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Type 'q()' to quit R. > install.packages("Rmpi",configure.args="--with-mpi=/packages/openmpi/4.1.8") checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed Trying to find mpi.h ... Found in /packages/openmpi/4.1.8/include Trying to find libmpi.so or libmpich.a ... Found libmpi in /packages/openmpi/4.1.8/lib checking for orted... yes checking for prted... no configure: creating ./config.status config.status: creating src/Makevars gcc -I"/home/th798/lib64/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/packages/openmpi/4.1.8/include -DMPI2 -DOPENMPI -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -g -O2 -c Rmpi.c -o Rmpi.o gcc -I"/home/th798/lib64/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/packages/openmpi/4.1.8/include -DMPI2 -DOPENMPI -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -g -O2 -c conversion.c -o conversion.o gcc -I"/home/th798/lib64/R/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/packages/openmpi/4.1.8/include -DMPI2 -DOPENMPI -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -g -O2 -c internal.c -o internal.o gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o Rmpi.so Rmpi.o conversion.o internal.o -L/packages/openmpi/4.1.8/lib -lmpi Loading required package: data.table Loading required package: data.table Loading required package: data.table -------------------------------------------------------------------------- WARNING: An invalid value was given for btl_tcp_if_include. This value will be ignored. Local host: wind Value: ib0 Message: Unknown interface name -------------------------------------------------------------------------- [wind:1160091:0:1160091] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil)) ==== backtrace (tid:1160091) ==== 0 /lib64/libucs.so.0(ucs_handle_error+0x2dc) [0x1475d161213c] 1 /lib64/libucs.so.0(+0x2c31c) [0x1475d161231c] 2 /lib64/libucs.so.0(+0x2c4ea) [0x1475d16124ea] 3 /packages/openmpi/4.1.8/lib/libopen-pal.so.40(+0x538d7) [0x1475dcdbf8d7] 4 /packages/openmpi/4.1.8/lib/libopen-pal.so.40(mca_base_var_register+0x27) [0x1475dcdc1477] 5 /packages/openmpi/4.1.8/lib/libopen-pal.so.40(mca_base_framework_var_register+0x3a) [0x1475dcdc150a] 6 /packages/openmpi/4.1.8/lib/libopen-pal.so.40(mca_base_framework_register+0x1c5) [0x1475dcdc7315] 7 /packages/openmpi/4.1.8/lib/libopen-pal.so.40(mca_base_framework_open+0x11) [0x1475dcdc73c1] 8 /packages/openmpi/4.1.8/lib/libopen-pal.so.40(mca_base_framework_components_open+0x16f) [0x1475dcdbd4ff] 9 /packages/openmpi/4.1.8/lib/libmpi.so.40(+0xf0a87) [0x1475dd3d9a87] 10 /packages/openmpi/4.1.8/lib/libopen-pal.so.40(mca_base_framework_open+0x81) [0x1475dcdc7431] 11 /packages/openmpi/4.1.8/lib/libmpi.so.40(ompi_mpi_init+0x634) [0x1475dd3e6bc4] 12 /packages/openmpi/4.1.8/lib/libmpi.so.40(MPI_Init+0x81) [0x1475dd36b561] 13 /projects/genomic-ml/lib64/R/library/00LOCK-Rmpi/00new/Rmpi/libs/Rmpi.so(mpi_initialize+0x3f) [0x1475dd63a25f] 14 /home/th798/lib64/R/bin/exec/R() [0x4a0182] 15 /home/th798/lib64/R/bin/exec/R() [0x4a0605] 16 /home/th798/lib64/R/bin/exec/R() [0x4d8021] 17 /home/th798/lib64/R/bin/exec/R(Rf_eval+0x140) [0x4e9440] 18 /home/th798/lib64/R/bin/exec/R() [0x4eb43f] 19 /home/th798/lib64/R/bin/exec/R(Rf_applyClosure+0x175) [0x4ec235] 20 /home/th798/lib64/R/bin/exec/R() [0x4e04f4] 21 /home/th798/lib64/R/bin/exec/R(Rf_eval+0x140) [0x4e9440] 22 /home/th798/lib64/R/bin/exec/R() [0x4e9ce0] 23 /home/th798/lib64/R/bin/exec/R() [0x4ea108] 24 /home/th798/lib64/R/bin/exec/R() [0x4df6f3] 25 /home/th798/lib64/R/bin/exec/R(Rf_eval+0x140) [0x4e9440] 26 /home/th798/lib64/R/bin/exec/R() [0x4e9ce0] 27 /home/th798/lib64/R/bin/exec/R() [0x4ea108] 28 /home/th798/lib64/R/bin/exec/R() [0x4df6f3] 29 /home/th798/lib64/R/bin/exec/R(Rf_eval+0x140) [0x4e9440] 30 /home/th798/lib64/R/bin/exec/R() [0x4e9ce0] 31 /home/th798/lib64/R/bin/exec/R() [0x4ea108] 32 /home/th798/lib64/R/bin/exec/R() [0x4df6f3] 33 /home/th798/lib64/R/bin/exec/R(Rf_eval+0x140) [0x4e9440] 34 /home/th798/lib64/R/bin/exec/R() [0x4e9ce0] 35 /home/th798/lib64/R/bin/exec/R() [0x4ea108] 36 /home/th798/lib64/R/bin/exec/R() [0x4df6f3] 37 /home/th798/lib64/R/bin/exec/R(Rf_eval+0x140) [0x4e9440] 38 /home/th798/lib64/R/bin/exec/R() [0x4eb43f] 39 /home/th798/lib64/R/bin/exec/R(Rf_applyClosure+0x175) [0x4ec235] 40 /home/th798/lib64/R/bin/exec/R() [0x4e04f4] 41 /home/th798/lib64/R/bin/exec/R(Rf_eval+0x140) [0x4e9440] 42 /home/th798/lib64/R/bin/exec/R() [0x4eb43f] 43 /home/th798/lib64/R/bin/exec/R(Rf_applyClosure+0x175) [0x4ec235] 44 /home/th798/lib64/R/bin/exec/R() [0x4e04f4] 45 /home/th798/lib64/R/bin/exec/R(Rf_eval+0x140) [0x4e9440] 46 /home/th798/lib64/R/bin/exec/R() [0x4eb43f] 47 /home/th798/lib64/R/bin/exec/R(Rf_applyClosure+0x175) [0x4ec235] 48 /home/th798/lib64/R/bin/exec/R() [0x4e04f4] 49 /home/th798/lib64/R/bin/exec/R(Rf_eval+0x140) [0x4e9440] 50 /home/th798/lib64/R/bin/exec/R() [0x4eb43f] 51 /home/th798/lib64/R/bin/exec/R(Rf_applyClosure+0x175) [0x4ec235] 52 /home/th798/lib64/R/bin/exec/R() [0x4e04f4] 53 /home/th798/lib64/R/bin/exec/R(Rf_eval+0x140) [0x4e9440] 54 /home/th798/lib64/R/bin/exec/R() [0x4eb43f] 55 /home/th798/lib64/R/bin/exec/R(Rf_applyClosure+0x175) [0x4ec235] 56 /home/th798/lib64/R/bin/exec/R() [0x4e04f4] 57 /home/th798/lib64/R/bin/exec/R(Rf_eval+0x140) [0x4e9440] 58 /home/th798/lib64/R/bin/exec/R() [0x4eb43f] 59 /home/th798/lib64/R/bin/exec/R(Rf_applyClosure+0x175) [0x4ec235] 60 /home/th798/lib64/R/bin/exec/R() [0x4e04f4] ================================= *** caught segfault *** address 0xa69b30011b39b, cause 'unknown' Traceback: 1: fun(libname, pkgname) 2: doTryCatch(return(expr), name, parentenv, handler) 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: tryCatchList(expr, classes, parentenv, handlers) 5: tryCatch(fun(libname, pkgname), error = identity) 6: runHook(".onLoad", env, package.lib, package) 7: loadNamespace(package, lib.loc) 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 11: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)}) 12: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) 13: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage")) 14: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)) 15: doTryCatch(return(expr), name, parentenv, handler) 16: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 17: tryCatchList(expr, classes, parentenv, handlers) 18: 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, nlines = 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))}) 19: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE))) 20: tools:::.test_load_package("Rmpi", "/projects/genomic-ml/lib64/R/library/00LOCK-Rmpi/00new") An irrecoverable exception occurred. R is aborting now ... > >