CSC Computing Environment

Installing a simple C code from source

💬 In this tutorial we will install the MCL Markov cluster algorithm program to the /projappl directory of the user on Puhti.

💭 This software is also available as an installation package (.deb, .rpm) for various Linux distributions, but these can not be used on Puhti. Instead, we install it from the source code.

☝🏻 To follow the instructions, first set an environment variable pointing to your project’s /projappl directory:

export PROJAPPL=/projappl/<project>   # replace <project> with your CSC project, e.g. project_2001234

Obtaining the source code

Create your own directory under $PROJAPPL (if not done already) and move there. Then, create and move to a new directory for the installation:

mkdir -p $PROJAPPL/$USER
cd $PROJAPPL/$USER
mkdir mcl
cd mcl

Downloading a distribution package

Download the distribution package:

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.

Unpack the file with the command:

tar -xvf mcl-latest.tar.gz

💬 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.

Alternative option: Get the software from GitHub

Clone source code from Github:

git clone https://github.com/JohannesBuchner/mcl.git

💬 After cloning, the ls command shows that a new directory called mcl has been created. This directory contains the actual installation files and documentation of the software.

Preparing to install

Create a new directory called version-14-137 under the mcl directory for the actual installation.

mkdir version-14-137

Move to the mcl-14-137 (or mcl if cloning from git) directory and study its contents:

cd mcl-14-137
ls

💬 Installation packages often contain short installation instructions. Typically, this instructions file is called INSTALL or README.

Read the INSTALL file to learn how the installation should be done.

less INSTALL

💡 Move in the file opened with less with up and down arrows, and exit with q.

Installation

💬 Many open source software tools are installed using the following three steps:

Configuring a so called Makefile with a ./configure command.
Running the make command that compiles the source code according to the instructions in Makefile
Installing the compiled executables with the command make install

💭 Normally, installation packages assume that the user has the required permissions to install the software to the locations where Linux binaries and libraries normally get installed.

However, at CSC this is not the case. You can install software only to your own (or project’s) disk areas.
Often you can use the option --prefix=<path> to tell to the configure script where the program should be installed (replacing <path> with the actual path).

💭 The ./configure command checks that all compilers and libraries that the software needs are available.

It is not uncommon that ./configure reports about missing libraries or incorrect compilation options.
In such cases you should check if the missing library or program could be made available by loading a suitable module.

🗯 The CSC computing environment has several compiler versions and HPC libraries available.

In some cases you may, for example, need to use a specific C compiler or Python version in order to install a software. Read the compilation instructions carefully and try different versions if needed.
If the compilation still fails, don’t hesitate to ask for help from the CSC Service Desk.

To compile mcl, load the GNU C compiler (gcc) version 9.4.0:

module load gcc/9.4.0

In this case we wish to install the software under the version-14-137 directory in your $PROJAPPL area. Thus, you need to specify the custom location for the installation using the --prefix option:

./configure --prefix=$PROJAPPL/$USER/mcl/version-14-137   # double check that the path is correct

Compile and install the software with the commands:

make
make install

☝🏻 If you intend to compile software packages larger than the rather small MCL example used here, please use the fast local disk ($TMPDIR) to avoid stressing the parallel file system. Compiling complex applications typically cause a lot of I/O load.

If the make and make install commands don’t give any error messages, you have successfully installed your software!

💭 Typically, the executables/binaries, i.e. the compiled programs that can be launched, are stored in a subdirectory called bin.

Check what binaries were installed with:

ls $PROJAPPL/$USER/mcl/version-14-137/bin

Running the software

💬 Although the software is now ready to be run, it is not automatically added to your $PATH. This means that running:

mcl --help

will give an error message bash: mcl: command not found.

💬 You need to tell the computer where to find that command.

Try running the software by providing the full path to the binary, i.e.

$PROJAPPL/$USER/mcl/version-14-137/bin/mcl --help

Add the path of the MCL executables to your $PATH environment variable. This is done with the command:

export PATH=$PROJAPPL/$USER/mcl/version-14-137/bin:$PATH   # double check that this path matches your actual installation path

‼️ When running export, note that the variable we are defining (first PATH) should not have a dollar sign. Also, note that we include the current $PATH at the end (with a dollar sign).

If we omit the current path the normal shell commands will stop working.

Now you can launch the program you have installed from anywhere with simply:

mcl --help

💬 Remember that the PATH variable must be set each time you login to the supercomputer before you can run the mcl command without providing the full path.

☝🏻 You need to run the correct export PATH=... command also in batch job files before launching self-installed programs without the full path.

💡 If you want to make the addition automatically, add the export PATH=... command to your .bashrc file in your $HOME directory.

‼️ Making changes to the .bashrc file may cause incompatibilities with software installed by CSC.

💭 If you wish to revert your .bashrc file (and your environment in general) back to default, you can use the csc-env command.

💡 Note that loading modules installed by CSC will automatically modify your $PATH as needed, so no exports are typically required if you only run pre-installed applications.

Cleaning up

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 can remove the mcl-latest.tar.gz package and the whole mcl-14-137 directory:

cd $PROJAPPL/$USER/mcl
rm mcl-latest.tar.gz
rm -r mcl-14-137

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