Maxwell : alphafold 2.1.1 - docker

#!/bin/bash
#SBATCH --partition=maxgpu
#SBATCH --constraint='(A100|V100)&BS'
#SBATCH --time=0-12:00
#SBATCH --job-name=T1050
unset LD_PRELOAD
AF_outdir=/beegfs/desy/user/$USER/ALPHAFOLD2.1 /software/alphafold/2.1.1/alphafold.sh \
        --fasta_paths=/software/alphafold/2.0/T1050.fasta --max_template_date=2020-05-1
# for a multimer:
AF_preset=multimer AF_outdir=/beegfs/desy/user/$USER/ALPHAFOLD2.1 /software/alphafold/2.1.1/alphafold.sh \
        --fasta_paths=/software/alphafold/2.0/T1050-2.fasta --max_template_date=2020-05-1
exit

#!/bin/bash

# basic setup
unset LD_PRELOAD
source /etc/profile.d/modules.sh
module purge
module load maxwell cuda/11.3

# alphafold basics 
export AF_NVL=/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/software/cuda/cuda-11.3/targets/x86_64-linux/lib:/software/cuda/cuda-11.3/lib64
export PATH=/software/alphafold/2.1.1/python3.6/bin:$PATH
export PYTHONPATH=/software/alphafold/2.1.1/python3.6:$PYTHONPATH

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}

# 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}"

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"
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_docker="${AF_docker:---gpus all -u `id -u`:`id -g` --userns=host --security-opt no-new-privileges}"
export AF_mount="${AF_mount:--v /tmp:/tmp -v $HOME:$HOME -v /beegfs/desy:/beegfs/desy -v /beegfs/cssb:/beegfs/cssb -v /software:/software}"
export AF_image="${AF_image:-gitlab.desy.de:5555/frank.schluenzen/alphafold:2.1.1}"
export AF_outdir="${AF_outdir:-/tmp/alphafold}"
export AF_models="${AF_models:-model_1,model_2,model_3,model_4,model_5}"
export AF_env="${AF_env:---env TF_FORCE_UNIFIED_MEMORY=1 --env XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 --env XLA_PYTHON_CLIENT_ALLOCATOR=platform}"

cat <<EOF
AlphaFold Setup
----------------------------------------------------------------------------------------------------
AF_datadir.:  $AF_datadir
AF_docker..:  $AF_docker
AF_mount...:  $AF_mount
AF_image...:  $AF_image
AF_outdir,,:  $AF_outdir
AF_models..:  $AF_models
AF_preset..:  $AF_preset
AF_env.....:  $AF_env

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:
----------------------------------------------------------------------------------------------------
docker run $AF_docker $AF_mount --env LD_LIBRARY_PATH=$AF_NVL $AF_env $AF_image \
--output_dir=$AF_outdir --data_dir=$AF_datadir --model_preset=$AF_preset $AF_dbs "$@"


EOF

docker run $AF_docker $AF_mount --env LD_LIBRARY_PATH=$AF_NVL $AF_env $AF_image \
           --output_dir=$AF_outdir --data_dir=$AF_datadir --model_preset=$AF_preset $AF_dbs "$@"

/sbin/ldconfig.real: Can't create temporary cache file /etc/ld.so.cache~: Permission denied
I1129 11:06:20.353542 140709785240512 templates.py:857] Using precomputed obsolete pdbs /beegfs/desy/group/it/ReferenceData/alphafold/pdb_mmcif/obsolete.dat.
I1129 11:06:21.219282 140709785240512 xla_bridge.py:231] Unable to initialize backend 'tpu_driver': Not found: Unable to find driver in registry given worker: 
I1129 11:06:21.684458 140709785240512 xla_bridge.py:231] Unable to initialize backend 'tpu': Invalid argument: TpuPlatform is not available.

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