libmkl_core.so: cannot open shared object file: No such file or directory

[krzjoa]

I installed ArrayFire via ArrayFire-v3.6.4_Linux_x86_64.sh script downloaded from the ArrayFire site. Then, I have tried to pass through RcppArrayFire installation procedure. Unfortunately, it fails with the following communicate:

** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘RcppArrayFire’ in dyn.load(file, DLLpath = DLLpath, ...):
cannot open shared object file '/home/krzysztof/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-RcppArrayFire/00new/RcppArrayFire/libs/RcppArrayFire.so':
libmkl_core.so: cannot open shared object file: No such file or directory

I saw a previous issue which seemed to be similar at glance, but it did't give my relevant answer to my question.

The environment I use looks like this:

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=pl_PL.UTF-8       LC_NUMERIC=C               LC_TIME=pl_PL.UTF-8        LC_COLLATE=pl_PL.UTF-8    
 [5] LC_MONETARY=pl_PL.UTF-8    LC_MESSAGES=pl_PL.UTF-8    LC_PAPER=pl_PL.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=pl_PL.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] drat_0.1.5     compiler_3.6.1 tools_3.6.1   

I hope I'll be able to install this great project on my machine 😎

[rstub]

This sounds a lot like arrayfire/arrayfire#2372. Does it help to add the LD_PRELOAD statement from the last comment? I generally use ArrayFire compiled from source, which removes this issue with linking to MKL.

[rstub]

The error messages are different, though. What is the output of these commands?

ldconfig --print-cache | grep libaf
ldconfig --print-cache | grep libmkl
ldd </path/to/libaf.so>

[krzjoa]

Thank you for quick answers!
I installed ArrayFire from source too.

Commands

ldconfig --print-cache | grep libaf
ldconfig --print-cache | grep libmkl

print nothing.

The last one, i.e:

ldd /usr/local/lib64/libaf.so

gives me following output:

   linux-vdso.so.1 (0x00007fff450f7000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f84125c2000)
    libmkl_core.so => not found
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f84123a3000)
    libmkl_intel_lp64.so => not found
    libmkl_gnu_thread.so => not found
    libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f8412174000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f8411dd6000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f8411bbe000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f84117cd000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f8412dbf000)

[rstub]

I installed ArrayFire from source too.

Originally you mentioned ArrayFire-v3.6.4_Linux_x86_64.sh, which installs a pre-compiled binary. Are you still using that?

Anyway, ldconfig not knowing about libaf is bad. Please have a look at this SO answer. Does that help?