fortran | Dr. Ravindra Shinde

Install and manage Intel oneAPI compiler and component tools using environment modules

Fri, 03 Dec 2021 08:41:00 +0000

Intel has recently changed their business model. Their suite of compilers, debuggers, toolkits, and libraries are given free of cost for personal or academic use. In an earlier post, I explained how to install them on Ubuntu linux and activate all the softwares using a single source command.

In this post, I will show you how to manage these compilers, libraries, and debuggers using the environment modules. So just using “module load icc” you could activate a single “icc” compoment. All the dependent modules will also be loaded automatically, if you follow the these steps.

Pre-requisites

Make sure that you have the following packages already installed on your ubuntu machine.

environment modules (i.e. the module command)
Intel oneapi basekit and/or hpckit (I am repeating the steps below)

Intel Repository Public Key

Get the Intel Repository public key and add it to your apt sources keyring so the packages will be trusted by ubuntu.

# use wget to fetch the Intel repository public key
wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
# add to your apt sources keyring so that archives signed with this key will be trusted.
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
# remove the public key
rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB

Configure apt client to use Intel repository

echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list

sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"

Install all the packages or selected packages.

All basic compilers (Fortran, C, C++, and Python)

sudo apt install intel-basekit

HPC toolkits

sudo apt install intel-hpckit

IoT (internet of things) toolkits

sudo apt install intel-iotkit

AI (Artificial Intelligence) analytics toolkits

sudo apt install intel-aikit

Rendering toolkit

sudo apt install intel-renderkit

After Installation

After you have installed the oneAPI kits, they can be activated using the following command written in the ~/.bashrc file.

Option 1: Activate all the components at once for all users (root access)

. /opt/intel/oneapi/setvars.sh

Option 2: Activate individual components using the environment modules

cd /opt/intel/oneapi/
You will see a modulefiles-setup.sh file. If we execute this file using bash it will create a folder named modulefiles in the same /opt/intel/oneapi/ folder.
Put the following line into your $HOME/.bashrc file
1. export MODULEPATH=${MODULEPATH}:/opt/intel/oneapi/modulefiles
2. . $HOME/.bashrc or close and reopen the terminal
If you type module avail, you will see all the components of Intel oneapi available for use.
You can load or unload individual components using module load icc or module load compiler etc.
You can create your own module file and put it in the modulefiles folder. Let us create a modulefile for intel python.
Copy the following content into a file /opt/intel/oneapi/modulefiles/python/latest

    #%Module1.0###################################################################
    set min_tcl_ver 8.4
    if { $tcl_version < $min_tcl_ver } {
        puts stderr " "
        puts stderr "ERROR: This modulefile requires tcl $min_tcl_ver or greater."
        puts stderr "Your system reports that tclsh version $tcl_version is installed."
        exit 1
    }

    proc ModulesHelp { } {
            puts stderr "\tAdds Intel Python 3 to your PATH environment variable\n"
    }

    module-whatis   "adds Intel Python 3 to your PATH environment variable"

    prepend-path    PATH    /opt/intel/oneapi/intelpython/latest/bin

Check the installed packages using module avail, check the loaded packages using module list, unload packages using module unload packagename

How to use Intel oneapi compilers on the Github actions workflow

Sat, 03 Jul 2021 11:51:00 +0000

Intel has recently changed their business model. Their suite of compilers, debuggers, toolkits, and libraries are given free of cost for personal or academic use. We can also use these compilers on the Github Actions workflow. This post gives details of the steps and a yml file which you can directly use on your Github repository to kick the automatic compilation and testing.

Step 1

Create a file with any name (but with a .yml extention) in the .github/workflows directory in your repository. If you want to use the Github website to create the action’s file, then

click actions
create new workflow
setup a workflow by yourself
Copy paste the following content

name: Intel OneAPI build

on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]
jobs:
  build_intel_champ_fparser:
    runs-on: ubuntu-20.04
    defaults:
      run:
        shell: bash --noprofile --norc {0}
    steps:
    - uses: actions/checkout@v2
    - name: setup repo
      run: |
        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
        rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
        sudo echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
        sudo apt-get update
    - name: install
      run: |
        sudo apt-get install -y intel-oneapi-common-vars
        sudo apt-get install -y intel-oneapi-compiler-fortran
        sudo apt-get install -y intel-oneapi-mkl
        sudo apt-get install -y intel-oneapi-mpi
        sudo apt-get install -y intel-oneapi-mpi-devel

    - name: Compile
      run: |
        source /opt/intel/oneapi/setvars.sh
        printenv >> $GITHUB_ENV
        ifort test.f90 -o test_program
        mpiifort test2.f90 -o mpitest

    - name: "Test the code"
      run: |
        echo "Running the tests using the Intel oneapi fortran compiler"
        cd tests/test01
        mpirun -np 1  $HOME/work/reponame/reponame/mpitest
        ./$HOME/work/reponame/reponame/test_program

Note that entire oneapi-basekit is not needed (and exceeds github’s docker size alloted to each user). Install the components as needed for your project and don’t forget to use “-y” option while installing using apt install

Installation of Intel oneAPI suite of compilers on Ubuntu Linux

Wed, 26 May 2021 22:51:00 +0000

Intel has recently changed their business model. Their suite of compilers, debuggers, toolkits, and libraries are given free of cost for personal or academic use. Here I explain how to install them on Ubuntu linux. All of these softwares are activated using a single source command.

Pre-requisites

Make sure that you have the following packages already installed on your ubuntu machine.

cmake
pkg-config
build-essential

If they are not installed, you can install using the following command:

sudo apt update
sudo apt -y install cmake pkg-config build-essential

Intel Repository Public Key

Get the Intel Repository public key and add it to your apt sources keyring so the packages will be trusted by ubuntu.

# use wget to fetch the Intel repository public key
wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
# add to your apt sources keyring so that archives signed with this key will be trusted.
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
# remove the public key
rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB

Configure apt client to use Intel repository

echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list

sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"

Install all the packages or selected packages.

All basic compilers (Fortran, C, C++, and Python)

sudo apt install intel-basekit

HPC toolkits

sudo apt install intel-hpckit

IoT (internet of things) toolkits

sudo apt install intel-iotkit

AI (Artificial Intelligence) analytics toolkits

sudo apt install intel-aikit

Rendering toolkit

sudo apt install intel-renderkit

After Installation

After you have installed the oneAPI kits, they can be activated using the following command written in the ~/.bashrc file.

For all users (root access)

. /opt/intel/oneapi/setvars.sh

For single user

. ~/intel/oneapi/setvars.sh

Octopus TDDFT code installation on the comet cluster at XSEDE, San Diego

Thu, 21 Nov 2019 18:46:00 +0000

Load Modules:

I chose Intel compiler and intelmpi to compile the mpi version of octopus on Comet (after the Rocks OS upgrade to Rocks 7).

The following modules need to be loaded first.

intel/2018.1.163
intelmpi/2018.1.163
gsl/2.5
mkl/2018.1.163

Install dependencies/libraries:

Install libxc-4.3.4 or above

Download the latest package of libxc. Use the following configure line:

./configure --prefix=/home/neelravi CC=mpicc FC=mpif90 FCFLAGS=-O3 CFLAGS=-O3
make 
make install
make check

Install fftw-3.3.8 or above

Do not use the pre-installed fftw package. Download the latest fftw package. Use the following configure line to compile.

I chose fftw-3.3.8.

./configure --prefix=/home/neelravi CC=mpicc CFLAGS=-O3 F77=mpif90 F77FLAGS=-O3
make 
make install
make check

Install octopus code

Download the stable version of the octopus. (i.e. octopus 9.1) Use the following configure script.

./configure --prefix=$HOME \
  CC=mpicc FC=mpif90 CFLAGS="-O3" FCFLAGS="-O3" \
--enable-mpi --enable-openmp \
--with-blas="-L${MKLROOT}/lib/intel64 -lmkl_rt -lpthread -lm -ldl" \
--with-libxc-prefix=$HOME \
--with-fftw-prefix=$HOME \
--with-blacs="-L${MKLROOT}/lib/intel64 -lmkl_rt -lpthread -lm -ldl" \
--with-scalapack="-L${MKLROOT}/lib/intel64 -lmkl_rt -lpthread -lm -ldl" \
--with-gsl-prefix="/opt/gsl/2.5/intel"

make 
make install
make check

The last command make check should either pass or fail all the tests. If some tests pass and some fail, then there is something wrong with the installation. Please note that a test corresponding to the glib may fail (probably this is used when Species are read from the picture file). You may ignore it.

Run a sample calculation with more than one node. The output file should show the parallelization and anticipated resource wastage.

Your octopus is ready!

Octopus TDDFT code installation on the XC40 Cray supercomputer

Thu, 06 Jul 2017 13:00:00 +0000

Load Modules in the PrgEnv-gnu:

I managed to install octopus in gnu programming environment with the following settings:

Modules loaded in the PrgEnv-gnu

modules/3.2.10.5
nodestat/2.2-1.0502.60539.1.31.ari
sdb/1.1-1.0502.63652.4.25.ari
alps/5.2.4-2.0502.9822.32.1.ari
lustre-cray_ari_s/2.5_3.0.101_0.46.1_1.0502.8871.20.1-1.0502.21538.30.1
udreg/2.3.2-1.0502.10518.2.17.ari
ugni/6.0-1.0502.10863.8.29.ari
gni-headers/4.0-1.0502.10859.7.8.ari
dmapp/7.0.1-1.0502.11080.8.76.ari
xpmem/0.1-2.0502.64982.5.3.ari
hss-llm/7.2.0
Base-opts/1.0.2-1.0502.60680.2.4.ari
gcc/6.1.0
craype/2.5.7
nodehealth/5.1-1.0502.65826.9.1.ari
cray-libsci/16.09.1
pmi/5.0.10-1.0000.11050.0.0.ari
atp/2.0.2
PrgEnv-gnu/5.2.82
pbs/12.2.404.152084
cray-parallel-netcdf/1.7.0
cray-netcdf-hdf5parallel/4.4.1
cray-hdf5-parallel/1.8.16
fftw/3.3.4.10
craype-network-aries
craype-haswell
cce/8.5.3
cray-shmem/7.4.3
cray-mpich/7.4.3

The LD LIBRARY PATH had following things in the path:

/opt/gcc/6.1.0/snos/lib64:/opt/cray/nodehealth/5.1-1.0502.65826.9.1.ari/lib64 /opt/cray/fftw/3.3.4.10/haswell/lib:/opt/cray/hdf5-parallel/1.8.16/GNU/5.1/lib:/opt/cray/netcdf-hdf5parallel/4.4.1/GNU/5.1/lib:/opt/cray/parallel-netcdf/1.7.0/GNU/5.1/lib:/opt/cray/pmi/5.0.10-1.0000.11050.0.0.ari/lib64:/opt/cray/libsci/16.09.1/GNU/5.1/x86_64/lib:/opt/cray/xpmem/0.1-2.0502.64982.5.3.ari/lib64:/opt/cray/dmapp/7.0.1-1.0502.11080.8.76.ari/lib64:/opt/cray/ugni/6.0-1.0502.10863.8.29.ari/lib64:/opt/cray/udreg/2.3.2-1.0502.10518.2.17.ari/lib64:/opt/cray/alps/5.2.4-2.0502.9822.32.1.ari/lib64

the configure script looks like:

set LD_LIBRARY_PATH=($LD_LIBRARY_PATH $CRAY_LD_LIBRARY_PATH)
setenv LIBS_BLAS /opt/cray/libsci/16.09.1/GNU/5.1/x86_64/lib/libsci_gnu_mpi_mp.a
setenv LIBS_LAPACK /opt/cray/libsci/16.09.1/GNU/5.1/x86_64/lib/libsci_gnu_mpi_mp.a
setenv LIBS_FFT /opt/cray/fftw/3.3.4.10/haswell/lib/libfftw3.a

./configure  --prefix=/mnt/lustre/mrc2/mrcravi/devel-basedir-test  \
--with-libxc-prefix=/mnt/lustre/mrc2/mrcravi/devel-basedir  \
--with-libxc-include=/mnt/lustre/mrc2/mrcravi/devel-basedir/include \
--with-gsl-prefix=/mnt/lustre/mrc2/mrcravi/devel-basedir \
--with-fftw-prefix=/opt/cray/fftw/3.3.4.10/haswell \
--enable-openmp --enable-mpi --host=cray

make -j 24
make install

The above script is for minimum working example. I managed to couple etsf, netcdf, hdf5 etc to octopus.

Install ETSF-IO libray on Cray XC40 supercomputer

Wed, 30 Nov 2016 00:00:00 +0000

Requirements:

ETSF IO library requires hdf5 and netcdf libraries. You can load them using the module load commands.

module load cray-parallel-netcdf

module load cray-netcdf-hdf5parallel

The path of the installed modules can be viewed using module show cray-parallel-netcdf command.

Configure:

./configure FC=ftn --prefix=installation-path \
--with-netcdf-libs="-L/opt/cray/parallel-netcdf/1.7.0/cray/8.3/lib -lnetcdff -lnetcdf" \
--with-netcdf-incs="-I/opt/cray/parallel-netcdf/1.7.0/cray/8.3/include" \
LDFLAGS="-L/opt/cray/parallel-netcdf/1.7.0/cray/8.3/lib" \
LIBS="-lnetcdff -lnetcdf"

compile

make

Install

make install

Install netcdf and netcdf-fortran required for ETSF-IO libray and octopus code

Thu, 03 Nov 2016 00:00:00 +0000

For installation of netcdf

Configure:

./configure CC=icc --prefix="/opt/etsf" \
--enable-static --enable-shared --disable-dap \
LT_SYS_LIBRARY_PATH="/opt/etsf/lib" \
LDFLAGS="-L/opt/etsf" \
--disable-netcdf-4

compile

make

Install

make install

Check the installation

make check

For installation of netcdf-fortran

Configure:

./configure FC=ifort CC=icc \
--prefix="/opt/etsf" \
CPPFLAGS="-I/opt/etsf/include" \
CPPFLAGS="-I/opt/include" \
LDFLAGS="-L/opt/lib"

compile

make

Install

make install

Check the installation

make check