Known Issues and Workarounds

Known Issues and Workarounds

Please check below for solutions to problems you might encounter on the upgraded CSF3.

If the documentation doesn’t allow you to solve the problem, please log a ticket, providing as much information as possible, including what you have tried to solve the problem that didn’t work: The HPC Connect Portal Form.

Logging in from a Mac

This problem has now been resolved – you should be able to login from a Mac, while on Eduroam WiFi and GlobalProtect, without problems.

Missing libraries when running applications

The O/S on the upgraded CSF3 may cause some applications to complain about missing libraries. We will provide workarounds if you see these errors in your job outputs. Please report any such errors to us.

Error: libssl or libcrypto

libssl.so.10: cannot open shared object file: No such file or directory
  or
libcrypto.so.10: cannot open shared object file: No such file or directory

Solution: Add to your jobscript:

module load libs/gcc/openssl/1.0.2k

Error: libblas

libblas.so.3: cannot open shared object file: No such file or directory

Solution: Add to your jobscript:

module load libs/gcc/lapack/3.5.0

Error: libgfortran

libgfortran.so.3: cannot open shared object file: No such file or directory

Solution: Add to your jobscript:

module load compilers/gcc/5.5.0

Error: libpng.so.15

libpng15.so.15: cannot open shared object file: No such file or directory

Solution: Add to your jobscript:

module load libs/gcc/libpng/1.5.30

Error: libpng.so.16

libpng16.so.16: cannot open shared object file: No such file or directory

Solution: Add to your jobscript:

module load libs/gcc/libpng/1.65.39

Emacs complains about libwebkit2gtk

If you are using emacs you may see this error:

emacs: symbol lookup error: /lib64/libwebkit2gtk-4.0.so.37: undefined symbol: gst_audio_format_info_fill_silence

We have identified that this can be caused by having an anaconda python modulefile loaded, and the libraries supplied with anaconda overriding the OS libraries. There are several possible workarounds – please use the one you prefer:

1. Have two login sessions open, one with the python modulefile loaded, the other without python loaded and run emacs in that, then switch to the other session for testing that the code executes.
2. Or: Run an interactive subshell in emacs:

   emacs -f shell # Alternatively, use `M-x shell'.

3. Or: Install a conda emacs in your env, for example,

   module load apps/binapps/anaconda3/2024.10
   conda install conda-forge::emacs
   

4. Or: Use emacs with no X11 libraries

   emacs-nox test