Amber20 update 12
ウェブページ
http://ambermd.org/

バージョン
Amber20 update 12, AmberTools 21 update 11

ビルド環境Intel Parallel Studio 2017 Update8 (MPI only)
GCC 7.3.1 (devtoolset-7)
CUDA 11.1 Update 1

ビルドに必要なファイル
Amber20.tar.bz2
AmberTools20.tar.bz2(Amber20 update.1-12 & AmberTools20 update.1-15 & AmberTools21 update.1-11; スクリプト内で取得)
patch-nmrat-gpu.cpp
http://archive.ambermd.org/202110/0206.html 参照。公式アップデートではパッチ確認できず--- src/pmemd/src/cuda/gpu.cpp.org

2022-01-06 16:02:15.915217989 +0900+++ src/pmemd/src/cuda/gpu.cpp 2022-01-06 16:02:26.857121731 +0900@@ -2849,7 +2849,7 @@}// torsions, resttype = 3
else if (resttype[i] == 3) {-if (nmrat[i][0] >= 0 && nmrat[i][1] >= 0 && nmrat[i][2] >= 0 && nmrat[3] >= 0) {+if (nmrat[i][0] >= 0 && nmrat[i][1] >= 0 && nmrat[i][2] >= 0 && nmrat[i][3] >= 0) {torsions++;}
else {

patch-cpptraj-configure
PNetCDF を強制的に off にするためのパッチ--- AmberTools/src/cpptraj/configure.org+++ AmberTools/src/cpptraj/configure2022-01-13 22:56:46.000000000 +0900
2022-01-13 22:57:10.000000000 +0900@@ -1771,8 +1771,6 @@if [ "${LIB_STAT[$LPARANC]}" != 'off' -a $USE_MPI -eq 0 ] ; then
WrnMsg "Parallel NetCDF enabled but MPI not specified. Assuming '-mpi'."
USE_MPI=1- elif [ $USE_MPI -ne 0 -a "${LIB_STAT[$LPARANC]}" = 'off' ] ; then-

LIB_STAT[$LPARANC]='enabled'fi# If we are using the bundled ARPACK then we will need C++/Fortran linking.
if [ "${LIB_STAT[$LARPACK]}" = 'bundled' ] ; thenpatch-configure_python
miniconda のかわりに miniforge を使うためのパッチ--- AmberTools/src/configure_python.org 2022-01-12 15:46:09.042775250 +0900+++ AmberTools/src/configure_python

2022-01-12 15:48:09.177986821 +0900@@ -107,8 +107,7 @@echo "Downloading the latest Miniconda distribution"
if [ $mac -eq 1 ]; then-curl -L -# https://repo.continuum.io/miniconda/Miniconda${version}-${MINICONDA_VERSION}-MacOSX-x86_64.sh > \+miniconda.sh:else

# Try to figure out if the machine builds 32- or 64-bit binaries,# respectively.
@@ -145,23 +144,23 @@;;
esac
if [ $bit -eq 32 ]; then-wget https://repo.continuum.io/miniconda/Miniconda${version}-${MINICONDA_VERSION}-Linux-x86.sh \--O miniconda.sh+exit 0else-

wget https://repo.continuum.io/miniconda/Miniconda${version}-${MINICONDA_VERSION}-Linux-x86_64.sh \--O miniconda.sh+wget https://github.com/conda-forge/miniforge/releases/${MINICONDA_VERSION}/download/Miniforge${version}-Linux-x86_64.sh \+-O miniforge.shfi

fi-if [ -d "$prefix/miniconda" ]; then-echo "Deleting existing miniconda at $prefix/miniconda"-/bin/rm -fr "$prefix/miniconda"+if [ -d "$prefix/miniforge" ]; then+echo "Deleting existing miniforge at $prefix/miniforge"+/bin/rm -fr "$prefix/miniforge"fiecho "Installing Miniconda Python."-bash miniconda.sh -b -p "$prefix/miniconda" || error "Installing miniconda failed"+bash miniforge.sh -b -p "$prefix/miniforge" || error "Installing miniconda failed"+ln -s ./miniforge ./miniconda-export PATH="$prefix/miniconda/bin":"$PATH"+export PATH="$prefix/miniforge/bin":"$PATH"
echo "Updating and installing required and optional packages..."$prefix/miniconda/bin/python -m pip install pip --upgrade@@ -172,7 +171,7 @@# Use pip to install matplotlib so we don't have to pull in the entire Qt# dependency. And cache inside the Miniconda directory, since we don't want to# be writing outside $AMBERHOME unless specifically requested to-$prefix/miniconda/bin/python -m pip --cache-dir=$prefix/miniconda/pkgs \+$prefix/miniconda/bin/python -m pip --cache-dir=$prefix/miniforge/pkgs \install matplotlib || install_matplotlib='yes'
if [ ! -z "$install_matplotlib" ]; then@@ -183,22 +182,22 @@mkdir -p $prefix/lib
cwd=`pwd`
cd "$prefix/bin"-ln -sf ../miniconda/bin/python amber.python || error "Linking Amber's Miniconda Python"-ln -sf ../miniconda/bin/conda amber.conda || error "Linking Amber's Miniconda conda"-ln -sf ../miniconda/bin/ipython amber.ipython || error "Linking Amber's Miniconda ipython"-ln -sf ../miniconda/bin/jupyter amber.jupyter || error "Linking Amber's Miniconda jupyter"-ln -sf ../miniconda/bin/pip amber.pip || error "Linking Amber's Miniconda pip"+ln -sf ../miniforge/bin/python amber.python || error "Linking Amber's Miniconda Python"+ln -sf ../miniforge/bin/conda amber.conda || error "Linking Amber's Miniconda conda"+ln -sf ../miniforge/bin/ipython amber.ipython || error "Linking Amber's Miniconda ipython"+ln -sf ../miniforge/bin/jupyter amber.jupyter || error "Linking Amber's Miniconda jupyter"+ln -sf ../miniforge/bin/pip amber.pip || error "Linking Amber's Miniconda pip"
cd "$prefix/lib"-for dir in ../miniconda/lib/tcl*; do+for dir in ../miniforge/lib/tcl*; doln -sf "$dir" || error "Linking TCL library folder $dir"
done-for dir in ../miniconda/lib/tk*; do+for dir in ../miniforge/lib/tk*; doln -sf "$dir" || error "Linking TK library folder $dir"
done
cd $cwdecho ""-echo "Done. Miniconda installed in $prefix/miniconda"+echo "Done. Miniforge installed in $prefix/miniforge"-/bin/rm -f miniconda.sh+/bin/rm -f miniforge.sh-$prefix/miniconda/bin/conda clean --all --yes+$prefix/miniforge/bin/conda clean --all --yes

ビルド手順#!/bin/sh
VERSION=20
TOOLSVERSION=20 # will be upgraded to 21
INSTALL_DIR="/local/apl/lx/amber20-up12"
TARBALL_DIR="/home/users/${USER}/Software/AMBER/20"
PATCH0=${TARBALL_DIR}/patch-nmrat-gpu.cpp
PATCH1=${TARBALL_DIR}/patch-cpptraj-configure
PATCHX=${TARBALL_DIR}/patch-configure_python
PARALLEL=12#---------------------------------------------------------------------module purge
module load intel_parallelstudio/2017update8
module load scl/devtoolset-7
module load cuda/11.1
export AMBERHOME=${INSTALL_DIR}
export CUDA_HOME="/local/apl/lx/cuda-11.1"
export LANG=C
export LC_ALL=C# install directory has to be prepared before running this script
if [ ! -d ${AMBERHOME} ]; thenecho "Create ${AMBERHOME} before running this script."
exit 1fi# the install directory must be empty
if [ "$(ls -A ${AMBERHOME})" ]; thenecho "Target directory ${AMBERHOME} not empty"
exit 2fi
ulimit -s unlimited# prep files
cd ${AMBERHOME}
bunzip2 -c ${TARBALL_DIR}/Amber${VERSION}.tar.bz2 | tar xf bunzip2 -c ${TARBALL_DIR}/AmberTools${TOOLSVERSION}.tar.bz2 | tar xf mv amber${VERSION}_src/* .
rmdir amber${VERSION}_src
patch -p0 < $PATCHX

# install python first. otherwise, update_amber failed to connect ambermd.org./AmberTools/src/configure_python -v 3
AMBER_PYTHON=$AMBERHOME/bin/amber.python# apply patches and update AmberTools
echo y | $AMBER_PYTHON ./update_amber --upgrade$AMBER_PYTHON ./update_amber --update# patch# see http://archive.ambermd.org/202110/0206.html
patch -p0 < $PATCH0# ad hoc something for pnetcdf
patch -p0 < $PATCH1# reaxff-puremd is openmp only (tentatively)# quick is tentatively not enabled; libstdc++ related issue?
echo "[GPU serial edition (two versions)]"
LANG=C ./configure --no-updates -cuda gnu
make -j${PARALLEL} install && make cleanecho "[GPU parallel edition (two versions)]"
LANG=C ./configure --no-updates -mpi -cuda gnu
make -j${PARALLEL} install && make cleanecho "[CPU serial edition]"
LANG=C ./configure --no-updates gnu
make -j${PARALLEL} install && make cleanecho "[CPU openmp edition]"
LANG=C ./configure --no-updates -mkl -reaxff-puremd-openmp -openmp gnu
make -j${PARALLEL} install && make cleanecho "[CPU parallel edition]"
LANG=C ./configure --no-updates -mkl -mpi gnu
make -j${PARALLEL} install && make clean# run tests. ${AMBERHOME}/amber.sh
cd ${AMBERHOME}# ad hoc work-around# https://github.com/Amber-MD/pdb4amber/issues/85#issuecomment-672812778
cd ${AMBERHOME}/lib/python*/site-packages
if [ -d ParmEd*/parmed ]; thenln -s ParmEd*/parmed ./parmedfiif [ -d pdb4amber*/pdb4amber ]; thenln -s pdb4amber*/pdb4amber ./pdb4amberfi
if [ -d pytraj*/pytraj ]; thenln -s pytraj*/pytraj ./pytrajfi# parallel tests first
cd ${AMBERHOME}
export DO_PARALLEL="mpirun -np 2"
make test.parallel && make clean.test
make test.cuda_parallel && make clean.test # DPFP
cd test; ./test_amber_cuda_parallel.sh SPFP; make clean; cd ../export DO_PARALLEL="mpirun -np 4"
cd test; make test.parallel.4proc; make clean; cd ../unset DO_PARALLEL# openmp tests
make test.openmp && make clean.test# serial tests
make test.serial && make clean.test
make test.cuda_serial && make clean.test # DPFP
cd test; ./test_amber_cuda_serial.sh SPFP; make clean; cd ../cd ${AMBERHOME}
chmod 700 src

テスト
結果は /local/apl/lx/amber20-up12/logs 以下にあります
ほとんどは軽微な数値エラー
test_at_serial において parmed 関連のエラーが２つ出ている。parmed の python パッケージの読み込みに失敗していることが原因？

メモ
cmake でビルドした場合、pbsa_cuda_cg テストがエラーになるため今回も configure を選択
miniconda のかわりに miniforge を利用
Quick については実行時にライブラリ(おそらくは libstdc++)関連のエラーが出たため今回は回避
詳細な検証は行っていません
reaxff-puremd は試験的に OpenMP 版で有効にPython のファイル配置がどうもおかしいため一部手動で修正
https://github.com/Amber-MD/pdb4amber/issues/85#issuecomment-672812778
amber.python で import parmed や import pdb4amber が正常に実行できることまでは確認しています。
nmrat の修正パッチは公式からは提供されていないものの、明らかに間違っていると思われるためパッチを適用
テスト結果に特筆すべきような影響は確認できていません
gcc8 や gcc10 を使うと一部テストが通らなくなるため、今回も gcc7 を利用(amber20 系では共通の事象)
GPU を使わない openmp 版と MPI 版では -mkl は問題無いようなので今回は有効に
cpptraj の PNetCDF は強制的に無効化している。テスト結果には悪影響は出ていないように見える。
上記パッチを適用しない場合は cpptraj.MPI 等のビルドに失敗してしまう(2022/6/1 更新) bin/parmed と bin/pdb4amber が正常に動いていなかったため更新。
中身を以前のバージョンと同じ形に手動で書き換え。とりあえず動作はするようになった。