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Exercises 1: Modules, the HPE Cray PE and EasyBuild

See the instructions to set up for the exercises.

Exercises on the use of modules

  1. The Bison program installed in the OS image is pretty old (version 3.0.4) and we want to use a newer one. Is there one available on LUMI?

    Click to see the solution.
    module spider Bison

    tells us that there are indeed newer versions available on the system.

    The versions that have a compiler name (usually gcc) in their name followed by some seemingly random characters are installed with Spack and not in the CrayEnv or LUMI environments.

    To get more information about Bison/3.8.2:

    module spider Bison/3.8.2

    tells us that Bison 3.8.2 is provided by a couple of buildtools modules and available in all partitions in several versions of the LUMI software stack and in CrayEnv.

    Alternatively, in this case

    module keyword Bison

    would also have shown that Bison is part of several versions of the buildtools module.

    The module spider command is often the better command if you use names that with a high likelihood could be the name of a package, while module keyword is often the better choice for words that are more a keyword. But if one does not return the solution it is a good idea to try the other one also.

  2. The htop command is a nice alternative for the top command with a more powerful user interface. However, typing htop on the command line produces an error message. Can you find and run htop?

    Click to see the solution.

    We can use either module spider htop or module keyword htop to find out that htop is indeed available on the system. With module keyword htop we'll find out immediately that it is in the systools modules and some of those seem to be numbered after editions of the LUMI stack suggesting that they may be linked to a stack, with module spider you'll first see that it is an extension of a module and see the versions. You may again see some versions installed with Spack.

    Let's check further for htop/3.2.1 that should exist according to module spider htop:

    module spider htop/3.2.1

    tells us that this version of htop is available in all partitions of LUMI/22.08 and LUMI/22.06, and in CrayEnv. Let us just run it in the CrayEnv environment:

    module load CrayEnv
    module load systools/22.08

    (You can quit htop by pressing q on the keyboard.)

  3. In the future LUMI will offer Open OnDemand as a browser-based interface to LUMI that will also enable running some graphical programs. At the moment the way to do this is through a so-called VNC server. Do we have such a tool on LUMI, and if so, how can we use it?

    Click to see the solution.

    module spider VNC and module keyword VNC can again both be used to check if there is software available to use VNC. Both will show that there is a module lumi-vnc in several versions. If you try loading the older ones of these (the version number points at the date of some scripts) you will notice that some produce a warning as they are deprecated. However, when installing a new version we cannot remove older ones in one sweep, and users may have hardcoded full module names in scripts they use to set their environment, so we chose to not immediate delete these older versions.

    One thing you can always try to get more information about how to run a program, is to ask for the help information of the module. For this to work the module must first be available, or you have to use module spider with the full name of the module. We see that version 20230110 is the newest version of the module, so let's try that one:

    module spider lumi-vnc/20230110

    The output may look a little strange as it mentions init-lumi as one of the modules that you can load. That is because this tool is available even outside CrayEnv or the LUMI stacks. But this command also shows a long help test telling you how to use this module (though it does assume some familiarity with how X11 graphics work on Linux).

    Note that if there is only a single version on the system, as is the case for the course in May 2023, the module spider VNC command without specific version or correct module name will already display the help information.

  4. Search for the bzip2 tool (and not just the bunzip2 command as we also need the bzip2 command) and make sure that you can use software compiled with the Cray compilers in the LUMI stacks in the same session.

    Click to see the solution.
    module spider bzip2

    shows that there are versions of bzip2 for several of the cpe* toolchains and in several versions of the LUMI software stack.

    Of course we prefer to use a recent software stack, the 22.08 or 22.12 (but as of early May 2023, there is a lot more software ready-to-install for 22.08). And since we want to use other software compiled with the Cray compilers also, we really want a cpeCray version to avoid conflicts between different toolchains. So the module we want to load is bzip2/1.0.8-cpeCray-22.08.

    To figure out how to load it, use

    module spider bzip2/1.0.8-cpeCray-22.08

    and see that (as expected from the name) we need to load LUMI/22.08 and can then use it in any of the partitions.

Exercises on compiling software by hand

These exercises are optional during the session, but useful if you expect to be compiling software yourself. The source files mentioned can be found in the subdirectory CPE of the download.

Compilation of a program 1: A simple "Hello, world" program

Four different implementations of a simple "Hello, World!" program are provided in the CPE subdirectory:

  • hello_world.c is an implementation in C,
  • is an implementation in C++,
  • hello_world.f is an implementation in Fortran using the fixed format source form,
  • hello_world.f90 is an implementation in Fortran using the more modern free format source form.

Try to compile these programs using the programming environment of your choice.

Click to see the solution.

We'll use the default version of the programming environment (22.12 at the moment of the course in May 2023), but in case you want to use a particular version, e.g., the 22.08 version, and want to be very sure that all modules are loaded correctly from the start you could consider using

module load cpe/22.08
module load cpe/22.08

So note that we do twice the same command as the first iteration does not always succeed to reload all modules in the correct version. Do not combine both lines into a single module load statement as that would again trigger the bug that prevents all modules to be reloaded in the first iteration.

The sample programs that we asked you to compile do not use the GPU. So there are three programming environments that we can use: PrgEnv-gnu, PrgEnv-cray and PrgEnv-aocc. All three will work, and they work almost the same.

Let's start with an easy case, compiling the C version of the program with the GNU C compiler. For this all we need to do is

module load PrgEnv-gnu
cc hello_world.c

which will generate an executable named a.out. If you are not comfortable using the default version of gcc (which produces the warning message when loading the PrgEnv-gnu module) you can always load the gcc/11.2.0 module instead after loading PrgEnv-gnu.

Of course it is better to give the executable a proper name which can be done with the -o compiler option:

module load PrgEnv-gnu
cc hello_world.c -o hello_world.x

Try running this program:


to see that it indeed works. We did forget another important compiler option, but we'll discover that in the next exercise.

The other programs are equally easy to compile using the compiler wrappers:

CC -o hello_world.x
ftn hello_world.f -o hello_world.x
ftn hello_world.f90 -o hello_world.x

Compilation of a program 2: A program with BLAS

In the CPE subdirectory you'll find the C program matrix_mult_C.c and the Fortran program matrix_mult_F.f90. Both do the same thing: a matrix-matrix multiplication using the 6 different orders of the three nested loops involved in doing a matrix-matrix multiplication, and a call to the BLAS routine DGEMM that does the same for comparison.

Compile either of these programs using the Cray LibSci library for the BLAS routine. Do not use OpenMP shared memory parallelisation. The code does not use MPI.

The resulting executable takes one command line argument, the size of the square matrix. Run the script using 1000 for the matrix size and see what happens.

Note that the time results may be very unreliable as we are currently doing this on the login nodes. In the session of Slurm you'll learn how to request compute nodes and it might be interesting to redo this on a compute node with a larger matrix size as the with a matrix size of 1000 all data may stay in the third level cache and you will not notice the differences that you should note. Also, because these nodes are shared with a lot of people any benchmarking is completely unreliable.

If this program takes more than half a minute or so before the first result line in the table, starting with ijk-variant, is printed, you've very likely done something wrong (unless the load on the system is extreme). In fact, if you've done things well the time reported for the ijk-variant should be well under 3 seconds for both the C and Fortran versions...

Click to see the solution.

Just as in the previous exercise, this is a pure CPU program so we can chose between the same three programming environments.

The one additional "difficulty" is that we need to link with the BLAS library. This is very easy however in the HPE Cray PE if you use the compiler wrappers rather than calling the compilers yourself: you only need to make sure that the cray-libsci module is loaded and the wrappers will take care of the rest. And on most systems (including LUMI) this module will be loaded automatically when you load the PrgEnv-* module.

To compile with the GNU C compiler, all you need to do is

module load PrgEnv-gnu
cc -O3 matrix_mult_C.c -o matrix_mult_C_gnu.x

will generate the executable matrix_mult_C_gnu.x.

Note that we add the -O3 option and it is very important to add either -O2 or -O3 as by default the GNU compiler will generate code without any optimization for debugging purposes, and that code is in this case easily five times or more slower. So if you got much longer run times than indicated this is likely the mistake that you made.

To use the Cray C compiler instead only one small change is needed: Loading a different programming environment module:

module load PrgEnv-cray
cc -O3 matrix_mult_C.c -o matrix_mult_C_cray.x

will generate the executable matrix_mult_C_cray.x.

Likewise for the AMD AOCC compiler we can try with loading yet another PrgEnv-* module:

module load PrgEnv-aocc
cc -O3 matrix_mult_C.c -o matrix_mult_C_aocc.x

but it turns out that this fails with linker error messages about not being able to find the sin and cos functions. When using the AOCC compiler the libm library with basic math functions is not linked automatically, but this is easily done by adding the -lm flag:

module load PrgEnv-aocc
cc -O3 matrix_mult_C.c -lm -o matrix_mult_C_aocc.x

For the Fortran version of the program we have to use the ftn compiler wrapper instead, and the issue with the math libraries in the AOCC compiler does not occur. So we get

module load PrgEnv-gnu
ftn -O3 matrix_mult_F.f90 -o matrix_mult_F_gnu.x

for the GNU Fortran compiler,

module load PrgEnv-cray
ftn -O3 matrix_mult_F.f90 -o matrix_mult_F_cray.x

for the Cray Fortran compiler and

module load PrgEnv-aocc
ftn -O3 matrix_mult_F.f90 -o matrix_mult_F_aocc.x

for the AMD Fortran compiler.

When running the program you will see that even though the 6 different loop orderings produce the same result, the time needed to compile the matrix-matrix product is very different and those differences would be even more pronounced with bigger matrices (which you can do after the session on using Slurm).

The exercise also shows that not all codes are equal even if they produce a result of the same quality. The six different loop orderings run at very different speed, and none of our simple implementations can beat a good library, in this case the BLAS library included in LibSci.

The results with the Cray Fortran compiler are particularly interesting. The result for the BLAS library is slower which we do not yet understand, but it also turns out that for four of the six loop orderings we get the same result as with the BLAS library DGEMM routine. It looks like the compiler simply recognized that this was code for a matrix-matrix multiplication and replaced it with a call to the BLAS library. The Fortran 90 matrix multiplication is also replaced by a call of the DGEMM routine. To confirm all this, unload the cray-libsci module and try to compile again and you will see five error messages about not being able to find DGEMM.

Compilation of a program 3: A hybrid MPI/OpenMP program

The file mpi_omp_hello.c is a hybrid MPI and OpenMP C program that sends a message from each thread in each MPI rank. It is basically a simplified version of the programs found in the lumi-CPEtools modules that can be used to quickly check the core assignment in a hybrid MPI and OpenMP job (see later in this tutorial). It is again just a CPU-based program.

Compile the program with your favourite C compiler on LUMI.

We have not yet seen how to start an MPI program. However, you can run the executable on the login nodes and it will then contain just a single MPI rank.

Click to see the solution.

In the HPE Cray PE environment, you don't use mpicc to compile a C MPI program, but you just use the cc wrapper as for any other C program. To enable MPI you have to make sure that the cray-mpich module is loaded. This module will usually be loaded by loading one of the PrgEnv-* modules, but only if the right network target module, which is craype-network-ofi, is also already loaded.

Compiling the program is very simple:

module load PrgEnv-gnu
cc -O3 -fopenmp mpi_omp_hello.c -o mpi_omp_hello_gnu.x

to compile with the GNU C compiler,

module load PrgEnv-cray
cc -O3 -fopenmp mpi_omp_hello.c -o mpi_omp_hello_cray.x

to compile with the Cray C compiler, and

module load PrgEnv-aocc
cc -O3 -fopenmp mpi_omp_hello.c -o mpi_omp_hello_aocc.x

to compile with the AMD AOCC compiler.

To run the executables it is not even needed to have the respective PrgEnv-* module loaded since the binaries will use a copy of the libraries stored in a default directory, though there have been bugs in the past preventing this to work with PrgEnv-aocc.

Information in the LUMI Software Library

Explore the LUMI Software Library.

  • Search for information for the package ParaView and quickly read through the page
Click to see the solution.

Link to the ParaView documentation

It is an example of a package for which we have both user-level and some technical information. The page will first show some license information, then the actual user information which in case of this package is very detailed and long. But it is also a somewhat complicated package to use. It will become easier when LUMI evolves a bit further, but there will always be some pain. Next comes the more technical part: Links to the EasyBuild recipe and some information about how we build the package.

We currently only provide ParaView in the cpeGNU toolchain. This is because it has a lot of dependencies that are not trivial to compile and to port to the other compilers on the system, and EasyBuild is strict about mixing compilers basically because it can cause a lot of problems, e.g., due to conflicts between OpenMP runtimes.

Installing software with EasyBuild

These exercises are based on material from the EasyBuild tutorials (and we have a special version for LUMI also).

Note: If you want to be able to uninstall all software installed through the exercises easily, we suggest you make a separate EasyBuild installation for the course, e.g., in /scratch/project_465000523/$USER/eb-course if you make the exercises during the course:

  • Start from a clean login shell with only the standard modules loaded.

    export EBU_USER_PREFIX=/scratch/project_465000523/$USER/eb-course

    You'll need to do that in every shell session where you want to install or use that software.

  • From now on you can again safely load the necessary LUMI and partition modules for the exercise.

  • At the end, when you don't need the software installation anymore, you can simply remove the directory that you just created.

    rm -rf /scratch/project_465000523/$USER/eb-course

Installing a simple program without dependencies with EasyBuild

The LUMI Software Library contains the package eb-tutorial. Install the version of the package for the cpeCray toolchain in the 22.08 version of the software stack.

At the time of this course, in early May 2023, we're still working on EasyBuild build recipes for the 22.12 version of the software stack.

Click to see the solution.
  • We can check the eb-tutorial page in the LUMI Software Library if we want to see more information about the package.

    You'll notice that there are versions of the EasyConfigs for cpeGNU and cpeCray. As we want to install software with the cpeCray toolchain for LUMI/22.08, we'll need the cpeCray-22.08 version which is the EasyConfig eb-tutorial-1.0.1-cpeCray-22.08.eb.

  • Obviously we need to load the LUMI/22.08 module. If we would like to install software for the CPU compute nodes, you need to also load partition/C. To be able to use EasyBuild, we also need the EasyBuild-user module.

    module load LUMI/22.08 partition/C
    module load EasyBuild-user
  • Now all we need to do is run the eb command from EasyBuild to install the software.

    Let's however take the slow approach and first check if what dependencies the package needs:

    eb eb-tutorial-1.0.1-cpeCray-22.08.eb -D

    We can do this from any directory as the EasyConfig file is already in the LUMI Software Library and will be located automatically by EasyBuild. You'll see that all dependencies are already on the system so we can proceed with the installation:

    eb eb-tutorial-1.0.1-cpeCray-22.08.eb 
  • After this you should have a module eb-tutorial/1.0.1-cpeCray-22.08 but it may not show up yet due to the caching of Lmod. Try

    module av eb-tutorial/1.0.1-cpeCray-22.08

    If this produces an error message complaining that the module cannot be found, it is time to clear the Lmod cache:

    rm -rf $HOME/.lmod.d/.cache
  • Now that we have the module, we can check what it actually does:

    module help eb-tutorial/1.0.1-cpeCray-22.08

    and we see that it provides the eb-tutorial command.

  • So let's now try to run this command:

    module load eb-tutorial/1.0.1-cpeCray-22.08

    Note that if you now want to install one of the other versions of this module, EasyBuild will complain that some modules are loaded that it doesn't like to see, including the eb-tutorial module and the cpeCray modules so it is better to unload those first:

    module unload cpeCray eb-tutorial

Installing an EasyConfig given to you by LUMI User Support

Sometimes we have no solution ready in the LUMI Software Library, but we prepare one or more custom EasyBuild recipes for you. Let's mimic this case. In practice we would likely send those as attachments to a mail from the ticketing system and you would be asked to put them in a separate directory (basically since putting them at the top of your home directory would in some cases let EasyBuild search your whole home directory for dependencies which would be a very slow process).

You've been given two EasyConfig files to install a tool called py-eb-tutorial which is in fact a Python package that uses the eb-tutorial package installed in the previous exercise. These EasyConfig files are in the EasyBuild subdirectory of the exercises for this course. In the first exercise you are asked to install the version of py-eb-tutorial for the cpeCray/22.08 toolchain.

Click to see the solution.
  • Go to the EasyBuild subdirectory of the exercises and check that it indeed contains the py-eb-tutorial-1.0.0-cpeCray-22.08-cray-python- and py-eb-tutorial-1.0.0-cpeGNU-22.08-cray-python- files. It is the first one that we need for this exercise.

    You can see that we have used a very long name as we are also using a version suffix to make clear which version of Python we'll be using.

  • Let's first check for the dependencies (out of curiosity):

    eb py-eb-tutorial-1.0.0-cpeCray-22.08-cray-python- -D

    and you'll see that all dependencies are found (at least if you made the previous exercise successfully). You may find it strange that it shows no Python module but that is because we are using the cray-python module which is not installed through EasyBuild and only known to EasyBuild as an external module.

  • And now we can install the package:

    eb py-eb-tutorial-1.0.0-cpeCray-22.08-cray-python-
  • To use the package all we need to do is to load the module and to run the command that it defines:

    module load py-eb-tutorial/1.0.0-cpeCray-22.08-cray-python-

    with the same remark as in the previous exercise if Lmod fails to find the module.

    You may want to do this step in a separate terminal session set up the same way, or you will get an error message in the next exercise with EasyBuild complaining that there are some modules loaded that should not be loaded.

Installing software with uninstalled dependencies

Now you're asked to also install the version of py-eb-tutorial for the cpeGNU toolchain in LUMI/22.08 (and the solution given below assumes you haven'ty accidentally installed the wrong EasyBuild recipe in one of the previous two exercises).

Click to see the solution.
  • We again work in the same environment as in the previous two exercises. Nothing has changed here. Hence if not done yet we need

    module load LUMI/22.08 partition/C
    module load EasyBuild-user
  • Now go to the EasyBuild subdirectory of the exercises (if not there yet from the previous exercise) and check what the py-eb-tutorial-1.0.0-cpeGNU-22.08-cray-python- needs:

    eb py-eb-tutorial-1.0.0-cpeGNU-22.08-cray-python- -D

    We'll now see that there are two missing modules. Not only is the py-eb-tutorial/1.0.0-cpeGNU-22.08-cray-python- that we try to install missing, but also the eb-tutorial/1.0.1-cpeGNU-22.08. EasyBuild does however manage to find a recipe from which this module can be built in the pre-installed build recipes.

  • We can install both packages separately, but it is perfectly possible to install both packages in a single eb command by using the -r option to tell EasyBuild to also install all dependencies.

    eb py-eb-tutorial-1.0.0-cpeGNU-22.08-cray-python- -r
  • At the end you'll now notice (with module avail) that both the module eb-tutorial/1.0.1-cpeGNU-22.08 and py-eb-tutorial/1.0.0-cpeGNU-22.08-cray-python- are now present.

    To run you can use

    module load py-eb-tutorial/1.0.0-cpeGNU-22.08-cray-python-