How to get software you need up and running on the clusters.
We recommend either use existing software modules, Anaconda, Singularity, or pre-compiled software where available. However, there are cases where compiling applications is necessary or desired. This can be because the pre-compiled version isn't readily available/compatible or because compiling applications on the cluster will make an appreciable difference in performance. It is also the case that many R packages are compiled at install time.
When compiling applications on the clusters, it is important to consider the ways in which you expect to run the application you are endeavoring to get working. If you want to be able to run jobs calling your application any node on the cluster, you will need to target the oldest hardware available so that newer optimizations are not used that will fail on some nodes. If your application is already quite specialized (e.g. needs GPUs or brand-new CPU instructions), you will want to compile it natively for the subset of compute nodes on which your jobs will run. This decision is often a trade-off between faster individual jobs or jobs that can run on more nodes at once.
Each of the cluster pages (see the clusters index for a list) has a "Compute Node Configurations" section where nodes are roughly listed from oldest to newest.
Illegal Instruction Instructions
You may find that software compiled on newer compute nodes will fail with the error
Illegal instruction (core dumped). This includes R/Python libraries that include code that compiles from source. To remedy this issue make sure to always either:
- Build or install software on the oldest available nodes. You can ensure you are on the oldest hardware by specifying the
--constraint oldest) in your job submission.
- Require that your jobs running the software in question request similar hardware to their build environment. If your software needs newer instructions using
avx512as a constraint will probably work, but limit the pool of nodes your job can run on.
Either way, you will want to control where your jobs run with job constraints.
Because you don't have admin/root/sudo privileges on the clusters, you won't be able to use
sudo and a package manager like
yum, etc.; You will need to adapt install instructions to allow for what is called a local or user install. If you prefer or require this method, you should create a singularity container image (see our Singularity guide), then run it on the cluster.
For things to work smoothly you will need to choose and stick with a prefix, or path to your installed applications and libraries. We recommend this be either in your home or project directory, something like
/path/to/project/software. Make sure you have created it before continuing.
If you choose a project directory prefix, it will be easier to share your applications with lab mates or other cluster users. Just make sure to use the true path (the one returned by
Once you've chosen a prefix you will want to add any directory with executables you want to run to your
PATH environment variable, and any directores with libraries that your application(s) link to your
LD_LIBRARY_PATH environment variable. Each of these tell your shell where to look when you call your application without specifying an absolute path to it. To set these variables permanently, add the following to the end of your
# local installs export MY_PREFIX=~/software export PATH=$MY_PREFIX/bin:$PATH export LD_LIBRARY_PATH=$MY_PREFIX/lib:$LD_LIBRARY_PATH
For the remainder of the guide we'll use the
$MY_PREFIX variable to refer to the prefix. See below or your application's install instructions for exactly how to specify your prefix at build/install time.
You will need to develop a build strategy that works for you and stay consistent. If you're happy using libraries and toolchains that are already available on the cluster as dependencies (recommended), feel free to create module collections that serve as your environments. If you prefer to completely build your own software tree, that is ok too. Whichever route you choose, try to stick with the same version of dependencies (e.g. MPI, zlib, numpy) and compiler you're using (e.g. GCC, intel). We find that unless absolutely necessary, the newest version of a compiler or library might not be the most compatible with a wide array of scientific software so you may want to step back a few versions or try using what was available at the time your application was being developed.
If your application includes instructions to run
make, it is using the GNU Build System.
If you are instructed to run
./configure to generate a Makefile, specify your prefix with the
--prefix option. This creates a file, usually named
Makefile that is a recipe for
make to use to build your application.
export MY_PREFIX=~/software ./configure --prefix=$MY_PREFIX
If your configure ran properly,
make install should properly place your application in your prefix directory. If there is no install target specified for your application, you can either run
make and copy the application to your
$MY_PREFIX/bin directory or build it somewhere in
$MY_PREFIX and add its relevant paths to your
LD_LIBRARY_PATH environment variables in your
~/.bashrc file as shown in the local install section.
CMake is a popular cross-platform build system. On a linux system, CMake will create a
Makefile in a step analogous to
./configure. It is common to create a build directory then run the
make commands from there. Below is what installing to your
$MY_DIRECTORY prefix might look like with CMake. CMake instructions also tend to link together the build process onto on line with
&&, which tells your shell to only continue to the next command if the previous one exited without error.
export MY_PREFIX=~/software mkdir build && cd build && cmake -DCMAKE_INSTALL_PREFIX=$MY_PREFIX .. && make && make install