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coderefinery · Oct 11, 2024 · 115fa5a · 115fa5a
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diff --git a/.buildinfo b/.buildinfo
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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: e4dd0cebedc9134d87f3c4373472ea75
+tags: d77d1c0d9ca2f4c8421862c7c5a0d620
diff --git a/.nojekyll b/.nojekyll
diff --git a/_downloads/07ab827005bb2435cfa6959d87adca94/accelerate_cuda.def b/_downloads/07ab827005bb2435cfa6959d87adca94/accelerate_cuda.def
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+Bootstrap: docker
+From: pytorch/pytorch:2.2.2-cuda12.1-cudnn8-runtime
+
+%post
+
+  pip install accelerate evaluate datasets scipy scikit-learn transformers
diff --git a/_downloads/69e350fcc7a533a6096e256764f8d27b/puhti-openmpi.def b/_downloads/69e350fcc7a533a6096e256764f8d27b/puhti-openmpi.def
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+Bootstrap: docker
+From: rockylinux:{{ OS_VERSION }}
+
+%arguments
+
+  NPROCS=4
+  OPENMPI_VERSION=4.1.4rc1
+  OSU_MICRO_BENCHMARKS_VERSION=7.4
+  GCC_VERSION=9
+  UCX_VERSION=1.13.0
+  OS_NAME=rhel
+  OS_VERSION=8.6
+  OFED_VERSION=5.6-2.0.9.0
+
+%post
+
+  ### Install OpenMPI dependencies
+
+  # Base tools and newer gcc version
+
+  dnf install -y dnf-plugins-core epel-release
+  dnf config-manager  --set-enabled powertools
+  dnf install -y make gdb wget numactl-devel which
+  dnf -y install gcc-toolset-{{ GCC_VERSION }}
+  source /opt/rh/gcc-toolset-{{ GCC_VERSION }}/enable
+
+  # Enable Mellanox OFED rpm repo
+
+  wget https://www.mellanox.com/downloads/ofed/RPM-GPG-KEY-Mellanox
+  rpm --import RPM-GPG-KEY-Mellanox
+  rm RPM-GPG-KEY-Mellanox
+  cd /etc/yum.repos.d/
+  wget https://linux.mellanox.com/public/repo/mlnx_ofed/{{ OFED_VERSION }}/{{ OS_NAME }}{{ OS_VERSION }}/mellanox_mlnx_ofed.repo
+  cd /
+
+  # Install network library components
+
+  dnf -y install rdma-core ucx-ib-{{ UCX_VERSION }} ucx-devel-{{ UCX_VERSION }} ucx-knem-{{ UCX_VERSION }} ucx-cma-{{ UCX_VERSION }} ucx-rdmacm-{{ UCX_VERSION }}
+
+  ### Install OpenMPI
+
+  dnf -y install openmpi-{{ OPENMPI_VERSION }}
+
+  ### Build example application
+
+  export OMPI_DIR=/usr/mpi/gcc/openmpi-{{ OPENMPI_VERSION }}
+  export PATH="$OMPI_DIR/bin:$PATH"
+  export LD_LIBRARY_PATH="$OMPI_DIR/lib:$LD_LIBRARY_PATH"
+
+  # Build osu benchmarks
+  cd /opt
+  wget -q http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}.tar.gz
+  tar xf osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}.tar.gz
+  cd osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}
+  ./configure --prefix=/opt/osu-micro-benchmarks CC=mpicc CFLAGS=-O3
+  make -j{{ NPROCS }}
+  make install
+  cd ..
+  rm -rf osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }} osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}.tar.gz
+
+%environment
+  export OMPI_DIR=/usr/mpi/gcc/openmpi-{{ OPENMPI_VERSION }}
+  export PATH="$OMPI_DIR/bin:$PATH"
+  export LD_LIBRARY_PATH="$OMPI_DIR/lib:$LD_LIBRARY_PATH"
+  export MANPATH="$OMPI_DIR/share/man:$MANPATH"
+
+%runscript
+  source /opt/rh/gcc-toolset-{{ GCC_VERSION }}/enable
+  /opt/osu-micro-benchmarks/libexec/osu-micro-benchmarks/mpi/pt2pt/osu_bw
+
diff --git a/_downloads/89af20c2d98096490dcc145892ed280d/run_lammps_indent.sh b/_downloads/89af20c2d98096490dcc145892ed280d/run_lammps_indent.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+#SBATCH --time=00:10:00
+#SBATCH --mem=2G
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+#SBATCH --output=lammps_indent.out
+
+# Copy example from image
+apptainer exec lammps-openmpi.sif cp -r /opt/lammps/examples/indent .
+
+cd indent
+
+# Load OpenMPI module
+module load openmpi
+
+# Run simulation
+srun apptainer run ../lammps-openmpi.sif -in in.indent
diff --git a/_downloads/b2789bd6fc9a1e97d79c827edc887d37/lammps-openmpi.def b/_downloads/b2789bd6fc9a1e97d79c827edc887d37/lammps-openmpi.def
@@ -0,0 +1,68 @@
+Bootstrap: docker
+From: ubuntu:latest
+
+%arguments
+
+  NPROCS=4
+  OPENMPI_VERSION=4.1.6
+  LAMMPS_VERSION=29Aug2024
+
+%post
+
+  ### Install OpenMPI dependencies
+
+  apt-get update
+  apt-get install -y wget bash gcc gfortran g++ make file bzip2 ca-certificates libucx-dev
+
+  ### Build OpenMPI
+
+  OPENMPI_VERSION_SHORT=$(echo {{ OPENMPI_VERSION }} | cut -f 1-2 -d '.')
+  cd /opt
+  mkdir ompi
+  wget -q https://download.open-mpi.org/release/open-mpi/v${OPENMPI_VERSION_SHORT}/openmpi-{{ OPENMPI_VERSION }}.tar.bz2
+  tar -xvf openmpi-{{ OPENMPI_VERSION }}.tar.bz2
+  # Compile and install
+  cd openmpi-{{ OPENMPI_VERSION }}
+  ./configure --prefix=/opt/ompi --with-ucx=/usr
+  make -j{{ NPROCS }}
+  make install
+  cd ..
+  rm -rf openmpi-{{ OPENMPI_VERSION }} openmpi-{{ OPENMPI_VERSION }}.tar.bz2
+
+  ### Build example application
+
+  # Install LAMMPS dependencies
+  apt-get install -y cmake
+
+  export OMPI_DIR=/opt/ompi
+  export PATH="$OMPI_DIR/bin:$PATH"
+  export LD_LIBRARY_PATH="$OMPI_DIR/lib:$LD_LIBRARY_PATH"
+  export CMAKE_PREFIX_PATH="$OMPI_DIR:$CMAKE_PREFIX_PATH"
+
+  # Build LAMMPS
+  cd /opt
+  wget -q https://download.lammps.org/tars/lammps-{{ LAMMPS_VERSION }}.tar.gz
+  tar xf lammps-{{ LAMMPS_VERSION }}.tar.gz
+  cd lammps-{{ LAMMPS_VERSION }}
+  cmake -S cmake -B build \
+    -DCMAKE_INSTALL_PREFIX=/opt/lammps \
+    -DBUILD_MPI=yes \
+    -DBUILD_OMP=yes
+  cmake --build build --parallel {{ NPROCS }} --target install
+  cp -r examples /opt/lammps/examples
+  cd ..
+  rm -rf lammps-{{ LAMMPS_VERSION }} lammps-{{ LAMMPS_VERSION }}.tar.gz
+
+%environment
+  export OMPI_DIR=/opt/ompi
+  export PATH="$OMPI_DIR/bin:$PATH"
+  export LD_LIBRARY_PATH="$OMPI_DIR/lib:$LD_LIBRARY_PATH"
+  export MANPATH="$OMPI_DIR/share/man:$MANPATH"
+
+  export LAMMPS_DIR=/opt/lammps
+  export PATH="$LAMMPS_DIR/bin:$PATH"
+  export LD_LIBRARY_PATH="$LAMMPS_DIR/lib:$LD_LIBRARY_PATH"
+  export MANPATH="$LAMMPS_DIR/share/man:$MANPATH"
+
+%runscript
+  exec /opt/lammps/bin/lmp "$@"
diff --git a/_downloads/c7c7f903ce66845641c48c1015bb49c9/lumi-mpich.def b/_downloads/c7c7f903ce66845641c48c1015bb49c9/lumi-mpich.def
@@ -0,0 +1,39 @@
+bootstrap: docker
+from: ubuntu:latest
+
+%arguments
+
+  NPROCS=4
+  MPICH_VERSION=3.1.4
+  OSU_MICRO_BENCHMARKS_VERSION=7.4
+
+%post
+
+  ### Install MPICH dependencies
+
+  apt-get update
+  apt-get install -y file g++ gcc gfortran make gdb strace wget ca-certificates --no-install-recommends
+
+  # Build MPICH
+
+  wget -q http://www.mpich.org/static/downloads/{{ MPICH_VERSION }}/mpich-{{ MPICH_VERSION }}.tar.gz
+  tar xf mpich-{{ MPICH_VERSION }}.tar.gz
+  cd mpich-{{ MPICH_VERSION }}
+  ./configure --disable-fortran --enable-fast=all,O3 --prefix=/usr
+  make -j{{ NPROCS }}
+  make install
+  ldconfig
+
+  # Build osu benchmarks
+  cd /opt
+  wget -q http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}.tar.gz
+  tar xf osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}.tar.gz
+  cd osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}
+  ./configure --prefix=/opt/osu-micro-benchmarks CC=mpicc CFLAGS=-O3
+  make -j{{ NPROCS }}
+  make install
+  cd ..
+  rm -rf osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }} osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}.tar.gz
+
+%runscript
+  /opt/osu-micro-benchmarks/libexec/osu-micro-benchmarks/mpi/pt2pt/osu_bw
diff --git a/_downloads/f8d6a1f0663067f2be980733bf38b45b/run_accelerate_parallel.sh b/_downloads/f8d6a1f0663067f2be980733bf38b45b/run_accelerate_parallel.sh
@@ -0,0 +1,16 @@
+#!/bin/bash
+#SBATCH --mem=32G
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --gpus-per-task=2
+#SBATCH --cpus-per-task=12
+#SBATCH --time=00:10:00
+#SBATCH --output=accelerate_run_parallel.out
+
+export OMP_NUM_THREADS=$(( $SLURM_CPUS_PER_TASK / $SLURM_GPUS_ON_NODE ))
+
+apptainer exec --nv accelerate_cuda.sif \
+  torchrun \
+    --nproc_per_node $SLURM_GPUS_ON_NODE \
+    ./nlp_example.py \
+    --mixed_precision fp16
diff --git a/_downloads/ff3d6a2935fcb472627a13145369a68b/triton-openmpi.def b/_downloads/ff3d6a2935fcb472627a13145369a68b/triton-openmpi.def
@@ -0,0 +1,56 @@
+Bootstrap: docker
+From: ubuntu:latest
+
+%arguments
+
+  NPROCS=4
+  OPENMPI_VERSION=4.1.6
+  OSU_MICRO_BENCHMARKS_VERSION=7.4
+
+%post
+
+  ### Install OpenMPI dependencies
+
+  apt-get update
+  apt-get install -y wget bash gcc gfortran g++ make file bzip2 ca-certificates libucx-dev
+
+  ### Build OpenMPI
+
+  OPENMPI_VERSION_SHORT=$(echo {{ OPENMPI_VERSION }} | cut -f 1-2 -d '.')
+  cd /opt
+  mkdir ompi
+  wget -q https://download.open-mpi.org/release/open-mpi/v${OPENMPI_VERSION_SHORT}/openmpi-{{ OPENMPI_VERSION }}.tar.bz2
+  tar -xvf openmpi-{{ OPENMPI_VERSION }}.tar.bz2
+  # Compile and install
+  cd openmpi-{{ OPENMPI_VERSION }}
+  ./configure --prefix=/opt/ompi --with-ucx=/usr
+  make -j{{ NPROCS }}
+  make install
+  cd ..
+  rm -rf openmpi-{{ OPENMPI_VERSION }} openmpi-{{ OPENMPI_VERSION }}.tar.bz2
+
+  ### Build example application
+
+  export OMPI_DIR=/opt/ompi
+  export PATH="$OMPI_DIR/bin:$PATH"
+  export LD_LIBRARY_PATH="$OMPI_DIR/lib:$LD_LIBRARY_PATH"
+
+  # Build osu benchmarks
+  cd /opt
+  wget -q http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}.tar.gz
+  tar xf osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}.tar.gz
+  cd osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}
+  ./configure --prefix=/opt/osu-micro-benchmarks CC=/opt/ompi/bin/mpicc CFLAGS=-O3
+  make -j{{ NPROCS }}
+  make install
+  cd ..
+  rm -rf osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }} osu-micro-benchmarks-{{ OSU_MICRO_BENCHMARKS_VERSION }}.tar.gz
+
+%environment
+  export OMPI_DIR=/opt/ompi
+  export PATH="$OMPI_DIR/bin:$PATH"
+  export LD_LIBRARY_PATH="$OMPI_DIR/lib:$LD_LIBRARY_PATH"
+  export MANPATH="$OMPI_DIR/share/man:$MANPATH"
+
+%runscript
+  /opt/osu-micro-benchmarks/libexec/osu-micro-benchmarks/mpi/pt2pt/osu_bw
diff --git a/_images/app_run_example.png b/_images/app_run_example.png
diff --git a/_images/apptainer_example.png b/_images/apptainer_example.png
diff --git a/_images/bind_example.png b/_images/bind_example.png
diff --git a/_images/build_example.png b/_images/build_example.png
diff --git a/_images/containerized_application.png b/_images/containerized_application.png
diff --git a/_images/default_mounts.png b/_images/default_mounts.png
diff --git a/_images/dockerfile_python_image.png b/_images/dockerfile_python_image.png
diff --git a/_images/dockerhub_python.png b/_images/dockerhub_python.png
diff --git a/_images/exec_example.png b/_images/exec_example.png
diff --git a/_images/image_explanation.png b/_images/image_explanation.png
diff --git a/_images/image_explanation_apptainer.png b/_images/image_explanation_apptainer.png
diff --git a/_images/instance_example.png b/_images/instance_example.png
diff --git a/_images/mpi_install_structure.png b/_images/mpi_install_structure.png
diff --git a/_images/mpi_job_structure.png b/_images/mpi_job_structure.png
diff --git a/_images/mpi_job_structure_bound.png b/_images/mpi_job_structure_bound.png
diff --git a/_images/mpi_job_structure_hybrid.png b/_images/mpi_job_structure_hybrid.png
diff --git a/_images/normal_application.png b/_images/normal_application.png
diff --git a/_images/nv_example.png b/_images/nv_example.png
diff --git a/_images/pull_example.png b/_images/pull_example.png
diff --git a/_images/rocm_example.png b/_images/rocm_example.png
diff --git a/_images/run_example.png b/_images/run_example.png
diff --git a/_images/shell_example.png b/_images/shell_example.png