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User's Manual Management Number:OUCMC-super-技術-007-06 National University Corporation Osaka University Cybermedia Center User's manual NEC First Government & Public Solutions Division Summary 1. System Overview ................................................................................................. 1 1.1. Overall System View ....................................................................................... 1 1.2. Thress types of Computiong Environments ........................................................ 2 1.2.1. General-purpose CPU environment .............................................................. 2 1.2.2. Vector computing environment ................................................................... 3 1.2.3. GPGPU computing environment .................................................................. 5 1.3. Three types of Storage Areas ........................................................................... 6 1.3.1. Features.................................................................................................. 6 1.3.2. Various Data Access Methods ..................................................................... 6 1.4. Three types of Front-end nodes ....................................................................... 7 1.4.1. Features.................................................................................................. 7 1.4.2. HPC Front-end ......................................................................................... 7 1.4.1. HPDA Front-end ....................................................................................... 8 1.5. 1.5. System usage environment ....................................................................... 9 1.5.1. Login method .......................................................................................... 9 1.5.2. Program development .............................................................................. 10 1.5.3. Program execution................................................................................... 11 1.5.4. Use container ......................................................................................... 11 2. Instructions for Front-end Login ............................................................................ 14 2.1. Login With SSH ............................................................................................. 14 2.1.1. Installation of 2-factor Authentication Application ......................................... 14 2.1.2. First Login .............................................................................................. 15 2.1.3. Second and subsequent Logins .................................................................. 19 2.1.4. Recovery instruction if Two-factor Authentication became unavailable ............. 21 2.2. How to login with GSI-SSH ............................................................................. 21 2.3. File Transfer ................................................................................................. 25 2.3.1. File Transfer On UNIX-based OS (Linux, MacOS) .......................................... 25 2.3.2. File Transfer on Windows® ....................................................................... 28 3. Front-end Environment ........................................................................................ 31 3.1. Common Instructions .................................................................................... 31 3.1.1. How to Use the File System ...................................................................... 31 3.1.2. How to check usage status ....................................................................... 32 3.1.3. Environment Settings ............................................................................... 34 i © NEC Corporation 2021 3.2. How to use the HPC Front-end ........................................................................ 37 3.2.1. Preparation for use .................................................................................. 37 3.2.2. Creating a virtual session of the NICE DCV server ........................................ 37 3.2.3. Starting the NICE DCV Client ..................................................................... 37 3.3. How to use the HPDA Front-end ...................................................................... 39 3.3.1. Preparation for Use .................................................................................. 39 3.3.2. Start Jupyter Container ............................................................................ 39 3.3.3. Access to Jupyter Container ...................................................................... 40 3.3.4. Customize Jupyter Container ..................................................................... 44 3.3.5. Stop Jupyter Container ............................................................................. 48 4. Program Development ......................................................................................... 49 4.1. Common Matters .......................................................................................... 49 4.1.1. Use of Compiler / MPI .............................................................................. 49 4.1.2. Use of The Library ................................................................................... 51 4.1.3. How to use Development Support Tool ....................................................... 52 4.2. compiling a program for General-purpose CPU environment ................................ 54 4.2.1. Serial Execution ...................................................................................... 54 4.2.2. Thread Parallel Execution .......................................................................... 54 4.2.3. MPI Parallel Execution .............................................................................. 55 4.2.4. How to Use Libraries ................................................................................ 55 4.3. compiling a program for Vector computing environment ..................................... 58 4.3.1. Serial Execution ...................................................................................... 58 4.3.2. Thread Parallel Execution .......................................................................... 60 4.3.3. How to Compile When Performing MPI Parallel Execution .............................. 60 4.3.4. How to Use Libraries ................................................................................ 61 4.4. compiling a program for GPGPU computing environment .................................... 64 4.4.1. Serial Execution ...................................................................................... 64 4.4.2. Thread Parallel Execution .......................................................................... 64 4.4.3. MPI Parallel Execution .............................................................................. 65 4.4.4. Compile For CUDA ................................................................................... 65 4.4.5. Options for OpenACC ............................................................................... 66 4.4.6. How to Use Libraries ................................................................................ 66 4.5. How to Use GNU Compiler Collection ................................................................ 69 4.5.1. Serial Execuion........................................................................................ 69 4.5.2. Thread Parallel Execution .......................................................................... 69 ii © NEC Corporation 2021 4.6. How to Use Containers .................................................................................. 71 4.6.1. Preparation of container image .................................................................. 71 4.6.2. Customize and Build Container Images ....................................................... 73 4.7. How to Use Python ........................................................................................ 77 4.7.1. Use in interactive mode ............................................................................ 77 4.7.2. Execute Program and Script ...................................................................... 78 4.7.3. Add Python Module .................................................................................. 79 4.7.4. Using python modules .............................................................................. 80 5. Program Execution Method ................................................................................... 85 5.1. Common Items ............................................................................................. 85 5.1.1. Explanation of Job Management System ..................................................... 85 5.1.2. Interactive Job Submission Method ............................................................ 85 5.1.3. Job Submission Method ............................................................................ 86 5.1.4. Job Management System Commands ......................................................... 89 5.2. Job Class ..................................................................................................... 91 5.2.1. Job Class for General-Purpose CPU Envirnment ............................................ 91 5.2.2. Job Class For Vector Computing Environment .............................................. 92 5.2.3. Job Class for GPGPU Computing Environment .............................................
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