error loading lantern with pre-built binaries on Linux

[tdhock]

related to #1398

I am trying to get torch working with CUDA on the Rorqual supercomputer (Linux).

I followed the instructions on https://torch.mlverse.org/docs/dev/articles/installation#pre-built and installation works but loading fails.

[thocking@rorqual3 ~]$ TORCH_INSTALL_DEBUG=1 R -e "torch::torch_tensor(pi)"

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Loading required namespace: data.table
> torch::torch_tensor(pi)
Torch libraries are installed but loading them was unsuccessful.
Torch libraries are installed but loading them was unsuccessful.
Error in torch_tensor_cpp(data, dtype, device, requires_grad, pin_memory) :
  Lantern is not loaded. Please use `install_torch()` to install additional dependencies.
Calls: <Anonymous> -> <Anonymous> -> <Anonymous> -> torch_tensor_cpp
Execution halted

so I used ldd to look for loading issues.

[thocking@rorqual3 ~]$ ldd R/x86_64-pc-linux-gnu-library/4.5/torch/lib/liblantern.so
        linux-vdso.so.1 (0x00007ffcd03e3000)
        libc10.so => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libc10.so (0x00007fcb302fd000)
        libc10_cuda.so => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libc10_cuda.so (0x00007fcb301a1000)
        libtorch_cpu.so => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libtorch_cpu.so (0x00007fcaf39a4000)
        libtorch_cuda.so => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libtorch_cuda.so (0x00007fca71ef8000)
        libcudart.so.12 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libcudart.so.12 (0x00007fca71c00000)
        libtorch.so => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libtorch.so (0x00007fca71ef1000)
        libstdc++.so.6 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libstdc++.so.6 (0x00007fca71a1e000)
        libm.so.6 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libm.so.6 (0x00007fca718cf000)
        libgcc_s.so.1 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libgcc_s.so.1 (0x00007fca71ed6000)
        libc.so.6 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libc.so.6 (0x00007fca716dd000)
        /cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/lib64/ld-linux-x86-64.so.2 (0x00007fcb316e3000)
        libdl.so.2 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libdl.so.2 (0x00007fca71ece000)
        libpthread.so.0 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libpthread.so.0 (0x00007fca716ba000)
        librt.so.1 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/librt.so.1 (0x00007fca71ec4000)
        libgomp-98b21ff3.so.1 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libgomp-98b21ff3.so.1 (0x00007fca71673000)
        libcudart-218eec4c.so.12 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libcudart-218eec4c.so.12 (0x00007fca71200000)
        libcublas-f6c022dc.so.12 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libcublas-f6c022dc.so.12 (0x00007fca6a000000)
        libcublasLt-4ef47ce6.so.12 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libcublasLt-4ef47ce6.so.12 (0x00007fca36200000)
        libcudnn.so.9 => /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/libcudnn.so.9 (0x00007fca35e00000)

nothing obvious above, so I followed the links. liblantern links to librt which seems to have an issue,

[thocking@rorqual3 ~]$ ldd R/x86_64-pc-linux-gnu-library/4.5/torch/lib/librt.so.1
R/x86_64-pc-linux-gnu-library/4.5/torch/lib/librt.so.1: /cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/lib64/libpthread.so.0: version `GLIBC_PRIVATE' not found (required by R/x86_64-pc-linux-gnu-library/4.5/torch/lib/librt.so.1)
        linux-vdso.so.1 (0x00007ffcd118c000)
        libpthread.so.0 => /cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/lib64/libpthread.so.0 (0x00007f4f015c9000)
        libc.so.6 => /cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/lib64/libc.so.6 (0x00007f4f013f4000)
        /cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/lib64/ld-linux-x86-64.so.2 (0x00007f4f01607000)

the link to libpthread seems to not work. Any idea how to fix?

Thanks in advance!!

[tdhock]

this is the code I used to follow all the links

library(data.table)
lib.file.vec <- Sys.glob("R/x86_64-pc-linux-gnu-library/4.5/torch/lib/*so")
lib.dt.list <- list()
msg.dt.list <- list()
for(lib.file in lib.file.vec){
  res <- system(paste("ldd", lib.file), intern=TRUE)
  if(length(res)){
    res_dt <- nc::capture_first_vec(
      res,
      "\t",
      source="[^ ]+",
      nc::quantifier(
        " => ",
        target="[^ ]+",
        "?"),
      " ",
      nomatch.error=FALSE)
    is.match <- !is.na(res_dt$target)
    if(any(is.match))
      lib.dt.list[[lib.file]] <- data.table(lib.file, res_dt[is.match])
    if(any(!is.match))
      msg.dt.list[[lib.file]] <- data.table(lib.file, res[!is.match])
  }
}
(lib.dt <- rbindlist(lib.dt.list))
(msg.dt <- rbindlist(msg.dt.list))

[jrosell]

In my case, this workaround worked #1360 (comment)

Give it a try if you want, and tell me.

[tdhock]

hi @jrosell thanks for writing.
It seems your error was different from mine.
And I tried to rename the librt, mv lib/librt.so.1 lib/librt.so.1.bak but that did not work, and in fact created a different warning from ldd,

[thocking@rorqual4 lib]$ ldd liblantern.so
./liblantern.so: 
 /home/thocking/R/x86_64-pc-linux-gnu-library/4.5/torch/lib/./libc.so.6: 
 version `GLIBC_ABI_DT_RELR' not found 
 (required by /cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/lib64/librt.so.1)