Changed to 6WQF structure.

loadem.py

@@ -6,12 +6,12 @@ from datetime import datetime
 
 test = False
 testone = False
-hopper = False
+hopper = True
 
 conn_retries = 0
 
 def stamp():
-    return datetime.now().strftime("%Y-%m-%d %H:%M:%S.%f") + " v1.0"
+    return datetime.now().strftime("%Y-%m-%d %H:%M:%S.%f") + " v1.1"
 
 def run_redis(host, fn):
     global conn_retries
@@ -49,7 +49,7 @@ def get_shard(host):
         return shard
     return shard.decode('utf8')
 
-out_pre = '/gpfs/alpine/world-shared/bif128/docked'
+out_pre = '/gpfs/alpine/world-shared/bif128/6WQF_docked'
 
 def main(argv):
     global conn_retries
@@ -60,6 +60,7 @@ def main(argv):
     username = os.environ['USER']
     jobid = os.environ['LSB_JOBID']
     ret = subprocess.call("mkdir -p %s/logs/%s"%(out_pre,jobid), shell=True)
+    ret = subprocess.call("rm -fr /mnt/bb/%s/%d"%(username, rank), shell=True)
     ofile = open('%s/logs/%s/rank%04x.log'%(out_pre,jobid,rank), "w")
 
     time.sleep(rank*0.0001) # 10k connections per second at startup

run_ad.sh

@@ -9,7 +9,7 @@
 
 export OMP_NUM_THREADS=7
 set -e
-version="run_ad.sh v1.0"
+version="run_ad.sh v1.1"
 
 if [ $# -ne 2 ]; then
     echo "Usage: $0 shard_name shard_segment"
@@ -23,14 +23,14 @@ if [ ! -s "$sfile" ]; then
     exit 1
 fi
 
-pfile=/gpfs/alpine/world-shared/bif128/final_Mpro_pdbqt_maps_for_1B.tgz
+pfile=/gpfs/alpine/world-shared/bif128/6WQF_maps_Josh.tgz
 if [ ! -s $pfile ]; then
     echo "Missing $pfile"
     exit 1
 fi
 
 HOST=`hostname`
-OUT_DIR=/gpfs/alpine/world-shared/bif128/docked/$LSB_JOBID/$HOST
+OUT_DIR=/gpfs/alpine/world-shared/bif128/6WQF_docked/$LSB_JOBID/$HOST
 mkdir -p $OUT_DIR
 
 log() {
@@ -55,7 +55,7 @@ if [ ! -s `basename $sfile` ]; then
     # final_Mpro_pdbqt_maps_for_1B.tgz
     # final_MPro_pdbqt_maps_for_1B
     # ligands
-    mv final_MPro_pdbqt_maps_for_1B/* .
+    [ -d final_MPro_pdbqt_maps_for_1B ] && mv final_MPro_pdbqt_maps_for_1B/* .
     ls ligands/* >liglist
     ls -1 ligands | cut -f 1 -d '.' >lignames
     log completed copyin

run_docking.lsf

-#BSUB -nnodes 90
-#BSUB -W 5:00
+#BSUB -nnodes 10
+#BSUB -W 1:20
 #BSUB -q batch
 #BSUB -P BIF128
-#BSUB -J ADv1.0
+#BSUB -J ADv1.1
 #BSUB -o %J.out
 #BSUB -alloc_flags "NVME"
 
@@ -10,7 +10,7 @@ source /ccs/proj/bif128/venvs/env.sh
 PROJ=/gpfs/alpine/bif128/proj-shared/redis
 gpus=$(( (LSB_MAX_NUM_PROCESSORS-1)/7 ))
 
-echo "Starting $((gpus/6)) node run of ADv1.0 at " `date`
+echo "Starting $((gpus/6)) node run of ADv1.1 at " `date`
 
 [ -s $PROJ/shards.rdb ]
 REMAKE=$?
@@ -27,6 +27,7 @@ for((i=0;i<120;i++)); do
   [ $? -eq 0 ] && break
   sleep 1
 done
+query set hopper $((gpus*2))
 
 echo "$memb initial members at " `date`
 

shards.conf

@@ -320,7 +320,7 @@ rdbcompression yes
 rdbchecksum yes
 
 # The filename where to dump the DB
-dbfilename shards.rdb
+dbfilename shards_6WQF.rdb
 
 # Remove RDB files used by replication in instances without persistence
 # enabled. By default this option is disabled, however there are environments