Exercises 1: Elementary access and the HPE Cray PE

See the instructions to set up for the exercises.

Accessing LUMI

1. Log on to an arbitrary login node of LUMI.

   Can you find how to check your quota and status of your allocation?

   Click to see the solution.

   How to check your quota and status of your allocation, is explained in the message-of-the-day at the bottom of the "Announcements" section: you can use the lumi-workspaces command.

2. How can you log on to a specific login node of LUMI, e.g., the login node "uan01"?

   Click to see the solution.

   To log in to the login node "uan01", use the hostname lumi-uan01.csc.fi instead of lumi.csc.fi.

   This may be useful if you use software on your desktop that tries to connect repeatedly to LUMI and then tries to find, e.g., a running server that it created before.

3. Create a shell on a login node using the Open OnDemand web interface?

   Click to see the solution.

   • Point your web browser to https://www.lumi.csc.fi. With some browsers it is sufficient to type lumi.csc.fi in the address bar while others require www.lumi.csc.fi.
   • Click the "Go to login" button. What you need to do here, depends on how you got your account. For the course you will have to proceed with the "MyAccessID" option "Login Puhuri" in most cases.
   • Once you're in the web interface, click on "Login node shell" (likely the third choice on the first line). It will open a new tab in the browser with a login shell on LUMI. Note that Open OnDemand uses a different set of login nodes.

4. Try to transfer a file from your desktop/laptop to your home directory via the Open OnDemand web interface.

   Click to see the solution.

   • Go back into Open OnDemand if you have left it after the previous exercise.
   • On the main screen of the web interface, choose "Home directory".
   • Depending on the browser and your system you may be able to just drag-and-drop files into the frame that shows your files, or you can click the blue "Upload" button towards the top of the screen.

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,
• hello_world.cc 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 (23.09 at the moment of the course in May 2024), but in case you want to use a particular version, e.g., the 22.12 version, and want to be very sure that all modules are loaded correctly from the start you could consider using

module load cpe/22.12
module load cpe/22.12

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:

./hello_world.x

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 hello_world.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.