In this example we install MCL Markov cluster algorithm program to users own projappl directory in Puhti.
This software would also be available as installation packages (.deb, .rpm) for various Linux distributions, but these can not be used in Puhti. Instead we install it from the source code.
To follow the instructions, set up environment variable to point to your projects /projappl folder (substitute “project_12345” with your project name):
export PROJAPPL=/projappl/project_12345
Move to your $PROJAPPL directory and create there a new directory called mcl
cd $PROJAPPL
mkdir mcl
Move to the newly created directory and download the distribution package:
cd mcl
wget https://micans.org/mcl/src/mcl-latest.tar.gz
In this case the installation package is a tar-archive file that has been compressed with gzip program. You can unpack this file with commands
tar xvf mcl-latest.tar
ls -l
After unpacking, the ls command shows that a new directory called mcl-14-137 has
been created. This directory contains the actual installation files and documentation of the
software.
Create a new empty directory called version-14-137 to the mcl directory. This vill be the actual
installation directory.
mkdir version-14-137
After this go to the mcl-14-137 directory and study its content
cd mcl-14-137
ls -l
Installation packages contain often a short installation instructions. Typically this instruction file is called as INSTALL or README. In this case you should read the INSTALL file to find out how the installation should be done.
less INSTALL
Many open source software tools are installed using following three steps:
1 Building up the so called Makefile with a ./configure command.
2 Running make command that compiles the source code according to the instructions in the
Makefile
3 Installing the compiled executables with command make install
Normally the installation packages assume that the user has permissions to install the software to
the locations where the standard linux commands and programs normally get installed. However,
at CSC this is not the case. You can install software only to your own disk areas. Often you can
use option --prefix=/path/ to tell to the configure command, where to the program should be
installed.
The ./configure command checks that all the compilers and libraries that the software needs, are
available. It is not uncommon that ./configure reports about missing libraries or incorrect
compilation options. In those cases you can check if the missing library or program can be taken in
use with the module system.
CSC environment has several compiler and program versions available. In some cases you may for example need to use certain C-compiler or python version in order to install the software. Try with different versions. If you still fail with the installation, ask help from the HelpDesk of CSC.
For mcl we choose gcc environment.
module load gcc/9.1.0
In this case we wish to install the software to the version-14-137 directory in you
$PROJAPPL area. Thus you must use following ./configure command:
./configure --prefix=$USERAPPL/mcl/version-14-137
Next we need to compile and install the software with commands:
make
make install
If make and make install commands don’t give any error messages, you have successfully
installed your software.
Typically the executables, i.e. the compiled programs that can be launched, are stored to a
subdirectory called bin.
Check what got installed with:
ls -l $PROJAPPL/mcl/version-14-137/bin
The software is now ready to run, but it is not in your $PATH. That means that if you try to run:
mcl --help
you get an error message bash: mcl: command not found.
You need to tell the computer where to find that command. You can do this by providing the path for the program, e.g.
$PROJAPPL/mcl/version-14-137/bin/mcl --help
You can also add the directory path of you executables to the $PATH environment variable. In this case
we add path ${USERAPPL}/mcl/version-14-137/bin to the $PATH variable. This is done with command:
export PATH=${PROJAPPL}/mcl/version-14-137/bin:${PATH}
Note that the first PATH word in the command above is without the dollar sign. Also note that we include
the current $PATH. If we omitted it, the normal shell commands would stop working.
Now you can launch the program you have installed with simply:
mcl --help
Remember that also in the future, when you log in to CSC, the PATH variable must be set up
before you can use mcl command without providing the path.
Also in the batch job files you need to run the correct export PATH command above before
executing the program you have installed yourself.
If you want to make the addition permanent, you can add the export PATH command to you .bashrc
file in your home directory. It should be noted, however, that making changes to the .bashrc can
couse incompatibilities with CSC installed software.
If you wish to revert your .bashrc (and your environment in general) back to default, you can use
the csc-env command.
If the software you have installed works correctly, you can remove the installation package and
temporary directories that were used during the compilation. In this case we could remove the
mcl-latest.tar.gz file and the directory mcl-14-137
cd $PROJAPPL/mcl
rm mcl-latest.tar.gz
rm -rf mcl-14-137