CUDA
CUDA (Compute Unified Device Architecture) is a parallel computing platform and application programming interface (API) model created by NVIDIA. It allows software developers to use a CUDA-enabled graphics processing unit (GPU) for general purpose processing, an approach known as General Purpose GPU (GPGPU) computing.
Usage
You need to first request one or more GPUs within an interactive session or batch job on a worker node.
To request say three unspecified public GPUs for a batch job you would include all the following in the header of your submission script:
#SBATCH --partition=gpu
#SBATCH --qos=gpu
#SBATCH --nodes=1
#SBATCH --gpus-per-node=3
Note
See Using GPUs on Bessemer for more information on how to request a GPU-enabled node for an interactive session or job submission.
You then need to ensure a version of the CUDA library (and compiler) is loaded. As with much software installed on the cluster, versions of CUDA are activated via the ‘module load’ command.
To load one of the currently available CUDA versions you can run one of the following commands:
module load CUDA/10.0.130
module load CUDA/10.1.105-GCC-8.2.0-2.31.1
module load CUDA/10.1.243
module load CUDA/10.1.243-GCC-8.3.0
module load CUDA/10.2.89-GCC-8.3.0
module load CUDAcore/11.0.2
module load CUDAcore/11.1.1
Warning
Please take care when loading these modules as some modules will load further software, libraries or toolchains. Further fosscuda toolchain modules also exist which are detailed below.
To load just CUDA 10.2 plus the GCC 8.3 compiler:
module load CUDA/10.2.89-GCC-8.3.0
To load CUDA 10.1 plus the GCC 8.x compiler, OpenMPI, OpenBLAS, SCALAPACK and FFTW:
module load fosscuda/2019b # includes GCC 8.3
module load fosscuda/2019a # includes GCC 8.2
To load just CUDA 10.1 and GCC 8.x:
module load CUDA/10.1.243-GCC-8.3.0 # subset of the fosscuda-2019b toolchain
module load CUDA/10.1.105-GCC-8.2.0-2.31.1 # subset of the fosscuda-2019a toolchain
To load just CUDA 10.0:
module load CUDA/10.0.130
Confirm which version of CUDA you are using via nvcc --version e.g.:
$ nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2019 NVIDIA Corporation
Built on Fri_Feb__8_19:08:17_PST_2019
Cuda compilation tools, release 10.1, V10.1.105
Compiling a simple CUDA program
An example of the use of nvcc (the CUDA compiler):
nvcc filename.cu
will compile the CUDA program contained in the file filename.cu.
Compiling the sample programs
You do not need to be using a GPU-enabled node to compile the sample programs but you do need at least one GPU to run them.
In this demonstration, we create a batch job that
Requests two GPUs, a single CPU core and 8GB RAM
Loads a module to provide CUDA 10.1
Downloads compatible NVIDIA CUDA sample programs
Compiles and runs an example that performs a matrix multiplication
#!/bin/bash
#SBATCH --partition=gpu
#SBATCH --qos=gpu
#SBATCH --nodes=1
#SBATCH --gpus-per-node=2 # Number of GPUs (per node)
#SBATCH --mem=8G
#SBATCH --time=0-00:05 # time (DD-HH:MM)
#SBATCH --job-name=gputest
module load fosscuda/2019a # provides CUDA 10.1
mkdir -p $HOME/examples
cd $HOME/examples
if ! [[ -f cuda-samples/.git ]]; then
git clone https://github.com/NVIDIA/cuda-samples.git cuda-samples
fi
cd cuda-samples
git checkout tags/10.1.1 # use sample programs compatible with CUDA 10.1
cd Samples/matrixMul
make
./matrixMul
GPU Code Generation Options
To achieve the best possible performance whilst being portable, GPU code should be generated for the architecture(s) it will be executed upon.
This is controlled by specifying -gencode arguments to NVCC which,
unlike the -arch and -code arguments,
allows for ‘fatbinary’ executables that are optimised for multiple device architectures.
Each -gencode argument requires two values,
the virtual architecture and real architecture,
for use in NVCC’s two-stage compilation.
For example, -gencode=arch=compute_70,code=sm_70 specifies a virtual architecture of compute_70 and real architecture sm_70.
To support future hardware of higher compute capability,
an additional -gencode argument can be used to enable Just in Time (JIT) compilation of embedded intermediate PTX code.
This argument should use the highest virtual architecture specified in other gencode arguments
for both the arch and code
i.e. -gencode=arch=compute_70,code=compute_70.
The minimum specified virtual architecture must be less than or equal to the Compute Capability of the GPU used to execute the code.
Most public and private GPU nodes in Bessemer contain Tesla V100 GPUs, which are Compute Capability 70.
To build a CUDA application which targets just the public GPUS nodes, use the following -gencode arguments:
nvcc filename.cu \
-gencode=arch=compute_70,code=sm_70 \
-gencode=arch=compute_70,code=compute_70
To build a CUDA application which targets just those nodes
you need CUDA >= 11 and need to supply the following -gencode arguments:
nvcc filename.cu \
-gencode=arch=compute_80,code=sm_80 \
-gencode=arch=compute_80,code=compute_80
Further details of these compiler flags can be found in the NVCC Documentation, along with details of the supported virtual architectures and real architectures.
Documentation
Nsight Systems
Nsight Systems is a system-wide performance analysis tool designed to visualize an application’s algorithms and identify the largest opportunities to optimize. It supports Pascal (SM 60) and newer GPUs.
A common use-case for Nsight Systems is to generate application timelines via the command line, which can later be visualised on a local computer using the GUI component. Nsight Systems, nsys, is provided by the following modules.
module load CUDAcore/11.0.2
module load CUDAcore/11.1.1
module load cuDNN/8.0.4.30-CUDA-11.0.2
module load cuDNN/8.0.4.30-CUDA-11.1.1
You should use a version of nsys that is at least as new as the CUDA toolkit used to compile your application (if appropriate).
To generate an application timeline with Nsight Systems CLI (nsys):
nsys profile -o timeline ./myapplication <arguments>
Nsight systems can trace mulitple APIs, such as CUDA and OpenACC. The --trace argument to specify which APIs should be traced. See the nsys profiling command switch options for further information.
nsys profile -o timeline --trace cuda,nvtx,osrt,openacc ./myapplication <arguments>
Once this file has been downloaded to your local machine, it can be opened in nsys-ui/nsight-sys via File > Open > timeline.qdrep
Nsight Compute
Nsight Compute is a kernel profiler for CUDA applications, which can also be used for API debugging. It supports Volta (SM 70) and newer GPUs.
A common use-case for using Nsight Compute is to capture all available profiling metrics via the command line, which can later be analysed on a local computer using the GUI component. Nsight Compute, ncu, is provided by the following modules.
module load CUDAcore/11.0.2
module load CUDAcore/11.1.1
module load cuDNN/8.0.4.30-CUDA-11.0.2
module load cuDNN/8.0.4.30-CUDA-11.1.1
You should use a versions of ncu that is at least as new as the CUDA toolkit used to compile your application.
To generate the default set of profile metrics with Nsight Compute CLI (ncu):
ncu -o metrics ./myapplication <arguments>
Nsight compute can capture many different metrics which are used to generate the different sections of the profiling report. The --set argument can be used to control which set of metrics and sections are captured. See the Nsight Compute CLI Command Line Options for further information.
ncu -o metrics --set full ./myapplication <arguments>
Once this file has been downloaded to your local machine, it can be opened in ncu-ui/nv-nsight-cu via File > Open File > metrics.ncu-rep
Profiling using nvprof
Prior to September 2020 nvprof, NVIDIA’s CUDA profiler, could not write its SQLite database outputs to the /fastdata filesystem.
This was because SQLite requires a filesystem that supports file locking
but file locking was not previously enabled on the (Lustre) filesystem mounted on /fastdata.
nvprof can now write output data to any user-accessible filesystem including /fastdata.
CUDA Training
The Research Software Engineering team have developed an undergraduate teaching module on CUDA; lecture notes and lecture recordings for that module are accessible here for anyone with a University account.
Determining the NVIDIA Driver version
Run the command:
cat /proc/driver/nvidia/version
Example output is:
NVRM version: NVIDIA UNIX x86_64 Kernel Module 418.67 Sat Apr 6 03:07:24 CDT 2019
GCC version: gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC)
Installation notes
These are primarily for system administrators.
Device driver
The NVIDIA device driver is installed and configured using the gpu-nvidia-driver systemd service (managed by puppet).
This service runs /usr/local/scripts/gpu-nvidia-driver.sh at boot time to:
Check the device driver version and uninstall it then reinstall the target version if required;
Load the
nvidiakernel module;Create several device nodes in
/dev/.
CUDA 11.1.1
Installed as a dependency of the cuDNN-8.0.4.30-CUDA-11.1.1 easyconfig.
Single GPU and compiler testing was conducted as above in the matrixMul batch job.
Inter-GPU performance was tested on all 4x V100 devices in bessemer-node026 (no NVLINK)
using nccl-tests and /NCCL/2.8.3-CUDA-11.1.1.
nccl-tests was run using ./build/all_reduce_perf -b 8 -e 128M -f 2 -g 4
Results:
# nThread 1 nGpus 4 minBytes 8 maxBytes 134217728 step: 2(factor) warmup iters: 5 iters: 20 validation: 1
#
# Using devices
# Rank 0 Pid 201685 on bessemer-node026 device 0 [0x3d] Tesla V100-PCIE-32GB
# Rank 1 Pid 201685 on bessemer-node026 device 1 [0x3e] Tesla V100-PCIE-32GB
# Rank 2 Pid 201685 on bessemer-node026 device 2 [0x3f] Tesla V100-PCIE-32GB
# Rank 3 Pid 201685 on bessemer-node026 device 3 [0x40] Tesla V100-PCIE-32GB
#
# out-of-place in-place
# size count type redop time algbw busbw error time algbw busbw error
# (B) (elements) (us) (GB/s) (GB/s) (us) (GB/s) (GB/s)
8 2 float sum 13.37 0.00 0.00 1e-07 14.59 0.00 0.00 0e+00
16 4 float sum 13.58 0.00 0.00 3e-08 13.35 0.00 0.00 3e-08
32 8 float sum 13.82 0.00 0.00 3e-08 13.46 0.00 0.00 3e-08
64 16 float sum 13.42 0.00 0.01 3e-08 13.45 0.00 0.01 3e-08
128 32 float sum 13.81 0.01 0.01 3e-08 13.21 0.01 0.01 3e-08
256 64 float sum 13.96 0.02 0.03 3e-08 13.63 0.02 0.03 3e-08
512 128 float sum 13.86 0.04 0.06 3e-08 13.56 0.04 0.06 1e-08
1024 256 float sum 13.77 0.07 0.11 1e-07 13.67 0.07 0.11 1e-07
2048 512 float sum 13.85 0.15 0.22 1e-07 13.92 0.15 0.22 1e-07
4096 1024 float sum 14.24 0.29 0.43 2e-07 13.75 0.30 0.45 2e-07
8192 2048 float sum 15.92 0.51 0.77 2e-07 15.23 0.54 0.81 2e-07
16384 4096 float sum 19.15 0.86 1.28 2e-07 18.81 0.87 1.31 2e-07
32768 8192 float sum 22.07 1.48 2.23 2e-07 21.74 1.51 2.26 2e-07
65536 16384 float sum 30.05 2.18 3.27 2e-07 29.71 2.21 3.31 2e-07
131072 32768 float sum 47.07 2.78 4.18 2e-07 46.60 2.81 4.22 2e-07
262144 65536 float sum 64.61 4.06 6.09 2e-07 63.70 4.12 6.17 2e-07
524288 131072 float sum 84.66 6.19 9.29 2e-07 85.23 6.15 9.23 2e-07
1048576 262144 float sum 156.5 6.70 10.05 2e-07 155.0 6.77 10.15 2e-07
2097152 524288 float sum 299.0 7.01 10.52 2e-07 299.0 7.01 10.52 2e-07
4194304 1048576 float sum 657.1 6.38 9.57 2e-07 651.5 6.44 9.66 2e-07
8388608 2097152 float sum 1313.2 6.39 9.58 2e-07 1308.3 6.41 9.62 2e-07
16777216 4194304 float sum 2671.5 6.28 9.42 2e-07 2671.4 6.28 9.42 2e-07
33554432 8388608 float sum 5349.2 6.27 9.41 2e-07 5351.0 6.27 9.41 2e-07
67108864 16777216 float sum 10712 6.26 9.40 2e-07 10711 6.27 9.40 2e-07
134217728 33554432 float sum 21410 6.27 9.40 2e-07 21407 6.27 9.40 2e-07
# Out of bounds values : 0 OK
# Avg bus bandwidth : 4.22207
#
CUDA 11.0.2
Installed as a dependency of the cuDNN-8.0.4.30-CUDA-11.0.2 easyconfig.
Single GPU and compiler testing was conducted as above in the matrixMul batch job.
Inter-GPU performance was tested on all 4x V100 devices in bessemer-node026 (no NVLINK)
using nccl-tests and /NCCL/2.8.3-CUDA-11.0.2.
nccl-tests was run using ./build/all_reduce_perf -b 8 -e 128M -f 2 -g 4
Results:
# nThread 1 nGpus 4 minBytes 8 maxBytes 134217728 step: 2(factor) warmup iters: 5 iters: 20 validation: 1
#
# Using devices
# Rank 0 Pid 200999 on bessemer-node026 device 0 [0x3d] Tesla V100-PCIE-32GB
# Rank 1 Pid 200999 on bessemer-node026 device 1 [0x3e] Tesla V100-PCIE-32GB
# Rank 2 Pid 200999 on bessemer-node026 device 2 [0x3f] Tesla V100-PCIE-32GB
# Rank 3 Pid 200999 on bessemer-node026 device 3 [0x40] Tesla V100-PCIE-32GB
#
# out-of-place in-place
# size count type redop time algbw busbw error time algbw busbw error
# (B) (elements) (us) (GB/s) (GB/s) (us) (GB/s) (GB/s)
8 2 float sum 13.23 0.00 0.00 1e-07 13.39 0.00 0.00 0e+00
16 4 float sum 13.31 0.00 0.00 3e-08 13.33 0.00 0.00 3e-08
32 8 float sum 13.55 0.00 0.00 3e-08 13.45 0.00 0.00 3e-08
64 16 float sum 13.40 0.00 0.01 3e-08 13.27 0.00 0.01 3e-08
128 32 float sum 13.51 0.01 0.01 3e-08 13.26 0.01 0.01 3e-08
256 64 float sum 13.68 0.02 0.03 3e-08 13.20 0.02 0.03 3e-08
512 128 float sum 13.69 0.04 0.06 3e-08 13.32 0.04 0.06 1e-08
1024 256 float sum 13.40 0.08 0.11 1e-07 13.15 0.08 0.12 1e-07
2048 512 float sum 14.14 0.14 0.22 1e-07 13.56 0.15 0.23 1e-07
4096 1024 float sum 14.45 0.28 0.43 2e-07 13.95 0.29 0.44 2e-07
8192 2048 float sum 16.36 0.50 0.75 2e-07 15.91 0.51 0.77 2e-07
16384 4096 float sum 19.80 0.83 1.24 2e-07 19.44 0.84 1.26 2e-07
32768 8192 float sum 23.24 1.41 2.11 2e-07 22.48 1.46 2.19 2e-07
65536 16384 float sum 31.39 2.09 3.13 2e-07 30.96 2.12 3.18 2e-07
131072 32768 float sum 50.30 2.61 3.91 2e-07 49.39 2.65 3.98 2e-07
262144 65536 float sum 69.78 3.76 5.64 2e-07 68.22 3.84 5.76 2e-07
524288 131072 float sum 86.08 6.09 9.14 2e-07 86.15 6.09 9.13 2e-07
1048576 262144 float sum 155.5 6.74 10.11 2e-07 156.3 6.71 10.06 2e-07
2097152 524288 float sum 298.7 7.02 10.53 2e-07 295.2 7.10 10.65 2e-07
4194304 1048576 float sum 646.5 6.49 9.73 2e-07 647.9 6.47 9.71 2e-07
8388608 2097152 float sum 1310.7 6.40 9.60 2e-07 1307.6 6.42 9.62 2e-07
16777216 4194304 float sum 2665.6 6.29 9.44 2e-07 2660.4 6.31 9.46 2e-07
33554432 8388608 float sum 5324.7 6.30 9.45 2e-07 5324.3 6.30 9.45 2e-07
67108864 16777216 float sum 10678 6.28 9.43 2e-07 10667 6.29 9.44 2e-07
134217728 33554432 float sum 21423 6.26 9.40 2e-07 21352 6.29 9.43 2e-07
# Out of bounds values : 0 OK
# Avg bus bandwidth : 4.18969
#
CUDA 10.1
Installed as a dependency of the fosscuda-2019a easyconfig.
Inter-GPU performance was tested on all 4x V100 devices in bessemer-node026 (no NVLINK)
using nccl-tests and NCCL/2.4.2-gcccuda-2019a.
nccl-tests was run using ./build/all_reduce_perf -b 8 -e 128M -f 2 -g 4
Results:
# nThread 1 nGpus 4 minBytes 8 maxBytes 134217728 step: 2(factor) warmup iters: 5 iters: 20 validation: 1
#
# Using devices
# Rank 0 Pid 31823 on bessemer-node026 device 0 [0x3d] Tesla V100-PCIE-32GB
# Rank 1 Pid 31823 on bessemer-node026 device 1 [0x3e] Tesla V100-PCIE-32GB
# Rank 2 Pid 31823 on bessemer-node026 device 2 [0x3f] Tesla V100-PCIE-32GB
# Rank 3 Pid 31823 on bessemer-node026 device 3 [0x40] Tesla V100-PCIE-32GB
#
# out-of-place in-place
# size count type redop time algbw busbw error time algbw busbw error
# (B) (elements) (us) (GB/s) (GB/s) (us) (GB/s) (GB/s)
8 2 float sum 16.36 0.00 0.00 1e-07 15.99 0.00 0.00 0e+00
16 4 float sum 183.5 0.00 0.00 3e-08 16.04 0.00 0.00 3e-08
32 8 float sum 15.99 0.00 0.00 3e-08 15.93 0.00 0.00 3e-08
64 16 float sum 16.13 0.00 0.01 3e-08 16.12 0.00 0.01 3e-08
128 32 float sum 255.5 0.00 0.00 3e-08 16.10 0.01 0.01 3e-08
256 64 float sum 16.23 0.02 0.02 3e-08 16.15 0.02 0.02 3e-08
512 128 float sum 16.13 0.03 0.05 3e-08 16.08 0.03 0.05 1e-08
1024 256 float sum 16.08 0.06 0.10 1e-07 16.28 0.06 0.09 1e-07
2048 512 float sum 16.44 0.12 0.19 1e-07 16.15 0.13 0.19 1e-07
4096 1024 float sum 16.41 0.25 0.37 2e-07 16.38 0.25 0.37 2e-07
8192 2048 float sum 16.56 0.49 0.74 2e-07 16.22 0.51 0.76 2e-07
16384 4096 float sum 19.62 0.84 1.25 2e-07 18.78 0.87 1.31 2e-07
32768 8192 float sum 29.21 1.12 1.68 2e-07 27.23 1.20 1.80 2e-07
65536 16384 float sum 46.77 1.40 2.10 2e-07 43.66 1.50 2.25 2e-07
131072 32768 float sum 51.53 2.54 3.82 2e-07 50.77 2.58 3.87 2e-07
262144 65536 float sum 67.61 3.88 5.82 2e-07 67.61 3.88 5.82 2e-07
524288 131072 float sum 100.3 5.23 7.84 2e-07 100.3 5.23 7.84 2e-07
1048576 262144 float sum 165.5 6.33 9.50 2e-07 165.1 6.35 9.52 2e-07
2097152 524288 float sum 301.1 6.96 10.45 2e-07 299.6 7.00 10.50 2e-07
4194304 1048576 float sum 588.3 7.13 10.69 2e-07 583.7 7.19 10.78 2e-07
8388608 2097152 float sum 1141.4 7.35 11.02 2e-07 1133.3 7.40 11.10 2e-07
16777216 4194304 float sum 2269.2 7.39 11.09 2e-07 2256.6 7.43 11.15 2e-07
33554432 8388608 float sum 4510.3 7.44 11.16 2e-07 4497.0 7.46 11.19 2e-07
67108864 16777216 float sum 9013.1 7.45 11.17 2e-07 8998.9 7.46 11.19 2e-07
134217728 33554432 float sum 18003 7.46 11.18 2e-07 17974 7.47 11.20 2e-07
# Out of bounds values : 0 OK
# Avg bus bandwidth : 4.42606
#
CUDA 10.0
Explicitly installed via the EasyBuild-provided CUDA/10.0.130 easyconfig.