From de21d05b148028ac80ed80e00c300db3fb62642e Mon Sep 17 00:00:00 2001
From: Spencer Bliven <spencer.bliven@psi.ch>
Date: Fri, 8 Oct 2021 15:19:17 +0200
Subject: [PATCH] Add submission scripts

---
 MX/alphafold/bin/submit.sh        | 91 +++++++++++++++++++++++++++++++
 MX/alphafold/bin/submit_merlin.sh | 23 ++++++++
 MX/alphafold/bin/submit_ra.sh     | 30 ++++++++++
 3 files changed, 144 insertions(+)
 create mode 100755 MX/alphafold/bin/submit.sh
 create mode 100755 MX/alphafold/bin/submit_merlin.sh
 create mode 100755 MX/alphafold/bin/submit_ra.sh

diff --git a/MX/alphafold/bin/submit.sh b/MX/alphafold/bin/submit.sh
new file mode 100755
index 0000000..de5e3c5
--- /dev/null
+++ b/MX/alphafold/bin/submit.sh
@@ -0,0 +1,91 @@
+#!/bin/bash
+
+# Generic alphafold submission script.
+# Set the ALPHAFOLD_DATA variable before running.
+# Usage: sbatch [slurm_opts] $ALPHAFOLD_DIR/bin/submit.sh fasta_file [max_template_date]
+#
+# Output will be in the same directory as the fasta_file.
+# Slurm logs will be in the current directory.
+#
+# 2021-08-09 Spencer Bliven, D.Ozerov
+#
+
+# Bash strict mode
+set -euo pipefail
+IFS=$'\n\t'
+
+usage () {
+    echo "Usage: sbatch [slurm_opts] \$ALPHAFOLD_DIR/bin/submit_merlin.sh fasta_file [max_template_date]"
+}
+
+# Parse parameters
+if [ "$#" -lt 1 ]
+then
+    echo "No fasta_file name" >&2
+    usage >&2
+    exit
+fi
+
+FASTA_FILE=`readlink -f $1`
+if [ ! -e ${FASTA_FILE} ] || [ "$FASTA_FILE" == "" ]
+then
+    echo "${FASTA_FILE} is not reachable (input argument was $1)"
+    exit
+fi
+
+DIR_QUERY=`dirname ${FASTA_FILE}`
+LOG="${DIR_QUERY}/alphafold.out"
+
+if [ "$#" -ge 2 ]
+then
+    MAX_TEMPLATE_DATE=$2
+else
+    MAX_TEMPLATE_DATE=$(date '+%Y-%m-%d')
+fi
+
+date     > "$LOG"
+hostname >> "$LOG"
+
+set +u # Allow unset variables in activate commands
+module purge
+module use MX unstable
+module load anaconda/2019.07 cuda/11.0.3 alphafold/2.0.0-b88f8da 2>> "$LOG"
+conda activate "${ALPHAFOLD_ENV:?"Error: ALPHAFOLD_ENV not set. Try 'module use MX unstable; module load alphafold'"}"
+set -u
+
+# Check the module loaded correctly
+if ! [ -d "${ALPHAFOLD_HOME}" ]; then
+    echo "Error: $ALPHAFOLD_HOME not available" >&2
+    exit 1
+fi
+
+# Data dir
+if ! [ -d "${ALPHAFOLD_DATA:?Set ALPHAFOLD_DATA before running}" ]; then
+    echo "Error: ALPHAFOLD_DATA directory not available ($ALPHAFOLD_DATA)" >&2
+    exit 1
+fi
+
+echo "GPUs: ${CUDA_VISIBLE_DEVICES:-None}" >> "$LOG"
+echo "Detecting GPUs with Tensorflow:" >> "$LOG"
+python -c 'import tensorflow as tf; tf.compat.v1.Session(config=tf.compat.v1.ConfigProto(log_device_placement=True))' 2>&1 |
+    sed -rn 's/^.* (Created TensorFlow device.*)$/\1/p' >> "$LOG"
+echo >> "$LOG"
+
+echo "Running alphafold from $PWD for fasta sequence : " >> "$LOG"
+cat ${FASTA_FILE} >> "$LOG"
+echo "and max_template_date : ${MAX_TEMPLATE_DATE} " >> "$LOG"
+echo >> "$LOG"
+
+
+cd "${ALPHAFOLD_HOME}"
+CMD=("./run_alphafold.sh" -p full_dbs -d "${ALPHAFOLD_DATA}" -o "${DIR_QUERY}" -m model_1,model_2,model_3,model_4,model_5 -f "${FASTA_FILE}" -t "${MAX_TEMPLATE_DATE}")
+if [ -z "${CUDA_VISIBLE_DEVICES:-}" ]
+then
+    CMD+=(-g false)
+else
+    CMD+=(-a "$CUDA_VISIBLE_DEVICES")
+fi
+
+echo "Run: ${CMD[@]}" >> "$LOG"
+echo >> "$LOG"
+( ( time "${CMD[@]}" ) 2>&1 ) >> "$LOG"
diff --git a/MX/alphafold/bin/submit_merlin.sh b/MX/alphafold/bin/submit_merlin.sh
new file mode 100755
index 0000000..2df1348
--- /dev/null
+++ b/MX/alphafold/bin/submit_merlin.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+#SBATCH -p gpu
+#SBATCH -J alphafold
+#SBATCH -M gmerlin6
+#SBATCH --gpus=1
+#SBATCH -n 1
+#SBATCH -c 10
+
+# Alphafold submission script for the merlin cluster
+# Usage: sbatch [slurm_opts] $ALPHAFOLD_DIR/bin/submit_merlin.sh fasta_file [max_template_date]
+#
+# Output will be in the same directory as the fasta_file.
+# Slurm logs will be in the current directory.
+#
+# 2021-08-09 Spencer Bliven, D.Ozerov
+#
+
+export ALPHAFOLD_DATA=/data/project/bio/shared/alphafold
+module purge
+module use MX unstable
+module load anaconda/2019.07 cuda/11.0.3 alphafold/2.0.0-b88f8da
+
+exec "${ALPHAFOLD_DIR:?Error loading module}/bin/submit.sh" "$@"
diff --git a/MX/alphafold/bin/submit_ra.sh b/MX/alphafold/bin/submit_ra.sh
new file mode 100755
index 0000000..3b8bb22
--- /dev/null
+++ b/MX/alphafold/bin/submit_ra.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+#SBATCH -p day
+#SBATCH -t 1-00:00:00
+#SBATCH -J alphafold
+#SBATCH -n 1
+#SBATCH -c 10
+
+# Alphafold submission script for the ra cluster
+# Usage: sbatch [slurm_opts] $ALPHAFOLD_DIR/bin/submit_merlin.sh fasta_file [max_template_date]
+#
+# Output will be in the same directory as the fasta_file.
+# Slurm logs will be in the current directory.
+#
+# 2021-08-09 Spencer Bliven, D.Ozerov
+#
+
+export ALPHAFOLD_DATA=/das/work/common/opt/alphafold/data
+
+# Need at least rc6 to see alphafold
+PMODULES_VERSION=1.0.0rc10;
+source /opt/psi/config/profile.bash;
+
+module --version
+
+module purge
+module use MX unstable Programming
+module load anaconda/2019.07 cuda/11.0.3 alphafold/2.0.0-b88f8da
+module list
+
+exec "${ALPHAFOLD_DIR:?Error loading module}/bin/submit.sh" "$@"