In this howto I’ll explain how to use a library provided by module and then how to compile as user a software on Baobab using this library.
On the cluster, a lot of libraries are provided by EasyBuild through module. In this howto, we’ll use zlib as example library.
First, load a compiler and the libraries:
module load foss/2018b zlib
If the library module is well written, you can use pkg-config to get the correct flags for compiler and linker.
For example to get the include path for the z library:
pkg-config zlib --cflags
-I/opt/ebsofts/Compiler/GCCcore/7.3.0/zlib/1.2.11/include
You can get as well the output for the linker:
pkg-config --libs zlib
-L/opt/ebsofts/Compiler/GCCcore/7.3.0/zlib/1.2.11/lib -lz
Depending on your build system, it’s maybe even not needed to add the include path as it’s already defined when you load the module. You can see that with a module command:
module show zlib
[...]
prepend_path("CPATH","/opt/ebsofts/Compiler/GCCcore/7.3.0/zlib/1.2.11/include")
prepend_path("LD_LIBRARY_PATH","/opt/ebsofts/Compiler/GCCcore/7.3.0/zlib/1.2.11/lib")
[...]
The output of module show may be useful as well if you need to figure out where the files are stored.
Let’s take a full example by compiling subread-1.6.4 from source as user in your home directory on Baobab. This soft needs a more recent version of zlib than provided by the system.
Download the source code:
wget https://downloads.sourceforge.net/project/subread/subread-1.6.4/subread-1.6.4-source.tar.gz
Decompress the archive:
tar xf subread-1.6.4-source.tar.gz
Load a recent compiler and zlib:
module load foss/2018b zlib
Go to the src directory:
cd subread-1.6.4-source/src
Edit the Makefile.Linux file to indicate the location of zlib. Replace the string -lz by $(shell pkg-config --libs zlib).
You can now build the software:
make -f Makefile.Linux
That’s it. The executable are copied to ../bin
HTH