Languages

27/1/2024 Update

Modules ceuadmin/deno/1.40.2 and ceuadmin/deno/1.40.2-icelake are available for JavaScript and TypeScript, with deno --version giving

deno 1.40.2 (release, x86_64-unknown-linux-gnu)
v8 12.1.285.6
typescript 5.3.3

See also bun, https://bun.sh/: curl -fsSL https://bun.sh/install | bash.

Ada

Web: https://www.adaic.org/

From hello.adb,

with Ada.Text_IO;

procedure Hello is
begin
   Ada.Text_IO.Put_Line ("Hello, World!");
end Hello;

We run

gnatmake hello
hello

C/C++

It is one of the critical software to use, e.g.,

module avail gcc
gcc --version

With module load gcc/8 we could compile this Timsort program.

#include <stdio.h>

#define MIN_RUN 32

// 插入排序算法
void insertionSort(int arr[], int left, int right) {
    for (int i = left + 1; i <= right; i++) {
        int key = arr[i];
        int j = i - 1;
        while (j >= left && arr[j] > key) {
            arr[j + 1] = arr[j];
            j--;
        }
        arr[j + 1] = key;
    }
}

// 归并函数
void merge(int arr[], int left, int mid, int right) {
    int len1 = mid - left + 1;
    int len2 = right - mid;
    int L[len1], R[len2];

    for (int i = 0; i < len1; i++)
        L[i] = arr[left + i];
    for (int j = 0; j < len2; j++)
        R[j] = arr[mid + 1 + j];

    int i = 0, j = 0, k = left;

    while (i < len1 && j < len2) {
        if (L[i] <= R[j])
            arr[k++] = L[i++];
        else
            arr[k++] = R[j++];
    }

    while (i < len1)
        arr[k++] = L[i++];
    while (j < len2)
        arr[k++] = R[j++];
}

// Timsort 算法
void timSort(int arr[], int n) {
    for (int i = 0; i < n; i += MIN_RUN)
        insertionSort(arr, i, (i + MIN_RUN - 1) < n ? (i + MIN_RUN - 1)
                      : (n - 1));

    for (int size = MIN_RUN; size < n; size *= 2) {
        for (int left = 0; left < n; left += 2 * size) {
            int mid = left + size - 1;
            int right = (left + 2 * size - 1) < (n - 1) ?
              (left + 2 * size - 1) : (n - 1);
            merge(arr, left, mid, right);
        }
    }
}

int main() {
    int arr[] = {12, 11, 13, 5, 6, 7};
    int n = sizeof(arr) / sizeof(arr[0]);
    printf("Original array: ");
    for (int i = 0; i < n; i++)
        printf("%d ", arr[i]);

    timSort(arr, n);

    printf("\nSorted array: ");
    for (int i = 0; i < n; i++)
        printf("%d ", arr[i]);
    return 0;
}

by gcc timsort.c -o timsort and timsort to get

Original array: 12 11 13 5 6 7
Sorted array: 5 6 7 11 12 13 14:40

C#

Mono

Our program is called Program.cs

using System;

namespace HelloWorldApp
{
    class Program
    {
        static void Main(string[] args)
        {
            Console.WriteLine("Hello, World!");
        }
    }
}

which is compiled and run as follows,

module load mono/5.0.1.1
csc Program.cs
mono Program.exe

We see

$ csc Program.cs
Microsoft (R) Visual C# Compiler version 2.0.0.61404
Copyright (C) Microsoft Corporation. All rights reserved.

$ mono Program.exe
Hello, World!

.NET

This is more desirable and done as follows.

We first create a new console application:

module avail ceuadmin/dotnet
module load ceuadmin/dotnet/6.0.423
dotnet new console -n HelloWorldApp
cd HelloWorldApp

where we change into a new directory called HelloWorldApp with a basic C# console application template but we continue our Program.cs, which is built and run as follows,

$ dotnet build
MSBuild version 17.3.4+a400405ba for .NET
  Determining projects to restore...
  All projects are up-to-date for restore.
  HelloWorldApp -> /rds/user/jhz22/hpc-work/genetics/HelloWorldApp/bin/Debug/net6.0/HelloWorldApp.dll

Build succeeded.
    0 Warning(s)
    0 Error(s)

Time Elapsed 00:00:03.80

$ dotnet run
Hello, World!

Fortran

Web: https://fortran-lang.org/

gfortran --version

Go

Web: https://go.dev/

It is avail from /usr/bin/go and also visible from module avail go.

A more recent version is available

module load ceuadmin/go
go version

giving go version go1.21.6 linux/amd64.

Haskell

Web: https://www.haskell.org/ghc/

The Glasgow Haskell Compiler is seen from module avail ghc, e.g.,

module load ghc/8.2.2
ghc --version

There is also module ceuadmin/ghc/8.6.5.

Java

module avail openjdk
java -version

JavaScript

Given hello.js containing these

// hello world
console.log('Hello World!');

called by

module load ceuadmin/node/16.14.0
node hello.js

and we get Hello World!.

Julia

Web: https://julialang.org/

The Julia compiler is visible from module avail julia, and by default it loads 1.6.2

module load gcc/9 julia
julia --version

Here is the "hello, world!" session,

               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.2 (2021-07-14)
 _/ |\__'_|_|_|\__'_|  |
|__/                   |

julia> println("Hello World")
Hello World

julia>

Pascal

Web: https://www.freepascal.org/

module load ceuadmin/fpc
fpc -help

Python

Web: https://www.python.org/

This can be invoked from a CSD3 console via python and python3. Libraries can be installed via pip and pip3 (or equivalently python -m pip install and python3 -m pip install), e.g., the script

pip install mygene --user
pip install tensorflow --user
pip install keras --user
pip install jupyter --user

installs libraries at $HOME/.local. To install package to a specific directory, use the --target= (or --install-option="--prefix=$PREFIX_PATH") option and flag in PYTHONPATH environmental variable.

There might be problem with pip,

pip install --upgrade mkdocs
Traceback (most recent call last):
  File "/rds/project/jmmh2/rds-jmmh2-public_databases/software/py38/bin/pip", line 6, in <module>
    from pip._internal.cli.main import main

so we can get around with

curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python3 get-pip.py

Recent version of packages such as fastapi-0.104.1 would complain about lack of setup.py but one can get around with pip install . which uses its pyproject.toml.

It is advised to use virual environments, i.e.,

# inherit system-wide packages as well
module load python/3.5
virtualenv --system-site-packages py35
source py35/bin/activate
# pip new packages
deactivate

An alternative syntax is python3 -m venv py37

Note that when this is set up, one only needs to restart from the source command. The pip is appropriate for installing small number of package; otherwise Anaconda (https://www.anaconda.com/) and Jupyter notebook (https://jupyter.org/) are useful.

We first load Anaconda and create virtual environments,

module avail miniconda
module load miniconda/2
conda create -n py27 python=2.7 ipykernel
source activate py27

for Python 2.7 at /home/$USER/.conda/envs/py27, where envs could be replaced with the --prefix option. These are only required once.

We can also load Anaconda and activate Python 3.51,

module load miniconda/3
conda create -n py35 python=3.5 ipykernel
source activate py35

and follow Autoencoder in Keras tutorial on data from http://yann.lecun.com/exdb/mnist/

The Jupyter notebook can be started as follows,

hostname
$HOME/.local/bin/jupyter notebook --ip=127.0.0.1 --no-browser --port 8081

If it fails to assign the port number, let the system choose (by dropping the --port option). The process which use the port can be shown with lsof -i:8081 or stopped by lsof -ti:8081 | xargs kill -9. The command hostname gives the name of the node. Once the port number is assigned, it is used by another ssh session elsewhere and the URL generated openable from a browser, e.g.,

ssh -4 -L 8081:127.0.0.1:8081 -fN <hostname>.hpc.cam.ac.uk
firefox <URL> &

paying attention to the port number as it may change.

An hello world example is hello.ipynb from which hello.html and hello.pdf were generated with jupyter nbconvert --to html|pdf hello.ipynb.

See also https://docs.hpc.cam.ac.uk/hpc/software-tools/python.html#using-anaconda-python and https://docs.hpc.cam.ac.uk/hpc/software-packages/jupyter.html.

See HPC docuementation for additional information on PyTorch, Tensorflow and GPU.

:star: Introduction to HPC in Python (GitHub).

R

Web: https://www.r-project.org/ and also https://bioconductor.org/

Under HPC, the default version is 3.3.3 with /usr/bin/R; alternatively choose the desired version of R from

module avail R
module avail r
# if you would also like to use RStudio
module avail rstudio

e.g., module load r-3.6.0-gcc-5.4.0-bzuuksv rstudio/1.1.383.

For information about Bioconductor installation, see https://bioconductor.org/install/.

Package installation

The following code installs package for weighted correlation network analysis (WGCNA).

# from CRAN
dependencies <- c("matrixStats", "Hmisc", "splines", "foreach", "doParallel",
                  "fastcluster", "dynamicTreeCut", "survival")
install.packages(dependencies)
# from Bioconductor
biocPackages <- c("GO.db", "preprocessCore", "impute", "AnnotationDbi")
# R < 3.5.0
source("http://bioconductor.org/biocLite.R")
biocLite(biocPackages)
# R >= 3.5.0
install.packages("BiocManager")
BiocManager::install(biocPackages)
install.packages("WGCNA")

A good alternative is to use remotes or devtools package, e.g.,

remotes::install_bioc("snpStats")

A separate example is from r-forge, e.g.,

rforge <- "http://r-forge.r-project.org"
install.packages("estimate", repos=rforge, dependencies=TRUE)

In case of difficulty it is still useful to install directly, e.g.,

wget http://master.bioconductor.org/packages//2.10/bioc/src/contrib/ontoCAT_1.8.0.tar.gz
R CMD INSTALL ontoCAT_1.8.0.tar.gz
# Alternatively,
R -e "install.packages('ontoCAT_1.8.0.tar.gz',repos=NULL)"

The package installation directory can be spefied explicitly with R_LIBS, i.e.,

export R_LIBS=/rds/user/$USER/hpc-work/R:/rds/user/$USER/hpc-work/R-3.6.1/library

To upgrade Bioconductor, we can specify as follows,

BiocManager::install(version = "3.14")

Integration with Rcpp

Template-Rcpp, https://github.com/stsds/Template-Rcpp (LinkedIn post)

ruby

Web: https://www.ruby-lang.org/en/

module load ceuadmin/ruby
ruby --version

Rust

Web: https://www.rust-lang.org/

module load ceuadmin/rust
rustc --version

This is necessary for package gifski.

Scala

Web https://www.scala-lang.org, https://ammonite.io/

module load ceuadmin/Scala

Assuming our Scala 3 program hello.sc containing @main def hello() = println("Hello, World!"), the code is run with

amm

amm hello.sc

scalac/scala

scalac hello.sc
ls -l
scala hello.sc

where scalac is analogous to Java's javac.

Swift

Web: https://www.swift.org/

module load ceuadmin/Swift
wsift --version
swift repl
1> print("Hello, World!")

TypeScript

Web: https://www.typescriptlang.org/

This can achieved with node

# Method 1
npm install -g typescript
tsc hello.ts
node hello.js
# Method 2
npm install -g ts-node
ts-node helloworld.ts

In the following, hello.ts use method 2 through /usr/bin/env

#!/usr/bin/env ts-node

console.log('Hello from TypeScript!');

which is effectively ts-node hello.ts.

  1. The following error

    CustomValidationError: Parameter channel_priority = 'flexible' declared in <<merged>> is invalid.
The value 'flexible' cannot be boolified.

    can be resolved with conda config --set channel_priority false. ↩