HOWTO: Run Python in Parallel
We can improve performace of python calculation by running python in parallel. In this turtorial we will be making use of the multithreading library to run python code in parallel.
Cardinal
HOWTO: Use GPU in Python
If you plan on using GPUs in tensorflow or pytorch see HOWTO: Use GPU with Tensorflow and PyTorch
This is an exmaple to utilize a GPU to improve performace in our python computations. We will make use of the Numba python library. Numba provides numerious tools to improve perfromace of your python code including GPU support.
Tinker
Tinker is a molecular modeling package. Tinker provides a general set of tools for molecular mechanics and molecular dynamics.
MRIcroGL
MRIcroGL is medical image viewer that allows you to load overlays (e.g. statistical maps), draw regions of interest (e.g. create lesion maps).
Availability and Restrictions
Versions
MRIcroGL is available on Pitzer cluster. These are the versions currently available:
dcm2nii
dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. The DICOM format is the standard image format generated by modern medical imaging devices. However, DICOM is very complicated and has been interpreted differently by different vendors. The NIfTI format is popular with scientists, it is very simple and explicit. However, this simplicity also imposes limitations (e.g. it demands equidistant slices).
NVHPC
NVHPC, or NVIDIA HPC SDK, C, C++, and Fortran compilers support GPU acceleration of HPC modeling and simulation applications with standard C++ and Fortran, OpenACC® directives, and CUDA®. GPU-accelerated math libraries maximize performance on common HPC algorithms, and optimized communications libraries enable standards-based multi-GPU and scalable systems programming. Performance profiling and debugging tools simplify porting and optimization of HPC applications, and containerization tools enable easy deployment on-premises or in the cloud.
NCCL
The NVIDIA Collective Communication Library (NCCL) implements multi-GPU and multi-node communication primitives optimized for NVIDIA GPUs and Networking. NCCL provides routines such as all-gather, all-reduce, broadcast, reduce, reduce-scatter as well as point-to-point send and receive that are optimized to achieve high bandwidth and low latency over PCIe and NVLink high-speed interconnects within a node and over NVIDIA Mellanox Network across nodes.
oneAPI
oneAPI is an open, cross-industry, standards-based, unified, multiarchitecture, multi-vendor programming model that delivers a common developer experience across accelerator architectures – for faster application performance, more productivity, and greater innovation. The oneAPI initiative encourages collaboration on the oneAPI specification and compatible oneAPI implementations across the ecosystem.
GSL
GSL is a library of mathematical methods for C and C++ languages.
Miniconda3
Miniconda3 is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages, including pip, zlib and a few others.
Availability and Restrictions
Versions
Miniconda is available on the Ascend Cluster. The versions currently available at OSC are:
