Useful Tools

• SSH -- connecting with ssh to the fu-berlin servers
• tmux 🔗 -- same as screen but newer and cooler
• fzf 🔗 -- quick file/folder selection, improve ctrl-r in shell and much more
• miniconda 🔗 -- install software in user space
• ncdu 🔗 -- interactive disk usage; e.g. ncdu -xr ~
• gdb -- gdb to debug your code (sometimes faster than printf)
• valgrind 🔗 -- tool to detect memory leaks and invalid reads before writes
• callgrind 🔗/kcachegrind 🔗 -- runtime profiling and visualization
• massif 🔗/massif-visualizer 🔗 -- heap memory profiling and visualization
• GraphViz
• cmp benchmarks -- The cmp_benchmarks.sh provides a wrapper around google/benchmark/tools/compare.py. It can be used to compare benchmarks between versions and to filter out significant differences in runtime. -> cmp_benchmarks:-Example-Usage

Useful bash commands

• Access problems: chmod a+rwX FILE (all users -> read(r), write(w) & search of directories (X))
• How much space do I use? du -sh * | sort -rh; or use ncdu
• How much memory is my program using? /usr/bin/time -v <your program> and check the "Maximum resident set size"

Useful page to interpret bash commands: https://explainshell.com/explain?cmd=du+-sm+*+%7C+sort+-rh

Git

If you prefer to use a Git GUI, we recommend sourcetree 🔗. You can also use a commit message template that looks like this:

~/Repos/seqan3$ less .git/commit_msg_template.txt

[FEATURE] Whenever you implement something new and shiny
[FIX]     Whenever you fix some wrong code in the source
[DOC]     Whenever you do something only(!) related to the documentation
[INFRA]   Whenever you change something of the build system or CI related
[TEST]    Whenever you do something related to the tests (unit or benchmark)
[MISC]    miscellaneous (=sonstiges) (style guide fixes) - Whenever it does not fit to any of the above

[INTERNAL] [I/O] [WIP] work in progress 
([NOP] not otherwise provided)

Using specific compiler on fu-servers:

Example for raptor and gcc-11. The same should work for most other SeqAn3 tools and gcc versions:

  git clone https://github.com/seqan/raptor.git --recursive
  mkdir raptor/build
  cd raptor/build
  export CC=/group/ag_abi/software/bin/gcc-11
  export CXX=/group/ag_abi/software/bin/g++-11
  cmake ..
  make -j8