User Programming Environment
A. Programming Tool Installation Status
※ We recommend using the Anaconda environment for the artificial intelligence framework of the Neuron system. We also plan to provide an environment that uses Singularity to run container images based on user requirements.
※ Using Singularity: Refer to “[Appendix 3] Method for Using Singularity Container Images”
※ Non-CUDA MPI libraries must be employed to use nodes that are not equipped with GPUs.
B. How to Use the Compilers
1. Compiler and MPI environment configuration (modules)
1) Module-related basic commands
Print a list of available modules You can check a list of available modules, such as compilers and libraries.
Add a module to be used You can add modules that you plan to use, such as compilers and libraries. Modules that will be used can be added simultaneously.
Delete used modules You can remove unnecessary modules. Several modules can be deleted simultaneously.
Print a list of used modules You can check the list of modules that are currently configured.
Delete all used modules simultaneously.
Check the module installation path.
2. Compiling sequential programs
A sequential program is a program that does not consider the parallel program environment. That is, it is a program that does not use a parallel program interface, such as OpenMP or MPI. A sequential program is run using only one processor in one node. Compiler-specific options used for compiling sequential programs are also used when compiling parallel programs. Hence, reference should be made to these options even if you are not interested in sequential programs.
1) Intel compiler
To use an Intel compiler, add the required version of the Intel compiler module. Available modules can be checked using the “module avail” command.
※ Check available versions by referring to the programming tool installation status table.
Compiler types
Intel compiler usage example
The following is an example of compiling a test sample file using an Intel compiler to generate a test.exe executable file.
※ You can copy a test sample file for job submission from /apps/shell/job_examples and use it.
2) GNU compiler
To use a GNU compiler, add the required version of the GNU compiler module. Available modules can be checked using the “module avail” command.
※ Check available versions by referring to the programming tool installation status table.
※ You must use version "gcc/4.8.5" or higher.
Compiler types
GNU compiler usage example
The following is an example of compiling a test sample file using a GNU compiler to generate a test.exe executable file.
※ You can copy a test sample file for job submission from /apps/shell/job_examples and use it.
3) PGI compiler
To use a PGI compiler, add the required version of the PGI compiler module. Available modules can be checked using the “module avail” command.
※ Check available versions by referring to the programming tool installation status table.
Compiler types
PGI compiler usage example
The following is an example of compiling a test sample file using a PGI compiler to generate a test.exe executable file.
※ You can copy a test sample file for job submission from /apps/shell/job_examples and use it.
3. Compiling parallel programs
1) OpenMP compiling
OpenMP is a technique that has been developed to utilize multi-threading by only using compiler directives. The compiler used to compile a parallel program using OpenMP is the same as the compiler used for a sequential program. Parallel compiling can be performed by adding compiler options, and most compilers currently support the OpenMP directives.
Example of compiling an OpenMP program (Intel compiler)
The following is an example of compiling a test_omp sample file using openMP with an Intel compiler to generate a test_omp.exe executable file.
Example of compiling an OpenMP program (GNU compiler)
The following is an example of compiling a test_omp sample file using openMP with a GNU compiler to generate a test_omp.exe executable file.
Example of compiling an OpenMP program (PGI compiler)
The following is an example of compiling a test_omp sample file using openMP with a PGI compiler to generate a test_omp.exe executable file.
2) MPI compiling
The user can run the MPI commands in the following table. These commands are a sort of wrapper, and the compiler that is specified by the .bashrc file compiles the source file.
Even if compiling is performed using mpicc, it is necessary to use the options that correspond to the original compiler being wrapped.
Example of compiling an MPI program (Intel compiler)
The following is an example of compiling a test_mpi sample file using MPI with an Intel compiler to generate a test_mpi.exe executable file.
Example of compiling an MPI program (GNU compiler)
The following is an example of compiling a test_mpi sample file using MPI with a GNU compiler to generate a test_mpi.exe executable file.
Example of compiling an MPI program (PGI compiler)
The following is an example of compiling a test_mpi sample file using MPI with a PGI compiler to generate a test_mpi.exe executable file.
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