165 lines
3.8 KiB
Markdown
165 lines
3.8 KiB
Markdown
# commands for compiling and running on HPCs
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## Gekko @ NTU
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### 1. Load necessary modules and select GNU compilers
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```bash
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module purge && module load cmake gnu/gcc-9.3.0
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```
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### 2. compiler openmpi and HDF5 with parallel option
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`./install_mpi_and_hdf5_local.sh`
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will create openmpi and hdf5 executables in external_libs/local_mpi_hdf5/bin
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### 3. Compile TomoATT
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```bash
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# make a build directory
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mkdir build
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# compile TomoATT
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cd build
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CC=/usr/local/gcc-9.3.0/bin/gcc CXX=/usr/local/gcc-9.3.0/bin/g++ cmake .. -DCMAKE_PREFIX_PATH=$(pwd)/../external_libs/local_mpi_hdf5
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make -j16
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```
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Then the executable TOMOATT is created in the build directory.
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## Fugaku @ RIKEN
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### 0. start interactive job on Fugaku (for accessing arch64 environment)
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```bash
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pjsub --interact -g hp220155 -L "node=1" -L "rscgrp=int" -L "elapse=1:00:00" --mpi "max-proc-per-node=12" --sparam "wait-time=600" -x PJM_LLIO_GFSCACHE=/vol0004 --no-check-directory
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```
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### 1. Load necessary modules
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```bash
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# prepare spack env
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. /vol0004/apps/oss/spack/share/spack/setup-env.sh
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# load Fujitsu mpi
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spack load /jfzaut5
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# or load gnu 11.2.0
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spack load /nphnrhl /cvur4ou
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```
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### 2. Download hdf5 source code and compile it
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```bash
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# every file will be placed in external_libs
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cd ./external_libs
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# make a local install pass
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mkdir local_mpi_hdf5
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# download hdf5 source
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wget https://gamma.hdfgroup.org/ftp/pub/outgoing/hdf5/snapshots/v112/hdf5-1.12.2-1.tar.gz
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#Extract the downloaded directory
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tar -xvf hdf5-1.12.2-1.tar.gz && cd hdf5-1.12.2-1
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# Configure the code. (the pathes to mpicc, mpicxx should vary on the environment)
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CC=mpifcc CFLAGS="-Nclang" CXX=mpiFCC CXXFLAGS="-Nclang" ./configure --enable-parallel --enable-unsupported --enable-shared --enable-cxx --prefix=$(pwd)/../local_mpi_hdf5
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# make
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make -j12 && make install
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# now hdf5 executables are in external_libs/local_mpi_hdf5/bin
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```
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or with gnu 11.2.0
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```bash
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# download hdf5 source
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wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.2/src/hdf5-1.13.2.tar.gz
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#Extract the downloaded directory
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tar -xvf hdf5-1.13.2.tar.gz
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cd hdf5-1.13.2
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# Configure the code. (the pathes to mpicc, mpicxx should vary on the environment)
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CC=mpicc CXX=mpic++ ./configure --enable-parallel --enable-unsupported --enable-shared --enable-cxx --prefix=$(pwd)/../local_mpi_hdf5
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# make
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make -j12 && make install
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```
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### 3. Compile TomoATT
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```bash
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# cd to TomoATT directory
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cd ../..
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# make a build directory
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mkdir build
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# compile TomoATT
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cd build
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CC=mpifcc CXX=mpiFCC cmake .. -DCMAKE_PREFIX_PATH=$(pwd)/../external_libs/local_mpi_hdf5
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# or for gnu 11.2.0
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cmake .. -DCMAKE_PREFIX_PATH=$(pwd)/../external_libs/local_mpi_hdf5
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make -j12
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```
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### 4. terminalte interactive job
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`Ctrl + D`
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## ASPIRE 1 @ NSCC
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### 0. load necessary modules
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```bash
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module purge
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export PATH=/app/gcc/9.5.0/bin:$PATH && export LD_LIBRARY_PATH=/app/gcc/9.5.0/lib:$LD_LIBRARY_PATH
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module load intel/19.0.0.117
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```
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### 1. Download hdf5 source code and compile it
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```bash
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# download openmpi and hdf5 source code on your LOCAL MACHINE
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wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.3/src/hdf5-1.13.3.tar.gz
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# then upload it to NSCC (for example)
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scp -rC hdf5-1.13.3.tar.gz aspire1:~/(where TomoATT placed)/external_libs/
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# on ASPIURE 1
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cd external_libs
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mkdir local_mpi_hdf5
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# extract tar file and cd to the directory
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tar -xvf hdf5-1.13.3.tar.gz && cd hdf5-1.13.3
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# configure the code
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CC=mpiicc CXX=mpiicpc \
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./configure --enable-parallel --enable-unsupported --enable-shared --enable-cxx --prefix=$(pwd)/../local_mpi_hdf5
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# make and install to the prefix
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make -j16 && make install
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```
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### 2. Compile TomoATT
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```bash
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# cd to TomoATT directory
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cd ../..
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# make a build directory
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mkdir build
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# compile TomoATT
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cd build
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CC=icc CXX=icpc cmake .. -DCMAKE_PREFIX_PATH=$(pwd)/../external_libs/local_mpi_hdf5
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make -j16
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```
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