Import content from N3PDF/external

containers/README.md

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+# Build container image
+
+Use the `Containerfile` file in this folder to build the `bench-<what>`
+container image.
+
+### Using an image
+
+This is the easy part: you just need to download the
+[image](https://github.com/N3PDF/external/pkgs/container/) and run with your
+favorite container tool.
+
+Here the explicit commands with `podman` [[1]](#docker)
+
+```sh
+podman pull ghcr.io/n3pdf/<image-name>:latest
+podman run ghcr.io/n3pdf/<image-name>
+```
+
+<a name="docker">[1]</a>: to use `docker` instead you can simply replace `podman -> docker`, they have compatible subcommands
+
+### Build an image
+
+_Use case_: if a new external installer is added, or some external code is
+updated, to receive the updates you need to regenerate the container (since they
+are pre-installed in the image itself)
+
+Update `Containerfile` (if needed [[2]](#container-update)), hen rerun:
+
+```sh
+./build.bash <folder>
+podman tag <image-id> ghcr.io/n3pdf/<folder>:<version>
+# login to GitHub registry with user credentials (not organization), see [3]
+echo ${PAT} | podman login ghcr.io -u <username> --password-stdin
+# finally publish
+podman push ghcr.io/n3pdf/<folder>:<version>
+# and publish the new latest (all layers already available, it's just an alias)
+podman push ghcr.io/n3pdf/<folder>:latest
+```
+
+Where `<folder>` is the name of one of the subfolders in this directory.
+
+<a name="container-update">[2]</a>: you need to update the container both to
+spell out new externals, but also to upgrade python version, or other build time
+dependencies (e.g. `gfortran`)
+<a name="github-registry-docs">[3]</a>: official [GitHub registry
+docs](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry)

containers/bench-dis/Containerfile

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+FROM docker.io/python:3.9
+
+# create a dedicated user
+RUN /bin/bash -c "apt update; \
+                  apt install -y wget patch autoconf libtool g++ gfortran make"
+
+RUN /bin/bash -c "useradd -m dis"
+
+USER dis
+ENV HOME=/home/dis
+WORKDIR $HOME
+
+RUN /bin/bash -c "pip install numpy"
+
+COPY --chown=dis packages/lhapdf $HOME/lhapdf
+COPY --chown=dis packages/apfel $HOME/apfel
+COPY --chown=dis packages/fonlldis $HOME/fonlldis
+COPY --chown=dis packages/qcdnum $HOME/qcdnum
+COPY --chown=dis packages/xspace-bench $HOME/xspace-bench
+# TODO: remove this dirty trick
+COPY --chown=dis packages/.backup/ $HOME/.backup
+
+ENV PREFIX=$HOME/.local
+ENV PATH=$PATH:$HOME/.local/bin
+
+RUN /bin/bash -c "cd lhapdf; sh install.sh"
+RUN /bin/bash -c "cd apfel; sh install.sh"
+RUN /bin/bash -c "cd fonlldis; sh install.sh"
+RUN /bin/bash -c "cd qcdnum; sh install.sh"
+RUN /bin/bash -c "cd xspace-bench; sh install.sh"
+
+# --------------------------------------------------------- #
+
+FROM docker.io/python:3.9-slim
+
+RUN /bin/bash -c "useradd -m dis"
+
+USER dis
+ENV HOME=/home/dis
+WORKDIR $HOME
+
+ENV LD_LIBRARY_PATH=$HOME/.local/lib
+
+COPY --from=0 /usr/lib/x86_64-linux-gnu/libquadmath* /usr/lib/x86_64-linux-gnu/
+COPY --from=0 /usr/lib/x86_64-linux-gnu/libgfortran* /usr/lib/x86_64-linux-gnu/
+COPY --from=0 /home/dis/.local/ $HOME/.local

containers/bench-evol/Containerfile

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+FROM docker.io/python:3.9
+
+# create a dedicated user
+RUN /bin/bash -c "apt update; \
+                  apt install -y wget patch autoconf libtool g++ gfortran make"
+
+RUN /bin/bash -c "useradd -m evol"
+
+USER evol
+ENV HOME=/home/evol
+WORKDIR $HOME
+
+RUN /bin/bash -c "pip install numpy"
+
+COPY --chown=evol packages/lhapdf $HOME/lhapdf
+COPY --chown=evol packages/apfel $HOME/apfel
+COPY --chown=evol packages/qcdnum $HOME/qcdnum
+COPY --chown=evol packages/pegasus $HOME/pegasus
+# TODO: remove this dirty trick
+COPY --chown=evol packages/.backup/ $HOME/.backup
+
+ENV PREFIX=$HOME/.local
+ENV PATH=$PATH:$HOME/.local/bin
+
+RUN /bin/bash -c "cd lhapdf; sh install.sh"
+RUN /bin/bash -c "cd apfel; sh install.sh"
+RUN /bin/bash -c "cd qcdnum; sh install.sh"
+RUN /bin/bash -c "cd pegasus; sh install.sh"
+
+# --------------------------------------------------------- #
+
+FROM docker.io/python:3.9-slim
+
+RUN /bin/bash -c "apt update; \
+                  apt install -y git curl"
+
+ENV LD_LIBRARY_PATH=/usr/local/lib
+
+COPY --from=0 /usr/lib/x86_64-linux-gnu/libquadmath* /usr/lib/x86_64-linux-gnu/
+COPY --from=0 /usr/lib/x86_64-linux-gnu/libgfortran* /usr/lib/x86_64-linux-gnu/
+COPY --from=0 /home/evol/.local/ /usr/local

containers/build.bash

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+#!/usr/bin/env bash
+
+pushd ..
+podman build -t ghcr.io/n3pdf/$1 -f containers/$1/Containerfile .
+popd

packages/.backup/update.sh

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+BACKUP_DIR=$(realpath $(dirname $0))
+ROOT=$(realpath $BACKUP_DIR/..)
+
+echo "Refetching all sources from: '$ROOT'"
+echo "  -> store them in '$BACKUP_DIR'"
+echo
+
+for ext in $ROOT/*/; do
+  if [ ! -f $ext/variables.sh ]; then
+    continue
+  fi
+
+  . $ext/variables.sh
+  sh $ext/download.sh $URL $BACKUP_DIR/$TARBALL
+done

packages/.gitignore

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+*.tar.gz
+!.backup/*.tar.gz

packages/README.md

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+# External
+
+This repo provides installer for the following software. 
+
+- [APFEL](https://github.com/scarrazza/apfel)
+- [LHAPDF](https://lhapdf.hepforge.org)
+- [QCDNUM](https://www.nikhef.nl/~h24/qcdnum/)
+- [FONLLdis](https://github.com/NNPDF/external)
+- [xspace-bench](https://github.com/NNPDF/external)
+- [pegasus](https://www.nikhef.nl/~avogt/pegasus.html)
+
+Installers share most of their structure, but since differences are unavoidable
+(and they are short and should not change frequently), it is far more flexible
+to have a separate independent copy of install script for each external.
+
+## Structure
+
+Each software is packaged providing installers in the subfolders of this repo
+(each one name after the program, but all lower case).
+
+The structure of each folder is the following:
+
+- `README.md` (optional): brief description and notes
+- `install.sh`: the actual installer, meant to be run by shell (`sh install.sh`)
+- `clean.sh`: a cleaner to remove files generated by the installer
+- `*.patch`: one or more patches (tiny corrections, or extensions, to the
+  original source)
+
+#### Clean
+
+If you clone this as a `git` repository and you run `install.sh` from within its
+own folder you should be able to clean also by running:
+
+```sh
+git clean -fd
+```
+
+If instead you download the script, or you run the script out of the repo, then
+running `sh clean.sh` in the same folder should clean up.
+
+## Disclaimer
+
+We are not the original authors of any of these software, all the rights are owned
+by them, and maintenance is up to them as well.

packages/apfel/.gitignore

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+APFEL-*
+scarrazza-apfel-*
+*.tar.gz

packages/apfel/README.md

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+# APFEL: A Partonic Function Evolution Library
+
+My fork of APFEL, just to store the working installation for my system
+
+## Fixes
+
+- replaced all the shebang containing `python` with `python2`
+
+# Install instructions
+
+## Dependencies
+
+- `swig`
+
+## Install for python2
+
+Uncomment in `configure.ac` the `python_incpath` definition for `python2`, then:
+
+```shell
+autoreconf -f -i
+chmod +x configure
+PYTHON=$(which python2) ./configure --prefix=$HOME/.local
+make clean
+make #-j4
+make install
+```
+
+## Install for python3
+
+Uncomment in `configure.ac` the `python_incpath` definition for `python3`, then:
+
+```shell
+autoreconf -f -i
+PYTHON=$(which python3) ./configure --prefix=$HOME/.local
+make clean
+make #-j4
+make install
+```
+
+---
+
+## Description
+
+APFEL is a library to perform the combined QCD+QED DGLAP
+evolution of parton distributions. It is written and maintained
+by Valerio Bertone (CERN), Stefano Carrazza (Milano) and Juan Rojo (CERN).
+
+## Manual and Instructions:
+
+    http://apfel.hepforge.org/
+    https://github.com/scarrazza/apfel
+
+## APFEL Web:
+
+    http://apfel.mi.infn.it

packages/apfel/clean.sh

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+# import variables
+. $(dirname $0)/variables.sh
+
+rm -rf $TARBALL
+rm -rf $SRC_DIR

packages/apfel/download.sh

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+URL=$1
+TARBALL=$2
+
+wget $URL -O $TARBALL

packages/apfel/install.sh

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+# early exit if errors occur
+set -e
+
+INSTALLER_DIR=$(realpath $(dirname $0))
+
+# import variables
+. $INSTALLER_DIR/variables.sh
+
+# download the code
+sh $INSTALLER_DIR/download.sh $URL $TARBALL
+
+# extract code
+tar -xvzf $TARBALL
+cd $SRC_DIR
+
+# apply patches
+# for p in $INSTALLER_DIR/*.patch; do
+# echo "Applying patch: '$p'"
+# patch <$p -p1
+# done
+
+# reconfigure
+autoreconf -f -i
+# if PREFIX is set use it, otherwise do the default
+if [ -z $PREFIX ]; then
+  PYTHON=$(which python3) ./configure
+else
+  echo "Installing in $PREFIX"
+  PYTHON=$(which python3) ./configure --prefix=$PREFIX
+fi
+
+# reset, compile, and install (includes python interface)
+make clean
+make -j
+make install

packages/apfel/variables.sh

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+VERSION=4426f689a95fbde94012083dd55a9af0edcc5928
+URL="https://github.com/scarrazza/apfel/tarball/$VERSION"
+TARBALL="APFEL-$VERSION.tar.gz"
+SRC_DIR="scarrazza-apfel-$(echo $VERSION | cut -c -7)"

packages/fonlldis/.gitignore

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+FONLLdis
+*.tar.gz

packages/fonlldis/README.md

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+# Installation
+
+Run
+
+```
+make clean
+make
+```
+
+Seems like gcc-9 is not working, please use gcc-10.
+
+To execute the original program run
+
+```
+./FONLLdis 
+```
+
+
+## Python bindings
+
+Run
+
+```sh
+cd pyWrap
+# activate your environment, so f2py already points to the correct thing
+sh f2py.sh
+pip install .
+```

packages/fonlldis/clean.sh

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+# import variables
+. $(dirname $0)/variables.sh
+
+rm -rf $TARBALL
+rm -rf $SRC_DIR

packages/fonlldis/download.sh

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+URL=$1
+TARBALL=$2
+
+INSTALLER_DIR=$(realpath $(dirname $0))
+cp $INSTALLER_DIR/../.backup/FONLLdis.tar.gz $TARBALL