biona001
commented
4 months ago Sorry, I just realized I opened this issue under bigstatsr rather than bigsnpr. Let me know if you want me to close this and reopen it under the right repo.
Closed biona001 closed 4 months ago
biona001
commented
4 months ago Sorry, I just realized I opened this issue under bigstatsr rather than bigsnpr. Let me know if you want me to close this and reopen it under the right repo.
privefl
commented
4 months ago Thanks for reporting. I've never encountered this issue before.
Could you please use debugonce(snp_ldsplit) and run the function again (you will be able to run line by line within the function), and tell me at which step you encounter this issue.
Also, do you get an error with the following code?
corr <- readRDS(runonce::download_file(
"https://figshare.com/ndownloader/files/24928052"))
library(bigsnpr)
THR_R2 <- 0.01
m <- ncol(corr)
SEQ <- round(seq_log(m / 30, m / 5, length.out = 10))
res <- snp_ldsplit(corr, thr_r2 = THR_R2, min_size = 100, max_size = SEQ) Hi @privefl, thank you for the quick response.
debugonce(snp_ldsplit) and hitting enter a bunch of times returned the following:
> res <- snp_ldsplit(corr, thr_r2 = THR_R2, min_size = 100, max_size = SEQ)
debugging in: snp_ldsplit(corr, thr_r2 = THR_R2, min_size = 100, max_size = SEQ)
debug: {
m <- ncol(corr)
stopifnot(min_size >= 1 && all(max_size <= m))
assert_lengths(pos_scaled, cols_along(corr))
corr <- Matrix::tril(corr)
stopifnot(all(Matrix::diag(corr) != 0))
max_cost <- min(max_cost, crossprod(corr@x) * 2)
prev_costs <- FBM(max_K, 1, init = Inf)
L <- corr %>% {
get_L(.@p, .@i, .@x, thr_r2 = thr_r2, max_r2 = max_r2)
} %>% {
Matrix::sparseMatrix(i = .$i, j = .$j, x = .$x, dims = c(m,
m + 1), triangular = FALSE, index1 = FALSE)
}
corr.p <- as.double(corr@p)
corr.i <- corr@i
rm(corr)
do.call("rbind", lapply(sort(max_size), function(one_max_size) {
cost_path <- get_C(L, min_size = min_size, max_size = one_max_size,
max_K = max_K, max_cost = max_cost, pos_scaled = pos_scaled)
reconstruct_paths(corr.p, corr.i, cost_path, min_size,
one_max_size, max_cost, prev_costs)
}))
}
Browse[2]>
debug: m <- ncol(corr)
Browse[2]>
debug: stopifnot(min_size >= 1 && all(max_size <= m))
Browse[2]>
debug: assert_lengths(pos_scaled, cols_along(corr))
Browse[2]>
debug: corr <- Matrix::tril(corr)
Browse[2]>
debug: stopifnot(all(Matrix::diag(corr) != 0))
Browse[2]>
debug: max_cost <- min(max_cost, crossprod(corr@x) * 2)
Browse[2]>
debug: prev_costs <- FBM(max_K, 1, init = Inf)
Browse[2]>
debug: L <- corr %>% {
get_L(.@p, .@i, .@x, thr_r2 = thr_r2, max_r2 = max_r2)
} %>% {
Matrix::sparseMatrix(i = .$i, j = .$j, x = .$x, dims = c(m,
m + 1), triangular = FALSE, index1 = FALSE)
}
Browse[2]>
debug: corr.p <- as.double(corr@p)
Browse[2]>
debug: corr.i <- corr@i
Browse[2]>
debug: rm(corr)
Browse[2]>
debug: do.call("rbind", lapply(sort(max_size), function(one_max_size) {
cost_path <- get_C(L, min_size = min_size, max_size = one_max_size,
max_K = max_K, max_cost = max_cost, pos_scaled = pos_scaled)
reconstruct_paths(corr.p, corr.i, cost_path, min_size, one_max_size,
max_cost, prev_costs)
}))
Browse[2]>
*** Error in `/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/bin/exec/R': free(): invalid pointer: 0x000000000c9d3e88 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x2b1b5ac28329]
/u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/bigsnpr/libs/bigsnpr.so(_Z31exception_to_condition_templateISt9exceptionEP7SEXPRECRKT_b+0x301)[0x2b1b6cbcdea1]
/u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/bigsnpr/libs/bigsnpr.so(_bigsnpr_get_C+0x1cb)[0x2b1b6cbcb39b]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x1014a4)[0x2b1b5a1974a4]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x14558d)[0x2b1b5a1db58d]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_eval+0x178)[0x2b1b5a1e9118]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x15496b)[0x2b1b5a1ea96b]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_applyClosure+0x1c1)[0x2b1b5a1eb6f1]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_eval+0x2ae)[0x2b1b5a1e924e]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x157a8a)[0x2b1b5a1eda8a]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_eval+0x51f)[0x2b1b5a1e94bf]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x15659e)[0x2b1b5a1ec59e]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_eval+0x51f)[0x2b1b5a1e94bf]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x15496b)[0x2b1b5a1ea96b]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_applyClosure+0x1c1)[0x2b1b5a1eb6f1]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(R_forceAndCall+0x17b)[0x2b1b5a1ee07b]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x86e3c)[0x2b1b5a11ce3c]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x1976f2)[0x2b1b5a22d6f2]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x143512)[0x2b1b5a1d9512]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_eval+0x178)[0x2b1b5a1e9118]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x15496b)[0x2b1b5a1ea96b]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_applyClosure+0x1c1)[0x2b1b5a1eb6f1]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_eval+0x2ae)[0x2b1b5a1e924e]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x153a8e)[0x2b1b5a1e9a8e]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x1529d2)[0x2b1b5a1e89d2]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_eval+0x178)[0x2b1b5a1e9118]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x15496b)[0x2b1b5a1ea96b]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_applyClosure+0x1c1)[0x2b1b5a1eb6f1]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_eval+0x2ae)[0x2b1b5a1e924e]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x15659e)[0x2b1b5a1ec59e]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_eval+0x51f)[0x2b1b5a1e94bf]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x15496b)[0x2b1b5a1ea96b]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_applyClosure+0x1c1)[0x2b1b5a1eb6f1]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_eval+0x2ae)[0x2b1b5a1e924e]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x157a8a)[0x2b1b5a1eda8a]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_eval+0x51f)[0x2b1b5a1e94bf]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(Rf_ReplIteration+0x252)[0x2b1b5a21e152]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(+0x1884c1)[0x2b1b5a21e4c1]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so(run_Rmainloop+0x48)[0x2b1b5a21e558]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/bin/exec/R(main+0x1b)[0x40075b]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b1b5abc9555]
/u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/bin/exec/R[0x40078b]
======= Memory map: ========
00400000-00401000 r-xp 00000000 00:34 6317251420151053054 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/bin/exec/R
00600000-00601000 r--p 00000000 00:34 6317251420151053054 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/bin/exec/R
00601000-00602000 rw-p 00001000 00:34 6317251420151053054 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/bin/exec/R
011e8000-194c8000 rw-p 00000000 00:00 0 [heap]
2b1b59e72000-2b1b59e94000 r-xp 00000000 08:03 284531 /usr/lib64/ld-2.17.so
2b1b59e94000-2b1b59e97000 rw-p 00000000 00:00 0
2b1b59e97000-2b1b59e98000 r--p 00000000 00:34 2254763068395539482 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/translations/en/LC_MESSAGES/R.mo
2b1b59e98000-2b1b59e99000 rw-p 00000000 00:00 0
2b1b59e99000-2b1b59e9a000 -w-s 00000000 08:04 17694761 /work/tmp/RtmpLiEN0M/filea5782822dd1b.bk
2b1b59e9a000-2b1b59ea1000 r--s 00000000 08:03 669524 /usr/lib64/gconv/gconv-modules.cache
2b1b59ea1000-2b1b59ea2000 r--s 00000000 08:04 17694761 /work/tmp/RtmpLiEN0M/filea5782822dd1b.bk
2b1b59ea2000-2b1b59ea3000 -w-s 00000000 08:04 17694763 /work/tmp/RtmpLiEN0M/filea57824bca57e.bk
2b1b59ea3000-2b1b59ea4000 rw-p 00000000 00:00 0
2b1b59eb9000-2b1b5a00b000 rw-p 00000000 00:00 0
2b1b5a093000-2b1b5a094000 r--p 00021000 08:03 284531 /usr/lib64/ld-2.17.so
2b1b5a094000-2b1b5a095000 rw-p 00022000 08:03 284531 /usr/lib64/ld-2.17.so
2b1b5a095000-2b1b5a096000 rw-p 00000000 00:00 0
2b1b5a096000-2b1b5a3c9000 r-xp 00000000 00:34 7697395682123609363 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so
2b1b5a3c9000-2b1b5a5c8000 ---p 00333000 00:34 7697395682123609363 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so
2b1b5a5c8000-2b1b5a5e6000 r--p 00332000 00:34 7697395682123609363 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so
2b1b5a5e6000-2b1b5a5f5000 rw-p 00350000 00:34 7697395682123609363 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/lib/libR.so
2b1b5a5f5000-2b1b5a75d000 rw-p 00000000 00:00 0
2b1b5a75d000-2b1b5a78a000 r-xp 00000000 00:34 7890178973220366635 /u/local/compilers/gcc/7.5.0/lib64/libgomp.so.1.0.0
2b1b5a78a000-2b1b5a989000 ---p 0002d000 00:34 7890178973220366635 /u/local/compilers/gcc/7.5.0/lib64/libgomp.so.1.0.0
2b1b5a989000-2b1b5a98a000 r--p 0002c000 00:34 7890178973220366635 /u/local/compilers/gcc/7.5.0/lib64/libgomp.so.1.0.0
2b1b5a98a000-2b1b5a98b000 rw-p 0002d000 00:34 7890178973220366635 /u/local/compilers/gcc/7.5.0/lib64/libgomp.so.1.0.0
2b1b5a98b000-2b1b5a9a2000 r-xp 00000000 08:03 283921 /usr/lib64/libpthread-2.17.so
2b1b5a9a2000-2b1b5aba1000 ---p 00017000 08:03 283921 /usr/lib64/libpthread-2.17.so
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2b1b5aba2000-2b1b5aba3000 rw-p 00017000 08:03 283921 /usr/lib64/libpthread-2.17.so
2b1b5aba3000-2b1b5aba7000 rw-p 00000000 00:00 0
2b1b5aba7000-2b1b5ad6b000 r-xp 00000000 08:03 284673 /usr/lib64/libc-2.17.so
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2b1b5bc89000-2b1b5bc94000 rw-p 00000000 00:00 0
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2b1b5d9a1000-2b1b5d9a5000 r--p 01b0d000 00:34 3970466220875599057 /u/local/compilers/intel/2020.4/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
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2b1b5d9f4000-2b1b61dd6000 r-xp 00000000 00:34 17415356185958232034 /u/local/compilers/intel/2020.4/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64_lin/libmkl_core.so
2b1b61dd6000-2b1b61fd5000 ---p 043e2000 00:34 17415356185958232034 /u/local/compilers/intel/2020.4/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64_lin/libmkl_core.so
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2b1b6200c000-2b1b62035000 rw-p 00000000 00:00 0
2b1b62035000-2b1b62037000 r-xp 00000000 08:03 284188 /usr/lib64/libdl-2.17.so
2b1b62037000-2b1b62237000 ---p 00002000 08:03 284188 /usr/lib64/libdl-2.17.so
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2b1b62239000-2b1b6233a000 r-xp 00000000 08:03 283234 /usr/lib64/libm-2.17.so
2b1b6233a000-2b1b62539000 ---p 00101000 08:03 283234 /usr/lib64/libm-2.17.so
2b1b62539000-2b1b6253a000 r--p 00100000 08:03 283234 /usr/lib64/libm-2.17.so
2b1b6253a000-2b1b6253b000 rw-p 00101000 08:03 283234 /usr/lib64/libm-2.17.so
2b1b6253b000-2b1b6265a000 r-xp 00000000 08:03 283152 /usr/lib64/libgfortran.so.3.0.0
2b1b6265a000-2b1b6285a000 ---p 0011f000 08:03 283152 /usr/lib64/libgfortran.so.3.0.0
2b1b6285a000-2b1b6285b000 r--p 0011f000 08:03 283152 /usr/lib64/libgfortran.so.3.0.0
2b1b6285b000-2b1b6285d000 rw-p 00120000 08:03 283152 /usr/lib64/libgfortran.so.3.0.0
2b1b6285d000-2b1b6289b000 r-xp 00000000 00:34 17540311835115103061 /u/local/compilers/gcc/7.5.0/lib64/libquadmath.so.0.0.0
2b1b6289b000-2b1b62a9a000 ---p 0003e000 00:34 17540311835115103061 /u/local/compilers/gcc/7.5.0/lib64/libquadmath.so.0.0.0
2b1b62a9a000-2b1b62a9b000 r--p 0003d000 00:34 17540311835115103061 /u/local/compilers/gcc/7.5.0/lib64/libquadmath.so.0.0.0
2b1b62a9b000-2b1b62a9c000 rw-p 0003e000 00:34 17540311835115103061 /u/local/compilers/gcc/7.5.0/lib64/libquadmath.so.0.0.0
2b1b62a9c000-2b1b62ad8000 r-xp 00000000 08:03 283553 /usr/lib64/libreadline.so.6.2
2b1b62ad8000-2b1b62cd8000 ---p 0003c000 08:03 283553 /usr/lib64/libreadline.so.6.2
2b1b62cd8000-2b1b62cda000 r--p 0003c000 08:03 283553 /usr/lib64/libreadline.so.6.2
2b1b62cda000-2b1b62ce0000 rw-p 0003e000 08:03 283553 /usr/lib64/libreadline.so.6.2
2b1b62ce0000-2b1b62ce2000 rw-p 00000000 00:00 0
2b1b62ce2000-2b1b62d58000 r-xp 00000000 08:03 284956 /usr/lib64/libpcre2-8.so.0.5.0
2b1b62d58000-2b1b62f57000 ---p 00076000 08:03 284956 /usr/lib64/libpcre2-8.so.0.5.0
2b1b62f57000-2b1b62f58000 r--p 00075000 08:03 284956 /usr/lib64/libpcre2-8.so.0.5.0
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2b1b62f59000-2b1b62f7e000 r-xp 00000000 08:03 284679 /usr/lib64/liblzma.so.5.2.2
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2b1b6f9bf000-2b1b6fa09000 r-xp 00000000 08:03 284967 /usr/lib64/libgssapi_krb5.so.2.2
2b1b6fa09000-2b1b6fc09000 ---p 0004a000 08:03 284967 /usr/lib64/libgssapi_krb5.so.2.2
2b1b6fc09000-2b1b6fc0a000 r--p 0004a000 08:03 284967 /usr/lib64/libgssapi_krb5.so.2.2
2b1b6fc0a000-2b1b6fc0c000 rw-p 0004b000 08:03 284967 /usr/lib64/libgssapi_krb5.so.2.2
2b1b6fc0c000-2b1b6fce5000 r-xp 00000000 08:03 284167 /usr/lib64/libkrb5.so.3.3
2b1b6fce5000-2b1b6fee4000 ---p 000d9000 08:03 284167 /usr/lib64/libkrb5.so.3.3
2b1b6fee4000-2b1b6fef2000 r--p 000d8000 08:03 284167 /usr/lib64/libkrb5.so.3.3
2b1b6fef2000-2b1b6fef5000 rw-p 000e6000 08:03 284167 /usr/lib64/libkrb5.so.3.3
2b1b6fef5000-2b1b6ff26000 r-xp 00000000 08:03 285267 /usr/lib64/libk5crypto.so.3.1
2b1b6ff26000-2b1b70125000 ---p 00031000 08:03 285267 /usr/lib64/libk5crypto.so.3.1
2b1b70125000-2b1b70127000 r--p 00030000 08:03 285267 /usr/lib64/libk5crypto.so.3.1
2b1b70127000-2b1b70128000 rw-p 00032000 08:03 285267 /usr/lib64/libk5crypto.so.3.1
2b1b70128000-2b1b7012b000 r-xp 00000000 08:03 283686 /usr/lib64/libcom_err.so.2.1
2b1b7012b000-2b1b7032a000 ---p 00003000 08:03 283686 /usr/lib64/libcom_err.so.2.1
2b1b7032a000-2b1b7032b000 r--p 00002000 08:03 283686 /usr/lib64/libcom_err.so.2.1
2b1b7032b000-2b1b7032c000 rw-p 00003000 08:03 283686 /usr/lib64/libcom_err.so.2.1
2b1b7032c000-2b1b7033a000 r-xp 00000000 08:03 282500 /usr/lib64/liblber-2.4.so.2.10.7
2b1b7033a000-2b1b70539000 ---p 0000e000 08:03 282500 /usr/lib64/liblber-2.4.so.2.10.7
2b1b70539000-2b1b7053a000 r--p 0000d000 08:03 282500 /usr/lib64/liblber-2.4.so.2.10.7
2b1b7053a000-2b1b7053b000 rw-p 0000e000 08:03 282500 /usr/lib64/liblber-2.4.so.2.10.7
2b1b7053b000-2b1b7058d000 r-xp 00000000 08:03 283482 /usr/lib64/libldap-2.4.so.2.10.7
2b1b7058d000-2b1b7078d000 ---p 00052000 08:03 283482 /usr/lib64/libldap-2.4.so.2.10.7
2b1b7078d000-2b1b7078f000 r--p 00052000 08:03 283482 /usr/lib64/libldap-2.4.so.2.10.7
2b1b7078f000-2b1b70790000 rw-p 00054000 08:03 283482 /usr/lib64/libldap-2.4.so.2.10.7
2b1b70790000-2b1b707f7000 r-xp 00000000 08:03 283287 /usr/lib64/libssl.so.1.0.2k
2b1b707f7000-2b1b709f7000 ---p 00067000 08:03 283287 /usr/lib64/libssl.so.1.0.2k
2b1b709f7000-2b1b709fb000 r--p 00067000 08:03 283287 /usr/lib64/libssl.so.1.0.2k
2b1b709fb000-2b1b70a02000 rw-p 0006b000 08:03 283287 /usr/lib64/libssl.so.1.0.2k
2b1b70a02000-2b1b70c39000 r-xp 00000000 08:03 284856 /usr/lib64/libcrypto.so.1.0.2k
2b1b70c39000-2b1b70e38000 ---p 00237000 08:03 284856 /usr/lib64/libcrypto.so.1.0.2k
2b1b70e38000-2b1b70e54000 r--p 00236000 08:03 284856 /usr/lib64/libcrypto.so.1.0.2k
2b1b70e54000-2b1b70e61000 rw-p 00252000 08:03 284856 /usr/lib64/libcrypto.so.1.0.2k
2b1b70e61000-2b1b70e65000 rw-p 00000000 00:00 0
2b1b70e65000-2b1b70e73000 r-xp 00000000 08:03 282706 /usr/lib64/libkrb5support.so.0.1
2b1b70e73000-2b1b71073000 ---p 0000e000 08:03 282706 /usr/lib64/libkrb5support.so.0.1
2b1b71073000-2b1b71074000 r--p 0000e000 08:03 282706 /usr/lib64/libkrb5support.so.0.1
2b1b71074000-2b1b71075000 rw-p 0000f000 08:03 282706 /usr/lib64/libkrb5support.so.0.1
2b1b71075000-2b1b71078000 r-xp 00000000 08:03 283484 /usr/lib64/libkeyutils.so.1.5
2b1b71078000-2b1b71277000 ---p 00003000 08:03 283484 /usr/lib64/libkeyutils.so.1.5
2b1b71277000-2b1b71278000 r--p 00002000 08:03 283484 /usr/lib64/libkeyutils.so.1.5
2b1b71278000-2b1b71279000 rw-p 00003000 08:03 283484 /usr/lib64/libkeyutils.so.1.5
2b1b71279000-2b1b7128f000 r-xp 00000000 08:03 283420 /usr/lib64/libresolv-2.17.so
2b1b7128f000-2b1b7148f000 ---p 00016000 08:03 283420 /usr/lib64/libresolv-2.17.so
2b1b7148f000-2b1b71490000 r--p 00016000 08:03 283420 /usr/lib64/libresolv-2.17.so
2b1b71490000-2b1b71491000 rw-p 00017000 08:03 283420 /usr/lib64/libresolv-2.17.so
2b1b71491000-2b1b71493000 rw-p 00000000 00:00 0
2b1b71493000-2b1b714af000 r-xp 00000000 08:03 282967 /usr/lib64/libsasl2.so.3.0.0
2b1b714af000-2b1b716ae000 ---p 0001c000 08:03 282967 /usr/lib64/libsasl2.so.3.0.0
2b1b716ae000-2b1b716af000 r--p 0001b000 08:03 282967 /usr/lib64/libsasl2.so.3.0.0
2b1b716af000-2b1b716b0000 rw-p 0001c000 08:03 282967 /usr/lib64/libsasl2.so.3.0.0
2b1b716b0000-2b1b716d4000 r-xp 00000000 08:03 284754 /usr/lib64/libselinux.so.1
2b1b716d4000-2b1b718d3000 ---p 00024000 08:03 284754 /usr/lib64/libselinux.so.1
2b1b718d3000-2b1b718d4000 r--p 00023000 08:03 284754 /usr/lib64/libselinux.so.1
2b1b718d4000-2b1b718d5000 rw-p 00024000 08:03 284754 /usr/lib64/libselinux.so.1
2b1b718d5000-2b1b718d7000 rw-p 00000000 00:00 0
2b1b718d7000-2b1b718df000 r-xp 00000000 08:03 284121 /usr/lib64/libcrypt-2.17.so
2b1b718df000-2b1b71ade000 ---p 00008000 08:03 284121 /usr/lib64/libcrypt-2.17.so
2b1b71ade000-2b1b71adf000 r--p 00007000 08:03 284121 /usr/lib64/libcrypt-2.17.so
2b1b71adf000-2b1b71ae0000 rw-p 00008000 08:03 284121 /usr/lib64/libcrypt-2.17.so
2b1b71ae0000-2b1b71b0e000 rw-p 00000000 00:00 0
2b1b71b0e000-2b1b71b6e000 r-xp 00000000 08:03 284281 /usr/lib64/libpcre.so.1.2.0
2b1b71b6e000-2b1b71d6e000 ---p 00060000 08:03 284281 /usr/lib64/libpcre.so.1.2.0
2b1b71d6e000-2b1b71d6f000 r--p 00060000 08:03 284281 /usr/lib64/libpcre.so.1.2.0
2b1b71d6f000-2b1b71d70000 rw-p 00061000 08:03 284281 /usr/lib64/libpcre.so.1.2.0
2b1b71d70000-2b1b71d72000 r-xp 00000000 08:03 283338 /usr/lib64/libfreebl3.so
2b1b71d72000-2b1b71f71000 ---p 00002000 08:03 283338 /usr/lib64/libfreebl3.so
2b1b71f71000-2b1b71f72000 r--p 00001000 08:03 283338 /usr/lib64/libfreebl3.so
2b1b71f72000-2b1b71f73000 rw-p 00002000 08:03 283338 /usr/lib64/libfreebl3.so
2b1b71f73000-2b1b71f74000 ---p 00000000 00:00 0
2b1b71f74000-2b1b72174000 rw-p 00000000 00:00 0
2b1b72174000-2b1b7217f000 r-xp 00000000 08:03 283433 /usr/lib64/libnss_nis-2.17.so
2b1b7217f000-2b1b7237e000 ---p 0000b000 08:03 283433 /usr/lib64/libnss_nis-2.17.so
2b1b7237e000-2b1b7237f000 r--p 0000a000 08:03 283433 /usr/lib64/libnss_nis-2.17.so
2b1b7237f000-2b1b72380000 rw-p 0000b000 08:03 283433 /usr/lib64/libnss_nis-2.17.so
2b1b72380000-2b1b72397000 r-xp 00000000 08:03 283314 /usr/lib64/libnsl-2.17.so
2b1b72397000-2b1b72596000 ---p 00017000 08:03 283314 /usr/lib64/libnsl-2.17.so
2b1b72596000-2b1b72597000 r--p 00016000 08:03 283314 /usr/lib64/libnsl-2.17.so
2b1b72597000-2b1b72598000 rw-p 00017000 08:03 283314 /usr/lib64/libnsl-2.17.so
2b1b72598000-2b1b7259a000 rw-p 00000000 00:00 0
2b1b7259a000-2b1b725a0000 r-xp 00000000 08:03 284073 /usr/lib64/libnss_dns-2.17.so
2b1b725a0000-2b1b7279f000 ---p 00006000 08:03 284073 /usr/lib64/libnss_dns-2.17.so
2b1b7279f000-2b1b727a0000 r--p 00005000 08:03 284073 /usr/lib64/libnss_dns-2.17.so
2b1b727a0000-2b1b727a1000 rw-p 00006000 08:03 284073 /usr/lib64/libnss_dns-2.17.so
2b1b727a1000-2b1b727f0000 r-xp 00000000 08:03 282668 /usr/lib64/libsoftokn3.so
2b1b727f0000-2b1b729f0000 ---p 0004f000 08:03 282668 /usr/lib64/libsoftokn3.so
2b1b729f0000-2b1b729f1000 r--p 0004f000 08:03 282668 /usr/lib64/libsoftokn3.so
2b1b729f1000-2b1b729f4000 rw-p 00050000 08:03 282668 /usr/lib64/libsoftokn3.so
2b1b729f4000-2b1b729f5000 rw-p 00000000 00:00 0
2b1b729f5000-2b1b72aa6000 r-xp 00000000 08:03 283592 /usr/lib64/libsqlite3.so.0.8.6
2b1b72aa6000-2b1b72ca5000 ---p 000b1000 08:03 283592 /usr/lib64/libsqlite3.so.0.8.6
2b1b72ca5000-2b1b72ca7000 r--p 000b0000 08:03 283592 /usr/lib64/libsqlite3.so.0.8.6
2b1b72ca7000-2b1b72caa000 rw-p 000b2000 08:03 283592 /usr/lib64/libsqlite3.so.0.8.6
2b1b72caa000-2b1b72d56000 r-xp 00000000 08:03 284053 /usr/lib64/libfreeblpriv3.so
2b1b72d56000-2b1b72f55000 ---p 000ac000 08:03 284053 /usr/lib64/libfreeblpriv3.so
2b1b72f55000-2b1b72f57000 r--p 000ab000 08:03 284053 /usr/lib64/libfreeblpriv3.so
2b1b72f57000-2b1b72f58000 rw-p 000ad000 08:03 284053 /usr/lib64/libfreeblpriv3.so
2b1b72f58000-2b1b72f5c000 rw-p 00000000 00:00 0
2b1b72f5c000-2b1b72f5e000 r-xp 00000000 08:03 282873 /usr/lib64/libnsssysinit.so
2b1b72f5e000-2b1b7315d000 ---p 00002000 08:03 282873 /usr/lib64/libnsssysinit.so
2b1b7315d000-2b1b7315e000 r--p 00001000 08:03 282873 /usr/lib64/libnsssysinit.so
2b1b7315e000-2b1b7315f000 rw-p 00002000 08:03 282873 /usr/lib64/libnsssysinit.so
2b1b7315f000-2b1b73188000 r-xp 00000000 08:03 283239 /usr/lib64/libnsspem.so
2b1b73188000-2b1b73388000 ---p 00029000 08:03 283239 /usr/lib64/libnsspem.so
2b1b73388000-2b1b73389000 r--p 00029000 08:03 283239 /usr/lib64/libnsspem.so
2b1b73389000-2b1b7338a000 rw-p 0002a000 08:03 283239 /usr/lib64/libnsspem.so
2b1b7338a000-2b1b733b0000 r-xp 00000000 00:34 18388101727159248012 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/grid/libs/grid.so
2b1b733b0000-2b1b735af000 ---p 00026000 00:34 18388101727159248012 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/grid/libs/grid.so
2b1b735af000-2b1b735b0000 r--p 00025000 00:34 18388101727159248012 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/grid/libs/grid.so
2b1b735b0000-2b1b735b1000 rw-p 00026000 00:34 18388101727159248012 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/grid/libs/grid.so
2b1b735b1000-2b1b735e7000 r-xp 00000000 00:3d 4256856905546022109 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/rlang/libs/rlang.so
2b1b735e7000-2b1b737e7000 ---p 00036000 00:3d 4256856905546022109 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/rlang/libs/rlang.so
2b1b737e7000-2b1b737e9000 r--p 00036000 00:3d 4256856905546022109 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/rlang/libs/rlang.so
2b1b737e9000-2b1b737ea000 rw-p 00038000 00:3d 4256856905546022109 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/rlang/libs/rlang.so
2b1b737ea000-2b1b737eb000 rw-p 00000000 00:00 0
2b1b737eb000-2b1b73812000 r-xp 00000000 00:34 15728348825865032304 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/cli/libs/cli.so
2b1b73812000-2b1b73a11000 ---p 00027000 00:34 15728348825865032304 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/cli/libs/cli.so
2b1b73a11000-2b1b73a12000 r--p 00026000 00:34 15728348825865032304 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/cli/libs/cli.so
2b1b73a12000-2b1b73a14000 rw-p 00027000 00:34 15728348825865032304 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/cli/libs/cli.so
2b1b73a14000-2b1b73a16000 rw-p 00000000 00:00 0
2b1b73a16000-2b1b73a18000 r-xp 00000000 00:34 17349876670123607500 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/glue/libs/glue.so
2b1b73a18000-2b1b73c18000 ---p 00002000 00:34 17349876670123607500 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/glue/libs/glue.so
2b1b73c18000-2b1b73c19000 r--p 00002000 00:34 17349876670123607500 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/glue/libs/glue.so
2b1b73c19000-2b1b73c1a000 rw-p 00003000 00:34 17349876670123607500 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/glue/libs/glue.so
2b1b73c1a000-2b1b73c24000 r-xp 00000000 00:34 2105445448758392764 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/colorspace/libs/colorspace.so
2b1b73c24000-2b1b73e24000 ---p 0000a000 00:34 2105445448758392764 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/colorspace/libs/colorspace.so
2b1b73e24000-2b1b73e25000 r--p 0000a000 00:34 2105445448758392764 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/colorspace/libs/colorspace.so
2b1b73e25000-2b1b73e26000 rw-p 0000b000 00:34 2105445448758392764 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/colorspace/libs/colorspace.so
2b1b73e26000-2b1b73e3f000 r--p 00000000 00:3d 17289150430478528354 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/bigstatsr/libs/bigstatsr.so
2b1b73e3f000-2b1b73ed9000 r-xp 00019000 00:3d 17289150430478528354 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/bigstatsr/libs/bigstatsr.so
2b1b73ed9000-2b1b73eef000 r--p 000b3000 00:3d 17289150430478528354 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/bigstatsr/libs/bigstatsr.so
2b1b73eef000-2b1b73ef0000 ---p 000c9000 00:3d 17289150430478528354 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/bigstatsr/libs/bigstatsr.so
2b1b73ef0000-2b1b73ef1000 r--p 000c9000 00:3d 17289150430478528354 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/bigstatsr/libs/bigstatsr.so
2b1b73ef1000-2b1b73ef3000 rw-p 000ca000 00:3d 17289150430478528354 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/bigstatsr/libs/bigstatsr.so
2b1b73ef3000-2b1b73ef6000 rw-p 00000000 00:00 0
2b1b74000000-2b1b74021000 rw-p 00000000 00:00 0
2b1b74021000-2b1b78000000 ---p 00000000 00:00 0
2b1b78000000-2b1b817fb000 rw-p 00000000 00:00 0
2b1b817fb000-2b1b81869000 r-xp 00000000 00:3d 4326294468325149910 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/vctrs/libs/vctrs.so
2b1b81869000-2b1b81a68000 ---p 0006e000 00:3d 4326294468325149910 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/vctrs/libs/vctrs.so
2b1b81a68000-2b1b81a6a000 r--p 0006d000 00:3d 4326294468325149910 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/vctrs/libs/vctrs.so
2b1b81a6a000-2b1b81a6b000 rw-p 0006f000 00:3d 4326294468325149910 /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/vctrs/libs/vctrs.so
2b1b81a6b000-2b1b81b30000 rw-p 00000000 00:00 0
2b1b81b30000-2b1b81b33000 r-xp 00000000 00:34 121383514300136850 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/magrittr/libs/magrittr.so
2b1b81b33000-2b1b81d32000 ---p 00003000 00:34 121383514300136850 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/magrittr/libs/magrittr.so
2b1b81d32000-2b1b81d33000 r--p 00002000 00:34 121383514300136850 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/magrittr/libs/magrittr.so
2b1b81d33000-2b1b81d34000 rw-p 00003000 00:34 121383514300136850 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/magrittr/libs/magrittr.so
2b1b81d34000-2b1b81d4c000 r-xp 00000000 00:34 17398956177741099208 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/fansi/libs/fansi.so
2b1b81d4c000-2b1b81f4c000 ---p 00018000 00:34 17398956177741099208 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/fansi/libs/fansi.so
2b1b81f4c000-2b1b81f4d000 r--p 00018000 00:34 17398956177741099208 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/fansi/libs/fansi.so
2b1b81f4d000-2b1b81f4e000 rw-p 00019000 00:34 17398956177741099208 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/fansi/libs/fansi.so
2b1b81f4e000-2b1b81f98000 r-xp 00000000 00:34 14987798028822578549 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/utf8/libs/utf8.so
2b1b81f98000-2b1b82197000 ---p 0004a000 00:34 14987798028822578549 /u/local/apps/R/4.2.2/gcc-4.8.5/intel-2020.4/lib64/R/library/utf8/libs/utf8.so
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Abortedmodule load R/4.2.2 (i.e. do not load gcc/7.5.0 intel/2020.4), then I cannot even load bigsnpr.
$ module load R/4.2.2
$ R
WARNING: ignoring environment value of R_HOMER version 4.2.2 (2022-10-31) -- "Innocent and Trusting" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)
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library("bigsnpr") Loading required package: bigstatsr Error: package or namespace load failed for ‘bigstatsr’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/bigstatsr/libs/bigstatsr.so': /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /u/home/b/biona001/R/x86_64-pc-linux-gnu-library/4.2.2/bigstatsr/libs/bigstatsr.so) Error: package ‘bigstatsr’ could not be loaded
biona001
commented
4 months ago @privefl I just tested the same code on the same data, but on a different cluster. Here I only module load R/4.0.2 and I am no longer getting this invalid pointer issue. Thus, I think the issue is indeed due to environment variables being set incorrectly. I'd be fine if you close this issue.
privefl
commented
4 months ago I guess it is something that has to do with the way the package has been installed on the cluster. You should contact the IT team responsible of the cluster to get some help.
I'm running
bigsnpron the cluster. MWE:module load R/4.2.2 gcc/7.5.0 intel/2020.4Rand run the followingimport PLINK data as FBM (file backed matrix) format
rdsfile <- paste0(fbmfile, ".rds") if (!file.exists(rdsfile)){snp_readBed2(plinkfile, backingfile = fbmfile)} x <- snp_attach(rdsfile)
estimate correlation matrix
corr <- snp_cor(x$genotypes, ind.col=1:1000, infos.pos=x$map$physical.pos[1:1000], ncores=1)
compute LD regions
THR_R2 <- 0.01 m <- ncol(corr) SEQ <- round(seq_log(m / 30, m / 5, length.out = 10)) res <- snp_ldsplit(corr, thr_r2 = THR_R2, min_size = 100, max_size = SEQ)