Using the Cirrus GPU Nodes¶

Cirrus has 38 GPU compute nodes each equipped with 4 NVIDIA V100 (Volta) GPU cards. This section of the user guide gives some details of the hardware; it also covers how to compile and run standard GPU applications.

The GPU cards on Cirrus do not support graphics rendering tasks; they are set to compute cluster mode and so only support computational tasks.

Hardware details¶

All of the Cirrus GPU nodes contain four Tesla V100-SXM2-16GB (Volta) cards. Each card has 16 GB of high-bandwidth memory, HBM, often referred to as device memory. Maximum device memory bandwidth is in the region of 900 GB per second. Each card has 5,120 CUDA cores and 640 Tensor cores.

There is one GPU Slurm partition installed on Cirrus called simply gpu. The 36 nodes in this partition have the Intel Cascade Lake architecture. Users concerned with host performance should add the specific compilation options appropriate for the processor.

The Cascade Lake nodes have two 20-core sockets (2.5 GHz) and a total of 384 GB host memory (192 GB per socket). Each core supports two threads in hardware.

For further details of the V100 architecture see, https://www.nvidia.com/en-gb/data-center/tesla-v100/ .

Compiling software for the GPU nodes¶

NVIDIA HPC SDK¶

NVIDIA now make regular releases of a unified HPC SDK which provides the relevant compilers and libraries needed to build and run GPU programs. Versions of the SDK are available via the module system.

$ module avail nvidia/nvhpc

NVIDIA encourage the use of the latest available version, unless there are particular reasons to use earlier versions. The default version is therefore the latest module version present on the system.

Each release of the NVIDIA HPC SDK may include several different versions of the CUDA toolchain. For example, the nvidia/nvhpc/21.2 module comes with CUDA 10.2, 11.0 and 11.2. Only one of these CUDA toolchains can be active at any one time and for nvhpc/22.11 this is CUDA 11.8.

Here is a list of available HPC SDK versions, and the corresponding version of CUDA:

Module	Supported CUDA Version
`nvidia/nvhpc/22.11`	CUDA 11.8
`nvidia/nvhpc/22.2`	CUDA 11.6

To load the latest NVIDIA HPC SDK use

$ module load nvidia/nvhpc

The following sections provide some details of compilation for different programming models.

CUDA¶

CUDA is a parallel computing platform and programming model developed by NVIDIA for general computing on graphical processing units (GPUs).

Programs, typically written in C or C++, are compiled with nvcc. As well as nvcc, a host compiler is required. By default, a gcc module is added when nvidia/nvhpc is loaded.

Compile your source code in the usual way.

nvcc -arch=sm_70 -o cuda_test.x cuda_test.cu

Note

The -arch=sm_70 compile option ensures that the binary produced is compatible with the NVIDIA Volta architecture.

Using CUDA with Intel compilers¶

You can load either the Intel 18 or Intel 19 compilers to use with nvcc.

module unload gcc
module load intel-compilers-19

You can now use nvcc -ccbin icpc to compile your source code with the Intel C++ compiler icpc.

nvcc -arch=sm_70 -ccbin icpc -o cuda_test.x cuda_test.cu

Compiling OpenACC code¶

OpenACC is a directive-based approach to introducing parallelism into either C/C++ or Fortran codes. A code with OpenACC directives may be compiled like so.

$ module load nvidia/nvhpc
$ nvc program.c

$ nvc++ program.cpp

Note that nvc and nvc++ are distinct from the NVIDIA CUDA compiler nvcc. They provide a way to compile standard C or C++ programs without explicit CUDA content. See man nvc or man nvc++ for further details.

CUDA Fortran¶

CUDA Fortran provides extensions to standard Fortran which allow GPU functionality. CUDA Fortran files (with file extension .cuf) may be compiled with the NVIDIA Fortran compiler.

$ module load nvidia/nvhpc
$ nvfortran program.cuf

See man nvfortran for further details.

OpenMP for GPUs¶

The OpenMP API supports multi-platform shared-memory parallel programming in C/C++ and Fortran and can offload computation from the host (i.e. CPU) to one or more target devices (such as the GPUs on Cirrus). OpenMP code can be compiled with the NVIDIA compilers in a similar manner to OpenACC. To enable this functionality, you must add -mp=gpu to your compile command.

$ module load nvidia/nvhpc
$ nvc++ -mp=gpu program.cpp

You can specify exactly which GPU to target with the -gpu flag. For example, the Volta cards on Cirrus use the flag -gpu=cc70.

During development it can be useful to have the compiler report information about how it is processing OpenMP pragmas. This can be enabled by the use of -Minfo=mp, see below.

nvc -mp=gpu -Minfo=mp testprogram.c
main:
24, #omp target teams distribute parallel for thread_limit(128)
24, Generating Tesla and Multicore code
Generating "nvkernel_main_F1L88_2" GPU kernel
26, Loop parallelized across teams and threads(128), schedule(static)

Submitting jobs to the GPU nodes¶

To run a GPU job, a SLURM submission must specify a GPU partition and a quality of service (QoS) as well as the number of GPUs required. You specify the number of GPU cards you want using the --gres=gpu:N option, where N is typically 1, 2 or 4.

Note

As there are 4 GPUs per node, each GPU is associated with 1/4 of the resources of the node, i.e., 10/40 physical cores and roughly 91/384 GB in host memory.

Allocations of host resources are made pro-rata. For example, if 2 GPUs are requested, sbatch will allocate 20 cores and around 190 GB of host memory (in addition to 2 GPUs). Any attempt to use more than the allocated resources will result in an error.

This automatic allocation by SLURM for GPU jobs means that the submission script should not specify options such as --ntasks and --cpus-per-task. Such a job submission will be rejected. See below for some examples of how to use host resources and how to launch MPI applications.

If you specify the --exclusive option, you will automatically be allocated all host cores and all memory from the node irrespective of how many GPUs you request. This may be needed if the application has a large host memory requirement.

If more than one node is required, exclusive mode --exclusive and --gres=gpu:4 options must be included in your submission script. It is, for example, not possible to request 6 GPUs other than via exclusive use of two nodes.

Warning

In order to run jobs on the GPU nodes your budget must have positive GPU hours and positive CPU core hours associated with it. However, only your GPU hours will be consumed when running these jobs.

Partitions¶

Your job script must specify a partition. The following table has a list of relevant GPU partition(s) on Cirrus.

Cirrus Partitions¶
Partition	Description	Maximum Job Size (Nodes)
gpu	GPU nodes with Cascade Lake processors	36

Quality of Service (QoS)¶

Your job script must specify a QoS relevant for the GPU nodes. Available QoS specifications are as follows.

GPU QoS¶
QoS Name	Jobs Running Per User	Jobs Queued Per User	Max Walltime	Max Size	Partition
gpu	No limit	128 jobs	4 days	64 GPUs	gpu
long	5 jobs	20 jobs	14 days	8 GPUs	gpu
short	1 job	2 jobs	20 minutes	4 GPUs	gpu
lowpriority	No limit	100 jobs	2 days	16 GPUs	gpu
largescale	1 job	4 jobs	24 hours	144 GPUs	gpu

Examples¶

Job submission script using one GPU on a single node¶

A job script that requires 1 GPU accelerator and 10 CPU cores for 20 minutes would look like the following.

#!/bin/bash
#
#SBATCH --partition=gpu
#SBATCH --qos=gpu
#SBATCH --gres=gpu:1
#SBATCH --time=00:20:00

# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]

# Load the required modules
module load nvidia/nvhpc

srun ./cuda_test.x

This will execute one host process with access to one GPU. If we wish to make use of the 10 host cores in this allocation, we could use host threads via OpenMP.

export OMP_NUM_THREADS=10
export OMP_PLACES=cores

srun --ntasks=1 --cpus-per-task=10 --hint=nomultithread ./cuda_test.x

The launch configuration is specified directly to srun because, for the GPU partitions, it is not possible to do this via sbatch.

Job submission script using multiple GPUs on a single node¶

A job script that requires 4 GPU accelerators and 40 CPU cores for 20 minutes would appear as follows.

#!/bin/bash
#
#SBATCH --partition=gpu
#SBATCH --qos=gpu
#SBATCH --gres=gpu:4
#SBATCH --time=00:20:00

# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]

# Load the required modules
module load nvidia/nvhpc

srun ./cuda_test.x

A typical MPI application might assign one device per MPI process, in which case we would want 4 MPI tasks in this example. This would again be specified directly to srun.

srun --ntasks=4 ./mpi_cuda_test.x

Job submission script using multiple GPUs on multiple nodes¶

See below for a job script that requires 8 GPU accelerators for 20 minutes.

#!/bin/bash
#
#SBATCH --partition=gpu
#SBATCH --qos=gpu
#SBATCH --gres=gpu:4
#SBATCH --nodes=2
#SBATCH --exclusive
#SBATCH --time=00:20:00

# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]

# Load the required modules
module load nvidia/nvhpc

srun ./cuda_test.x

An MPI application with four MPI tasks per node would be launched as follows.

srun --ntasks=8 --tasks-per-node=4 ./mpi_cuda_test.x

Again, these options are specified directly to srun rather than being declared as sbatch directives.

Attempts to oversubscribe an allocation (10 cores per GPU) will fail, and generate an error message.

srun: error: Unable to create step for job 234123: More processors requested
than permitted

Debugging GPU applications¶

Applications may be debugged using cuda-gdb. This is an extension of gdb which can be used with CUDA. We assume the reader is familiar with gdb.

First, compile the application with the -g -G flags in order to generate debugging information for both host and device code. Then, obtain an interactive session like so.

$ srun --nodes=1 --partition=gpu --qos=short --gres=gpu:1 \
       --time=0:20:0 --account=[budget code] --pty /bin/bash

Next, load the NVIDIA HPC SDK module and start cuda-gdb for your application.

$ module load nvidia/nvhpc
$ cuda-gdb ./my-application.x
NVIDIA (R) CUDA Debugger
...
(cuda-gdb)

Debugging then proceeds as usual. One can use the help facility within cuda-gdb to find details on the various debugging commands. Type quit to end your debug session followed by exit to close the interactive session.

Note, it may be necessary to set the temporary directory to somewhere in the user space (e.g., export TMPDIR=$(pwd)/tmp) to prevent unexpected internal CUDA driver errors.

For further information on CUDA-GDB, see https://docs.nvidia.com/cuda/cuda-gdb/index.html.

Profiling GPU applications¶

NVIDIA provide two useful tools for profiling performance of applications: Nsight Systems and Nsight Compute; the former provides an overview of application performance, while the latter provides detailed information specifically on GPU kernels.

Using Nsight Systems¶

Nsight Systems provides an overview of application performance and should therefore be the starting point for investigation. To run an application, compile as normal (including the -g flag) and then submit a batch job.

#!/bin/bash

#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --exclusive
#SBATCH --partition=gpu
#SBATCH --qos=short
#SBATCH --gres=gpu:1

# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]

module load nvidia/nvhpc

srun -n 1 nsys profile -o prof1 ./my_application.x

The run should then produce an additional output file called, in this case, prof1.qdrep. The recommended way to view the contents of this file is to download the NVIDIA Nsight package to your own machine (you do not need the entire HPC SDK). Then copy the .qdrep file produced on Cirrus so that if can be viewed locally.

Note, a profiling run should probably be of a short duration so that the profile information (contained in the .qdrep file) does not become prohibitively large.

Details of the download of Nsight Systems and a user guide can be found via the links below.

https://developer.nvidia.com/nsight-systems

https://docs.nvidia.com/nsight-systems/UserGuide/index.html

If your code was compiled with the tools provided by nvidia/nvhpc/21.2 you should download and install Nsight Systems v2020.5.1.85.

Using Nsight Compute¶

Nsight Compute may be used in a similar way as Nsight Systems. A job may be submitted like so.

#!/bin/bash

#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --exclusive
#SBATCH --partition=gpu
#SBATCH --qos=short
#SBATCH --gres=gpu:1

# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]

module load nvidia/nvhpc

srun -n 1 nv-nsight-cu-cli --section SpeedOfLight_RooflineChart \
                           -o prof2 -f ./my_application.x

In this case, a file called prof2.ncu-rep should be produced. Again, the recommended way to view this file is to download the Nsight Compute package to your own machine, along with the .ncu-rep file from Cirrus. The --section option determines which statistics are recorded (typically not all hardware counters can be accessed at the same time). A common starting point is --section MemoryWorkloadAnalysis.

Consult the NVIDIA documentation for further details.

https://developer.nvidia.com/nsight-compute

https://docs.nvidia.com/nsight-compute/2021.2/index.html

Nsight Compute v2021.3.1.0 has been found to work for codes compiled using nvhpc versions 21.2 and 21.9.

Monitoring the GPU Power Usage¶

NVIDIA also provides a useful command line utility for the management and monitoring of NVIDIA GPUs: the NVIDIA System Management Interface nvidia-smi.

The nvidia-smi command queries the available GPUs and reports current information, including but not limited to: driver versions, CUDA version, name, temperature, current power usage and maximum power capability. In this example output, there is one available GPU and it is idle:

::

NVIDIA-SMI 510.47.03 Driver Version: 510.47.03 CUDA Version: 11.6

——————————-+———————-+———————-

GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M.

| MIG M.

===============================+======================+======================

0 Tesla V100-SXM2… Off | 00000000:1C:00.0 Off | Off

N/A 38C P0 57W / 300W | 0MiB / 16384MiB | 1% Default: | N/A

Processes:

GPU GI CI PID Type Process name GPU Memory

ID ID Usage

No running processes found

To monitor the power usage throughout the duration of a job, the output of nvidia-smi will report data at every specified interval with the --loop=SEC option with the tool sleeping in-between queries. The following command will print the output of nvidia-smi every 10 seconds in the specified output file.

nvidia-smi --loop=10 --filename=out-nvidia-smi.txt &

Example submission script:

#!/bin/bash --login

# Slurm job options (name, compute nodes, job time)
#SBATCH --job-name=lammps_Example
#SBATCH --time=00:20:00
#SBATCH --nodes=1
#SBATCH --gres=gpu:4

# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]
#SBATCH --partition=gpu
#SBATCH --qos=gpu

# Load the required modules
module load nvidia/nvhpc

# Save the output of NVIDIA-SMI every 10 seconds
nvidia-smi --loop=10 --filename=out-nvidia-smi.txt &
srun ./cuda_test.x

This submission script uses 4 GPU accelerators for 20 minutes, printing the output of nvidia-smi every 10 seconds to the nvidia-smi.txt output file. The & means the shell executes the command in the background.

Consult the NVIDIA documentation for further details.

https://developer.nvidia.com/nvidia-system-management-interface

Compiling and using GPU-aware MPI¶

For applications using message passing via MPI, considerable improvements in performance may be available by allowing device memory references in MPI calls. This allows replacement of relevant host device transfers by direct communication within a node via NVLink. Between nodes, MPI communication will remain limited by network latency and bandwidth.

Version of OpenMPI with both CUDA-aware MPI support and SLURM support are available, you should load the following modules:

module load openmpi/4.1.4-cuda-11.8
module load nvidia/nvhpc-nompi/22.11

The command you use to compile depends on whether you are compiling C/C++ or Fortran.

Compiling C/C++¶

The location of the MPI include files and libraries must be specified explicitly, e.g.,

nvcc -I${MPI_HOME}/include  -L${MPI_HOME}/lib -lmpi -o my_program.x my_program.cu

This will produce an executable in the usual way.

Compiling Fortran¶

Use the mpif90 compiler wrapper to compile Fortran code for GPU. e.g.

mpif90 -o my_program.x my_program.f90

This will produce an executable in the usual way.

Run time¶

A batch script to use such an executable might be:

#!/bin/bash

#SBATCH --time=00:20:00

#SBATCH --nodes=1
#SBATCH --partition=gpu
#SBATCH --qos=gpu
#SBATCH --gres=gpu:4

# Load the appropriate modules, e.g.,
module load openmpi/4.1.4-cuda-11.8
module load nvidia/nvhpc-nompi/22.2

export OMP_NUM_THREADS=1

# Note the addition
export OMPI_MCA_pml=ob1

srun --ntasks=4 --cpus-per-task=10 --hint=nomultithread ./my_program

Note the addition of the environment variable OMPI_MCA_pml=ob1 is required for correct operation. As before, MPI and placement options should be directly specified to srun and not via SBATCH directives.