panczak

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May 2, 2022, 5:07:01 AMMay 2
to R-inla discussion group
Thank you Håvard, already tried this. No luck. 

Radoslaw Panczak

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May 10, 2022, 10:43:26 AMMay 10
to R-inla discussion group
I'm sorry I realize I was answering to helpdesk email not the group. 

Here are more details. 

I restarted the whole installation process one more time. Came back to the same error as specified above. 

Searching for the three missing libraries I realized they are part of the ICU package, as listed here
Which seems to be this

I tried tracking down this module on our cluster and I can get the version that should be correct one:
ICU/69.1-GCCcore-10.3.0

That changes error message to this:

 *** caught illegal operation ***
address 0x7f4085934a2e, cause 'illegal operand'

Traceback:
 1: validityMethod(as(object, superClass))
 2: isTRUE(x)
 3: anyStrings(validityMethod(as(object, superClass)))
 4: validObject(.Object)
 5: .nextMethod(.Object = .Object, ... = ...)
 6: callNextMethod()
 7: initialize(value, ...)
 8: initialize(value, ...)
 9: new("dgCMatrix", i = 0:(n - 1L), p = c(0L, n), Dim = c(n, 1L),     x = rep.int(1, n))
10: model.spmatrix(t, data, transpose = transpose, drop.unused.levels = drop.unused.levels,     row.names = row.names, sep = sep, verbose = verbose)
11: sparse.model.matrix(object, data = data, contrasts.arg = contrasts.arg,     drop.unused.levels = drop.unused.levels, xlev = xlev, ...)
12: MatrixModels::model.Matrix(new.fix.formula, data = model.frame(new.fix.formula,     data.same.len, na.action = inla.na.action), contrasts.arg = contrasts,     sparse = TRUE)
13: inla.core(formula = formula, family = family, contrasts = contrasts,     data = data, quantiles = quantiles, E = E, offset = offset,     scale = scale, weights = weights, Ntrials = Ntrials, strata = strata,     lp.scale = lp.scale, link.covariates = link.covariates, verbose = verbose,     lincomb = lincomb, selection = selection, control.compute = control.compute,     control.predictor = control.predictor, control.family = control.family,     control.inla = control.inla, control.fixed = control.fixed,     control.mode = control.mode, control.expert = control.expert,     control.hazard = control.hazard, control.lincomb = control.lincomb,     control.update = control.update, control.lp.scale = control.lp.scale,     control.pardiso = control.pardiso, only.hyperparam = only.hyperparam,     inla.call = inla.call, inla.arg = inla.arg, num.threads = num.threads,     blas.num.threads = blas.num.threads, keep = keep, working.directory = working.directory,     silent = silent, inla.mode = inla.mode, safe = FALSE, debug = debug,     .parent.frame = .parent.frame)
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
18: try(inla.core(formula = formula, family = family, contrasts = contrasts,     data = data, quantiles = quantiles, E = E, offset = offset,     scale = scale, weights = weights, Ntrials = Ntrials, strata = strata,     lp.scale = lp.scale, link.covariates = link.covariates, verbose = verbose,     lincomb = lincomb, selection = selection, control.compute = control.compute,     control.predictor = control.predictor, control.family = control.family,     control.inla = control.inla, control.fixed = control.fixed,     control.mode = control.mode, control.expert = control.expert,     control.hazard = control.hazard, control.lincomb = control.lincomb,     control.update = control.update, control.lp.scale = control.lp.scale,     control.pardiso = control.pardiso, only.hyperparam = only.hyperparam,     inla.call = inla.call, inla.arg = inla.arg, num.threads = num.threads,     blas.num.threads = blas.num.threads, keep = keep, working.directory = working.directory,     silent = silent, inla.mode = inla.mode, safe = FALSE, debug = debug,     .parent.frame = .parent.frame))
19: run.inla()
20: inla.core.safe(formula = formula, family = family, contrasts = contrasts,     data = data, quantiles = quantiles, E = E, offset = offset,     scale = scale, weights = weights, Ntrials = Ntrials, strata = strata,     lp.scale = lp.scale, link.covariates = link.covariates, verbose = verbose,     lincomb = lincomb, selection = selection, control.compute = control.compute,     control.predictor = control.predictor, control.family = control.family,     control.inla = control.inla, control.fixed = control.fixed,     control.mode = control.mode, control.expert = control.expert,     control.hazard = control.hazard, control.lincomb = control.lincomb,     control.update = control.update, control.lp.scale = control.lp.scale,     control.pardiso = control.pardiso, only.hyperparam = only.hyperparam,     inla.call = inla.call, inla.arg = inla.arg, num.threads = num.threads,     blas.num.threads = blas.num.threads, keep = keep, working.directory = working.directory,     silent = silent, inla.mode = inla.mode, safe = FALSE, debug = debug,     .parent.frame = .parent.frame)
21: inla(formula, family = "gaussian", data = data)

Helpdesk

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May 12, 2022, 6:32:01 AMMay 12
to Radoslaw Panczak, R-inla discussion group
it seems that this is happeningin the R code, hence nothing to do in the
inla-binary
Håvard Rue
he...@r-inla.org
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