Maxwell : alphafold 2.1.1L

#!/bin/bash
#SBATCH --partition=allgpu
#SBATCH --constraint='A100|V100'
#SBATCH --time=0-12:00
#SBATCH --job-name=T1050-dimer
#SBATCH --output=slurm.T1050-dimer.out
unset LD_PRELOAD
export AF_preset=multimer 
export AF_outdir=/beegfs/desy/user/$USER/ALPHAFOLD2.1/local 

/software/alphafold/2.1.1L/alphafold.sh --fasta_paths=/software/alphafold/2.1.1L/T1050-2.fasta

#!/bin/bash
# basic setup
unset LD_PRELOAD

source /etc/profile.d/modules.sh
module purge
module load maxwell cuda/11.3

# alphafold basics 
export PATH=/software/alphafold/2.1.1L/envs/af2.1/bin:$PATH
export TF_FORCE_UNIFIED_MEMORY=1

export AF_datadir=${AF_datadir:-/beegfs/desy/group/it/ReferenceData/alphafold}

# databases
AF_uniref90=${AF_uniref90:-$AF_datadir/uniref90/uniref90.fasta}
AF_bfd=${AF_bfd:-$AF_datadir/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt}
AF_mmcif=${AF_mmcif:-$AF_datadir/pdb_mmcif/mmcif_files}
AF_obsolete=${AF_obsolete:-$AF_datadir/pdb_mmcif/obsolete.dat}
AF_pdb70=${AF_pdb70:-$AF_datadir/pdb70/pdb70}
AF_mgnify=${AF_mgnify:-$AF_datadir/mgnify/mgy_clusters.fa}
AF_uniclust30=${AF_uniclust30:-$AF_datadir/uniclust30/uniclust30_2018_08/uniclust30_2018_08}
AF_uniprot=${AF_uniprot:-$AF_datadir/uniprot/uniprot.fasta}
AF_pdbseqres=${AF_pdbseqres:-$AF_datadir/pdb_seqres/pdb_seqres.txt}
AF_template_date=${AF_template_date:-$(date +%Y-%m-%d)}

# make sure they all exist
for e in $( /usr/bin/env | grep "$AF_datadir" | cut -d= -f2 ) ; do
    if [[ ! -e $e ]]; then
	echo "missing $e -- check your environment "
	exit
    fi
done

export AF_preset="${AF_preset:-monomer}"

if [[ $AF_preset =~ monomer ]]; then
    export AF_dbs="--uniref90_database_path=$AF_uniref90 --bfd_database_path=$AF_bfd --template_mmcif_dir=$AF_mmcif"
    export AF_dbs="$AF_dbs --obsolete_pdbs_path=$AF_obsolete --pdb70_database_path=$AF_pdb70 --mgnify_database_path=$AF_mgnify"
    export AF_dbs="$AF_dbs --uniclust30_database_path=$AF_uniclust30"
else
    export AF_dbs="--uniref90_database_path=$AF_uniref90 --bfd_database_path=$AF_bfd --template_mmcif_dir=$AF_mmcif"
    export AF_dbs="$AF_dbs --obsolete_pdbs_path=$AF_obsolete --mgnify_database_path=$AF_mgnify"
    export AF_dbs="$AF_dbs --uniclust30_database_path=$AF_uniclust30 --uniprot_database_path=$AF_uniprot --pdb_seqres_database_path=$AF_pdbseqres"
fi
# user customizable setup
export AF_outdir="${AF_outdir:-/tmp/alphafold}"

cat <<EOF
AlphaFold Setup
----------------------------------------------------------------------------------------------------
AF_datadir.:  $AF_datadir
AF_outdir,,:  $AF_outdir
AF_preset..:  $AF_preset

Hardware Setup
----------------------------------------------------------------------------------------------------
Host.......:  $(hostname)
CPU........:  $(grep "model name" /proc/cpuinfo  | head -1 | cut -d: -f2 | grep -o '[a-Z].*')
GPU........:  $(nvidia-smi -L |cut -d'(' -f1 | tr '\n' ' ')
Cores......:  $(nproc)
Memory.....:  $(free -g | grep Mem | awk '{print $2}')

Time.......:  $(date)

Execute:
----------------------------------------------------------------------------------------------------
python3 /software/alphafold/2.1.1L/alphafold/run_alphafold.py \
        --output_dir=$AF_outdir \
        --data_dir=$AF_datadir \
        --model_preset=$AF_preset \
        --max_template_date=$AF_template_date \
        $AF_dbs \
        "$@"

EOF

python3 /software/alphafold/2.1.1L/alphafold/run_alphafold.py --output_dir=$AF_outdir --data_dir=$AF_datadir --model_preset=$AF_preset --max_template_date=$AF_template_date $AF_dbs "$@"

>1WUF_1|Chains A|hypothetical protein lin2664|Listeria innocua (272626)
GHHHHHHHHHHGLVPRGSHMYFQKARLIHAELPLLAPFKTSYGELKSKDFYIIELINEEGIHGYGELEAFPLPDYTEETLSSAILIIKEQLLPLLAQRKIRKPEEIQELFSWIQGNEMAKAAVELAVWDAFAKMEKRSLAKMIGATKESIKVGVSIGLQQNVETLLQLVNQYVDQGYERVKLKIAPNKDIQFVEAVRKSFPKLSLMADANSAYNREDFLLLKELDQYDLEMIEQPFGTKDFVDHAWLQKQLKTRICLDENIRSVKDVEQAHSIGSCRAINLKLARVGGMSSALKIAEYCALNEILVWCGGMLEAGVGRAHNIALAARNEFVFPGDISASNRFFAEDIVTPAFELNQGRLKVPTNEGIGVTLDLKVLKKYTKSTEEILLNKGWS
>1WUF_2|Chains B|hypothetical protein lin2664|Listeria innocua (272626)
GHHHHHHHHHHGLVPRGSHMYFQKARLIHAELPLLAPFKTSYGELKSKDFYIIELINEEGIHGYGELEAFPLPDYTEETLSSAILIIKEQLLPLLAQRKIRKPEEIQELFSWIQGNEMAKAAVELAVWDAFAKMEKRSLAKMIGATKESIKVGVSIGLQQNVETLLQLVNQYVDQGYERVKLKIAPNKDIQFVEAVRKSFPKLSLMADANSAYNREDFLLLKELDQYDLEMIEQPFGTKDFVDHAWLQKQLKTRICLDENIRSVKDVEQAHSIGSCRAINLKLARVGGMSSALKIAEYCALNEILVWCGGMLEAGVGRAHNIALAARNEFVFPGDISASNRFFAEDIVTPAFELNQGRLKVPTNEGIGVTLDLKVLKKYTKSTEEILLNKGWS

# see /software/alphafold/2.1.1L/alphafold/docker/Dockerfile for the basic setup
# some parts adopted from https://pythonrepo.com/repo/kuixu-alphafold

tmpdir=/scratch/$USER
inst_dir=/software/alphafold/2.1.1L

#
# install miniconda
#
pushd $tmpdir
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p $inst_dir
export PATH=$inst_dir/bin:$PATH
# don't want to polute my environment, used /software/alphafold/2.1.1L/bin/conda-init instead. has to be created
. conda-init

#
#  setup alphafold conda environment
#
conda create -n af2.1 python=3.8
conda activate af2.1
conda install -y -c nvidia          cudnn==8.0.4
conda install -y -c bioconda        hmmer hhsuite==3.3.0 kalign2
conda install -y -c conda-forge     openmm=7.5.1 pdbfixer pip

#
#  alphafold itself
#
wget https://github.com/deepmind/alphafold/archive/refs/tags/v2.1.1.tar.gz -O alphafold-2.1.1.tar.gz
tar xf alphafold-2.1.1.tar.gz
mv alphafold-2.1.1 $inst_dir/alphafold
rm alphafold-2.1.1.tar.gz 
pip3 install -r $inst_dir/alphafold/requirements.txt 
# both jax and jaxlib versions have to be explicit, will cause problems otherwise
pip3 install --upgrade jax==0.2.21 jaxlib==0.1.69+cuda111 -f https://storage.googleapis.com/jax-releases/jax_releases.html
popd

#
#  patch
#
pushd $inst_dir/lib/python3.8/site-packages
patch -p0 < $inst_dir/alphafold/docker/openmm.patch
popd

#
#  get stereo_chemical_props.txt
#
wget -P $inst_dir/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt --no-check-certificate