Final updates for scale test.

breaker.sh

@@ -4,14 +4,15 @@
 #SBATCH -n64
 #SBATCH -J breakup
 #SBATCH -o %x.%A_%a.out
-#SBATCH --array=1-2
+#SBATCH --array=1-5
 
+echo "Starting $SLURM_JOB_NAME-$SLURM_ARRAY_TASK_ID at" `date`
 source /apps/dock_env/env.sh
 
 export OMP_NUM_THREADS=1
 
 DIR=/apps/launchad
 cd /dev/shm
-srun -n64 -N1 --exclusive \
-     $DIR/loadem.py ccddc-controller $SLURM_JOB_NAME
+srun -n64 -N1 $DIR/loadem.py ccddc-controller $SLURM_JOB_NAME
 
+echo "Completed $SLURM_JOB_NAME-$SLURM_ARRAY_TASK_ID at" `date`

create_inp.py

 #!/usr/bin/env python3
 
+# Note: we need to prune the metadata on the ligands
+# down to the stuff from ROOT .. TER
+
+import re
 import pandas as pd
 
+expr = re.compile('ROOT\n.*?\nTER\n', re.DOTALL)
+# essentially we have to strip all 'MODEL', 'USER' and 'ENDMDL' lines
+
+def fix(s):
+    #return s
+    s = s.replace('\r', '')
+    m = expr.search(s)
+    if m is not None:
+        return m[0]
+    return s[s.index("ROOT"):]
+
 def main(argv):
     assert len(argv) == 2, "Usage: %s <ligs.pq>"
 
     df = pd.read_parquet(argv[1])
     for lig in df.itertuples():
-        fname = lig.name + '.pdbqt'
+        fname = lig[0] + '.pdbqt'
         with open(fname, "w") as f:
-            f.write(lig.pdbqt)
-        print( "%s\n%s"%(lig.name, fname) )
+            f.write( fix(lig[1]) )
+        print( "%s\n%s"%(lig[0], fname) )
 
 if __name__=="__main__":
     import sys

docker.sh

@@ -5,14 +5,15 @@
 #SBATCH --gres gpu:1
 #SBATCH -J dock
 #SBATCH -o %x.%A_%a.out
-#SBATCH --array=1-2
+#SBATCH --array=1-1000
 
+echo "Starting $SLURM_JOB_NAME-$SLURM_ARRAY_TASK_ID at" `date`
 source /apps/dock_env/env.sh
 
-export OMP_NUM_THREADS=2
-
+export OMP_NUM_THREADS=1
 DIR=/apps/launchad
 cd /dev/shm
 srun -n1 -N1 --gres=gpu:1 --cpus-per-task=2 --exclusive \
      $DIR/loadem.py ccddc-controller $SLURM_JOB_NAME
 
+echo "Completed $SLURM_JOB_NAME-$SLURM_ARRAY_TASK_ID at" `date`

helpers.py

@@ -39,9 +39,9 @@ def xml_to_energy(f):
 def grep_all(f, *keys):
     out = dict((k,[]) for k in keys)
     for line in f:
-        line = line.decode('utf8')
+        #line = line.decode('utf8')
         for k in keys:
-            if k in line:
+            if len(line) >= len(k) and line[:len(k)] == k:
                 out[k].append(line)
     return out
 
@@ -64,6 +64,7 @@ def dlg_to_confs(lines):
     en = None
     for s in lines:
         conf.append( s[8:].strip() )
+        #print(s[8:].strip())
         # DOCKED: USER    Estimated Free Energy of Binding    =  -7.85 kcal/mol
         if "Estimated Free Energy of Binding" in s:
             tok = s.replace('=','').split()

loadem.py

@@ -10,8 +10,7 @@ rules = yaml.safe_load(open(base / 'rules.yaml'))
 bucket = 'gs://ccddc'
 
 test   = False
-testone = False
-hopper = False
+hopper = True
 
 conn_retries = 0
 
@@ -54,12 +53,20 @@ def get_item(host, db, assigned):
         return item
     return item.decode('utf8')
 
+def gsutil(cmd):
+    args = ["gsutil", "-o", "GSUtil:parallel_process_count=1",
+                      "-o", "GSUtil:parallel_thread_count=1",
+                      "-o", "GSUtil:state_dir=%s"%str(base / "gsutil")
+           ] + cmd
+    return subprocess.call( args )
+
 def copyin(name, bucket = bucket, static=False):
     base = PurePosixPath(name).name
-    static = base[-4:] == '.tgz' # hack for tgz
+    static = (base[-4:] == '.tgz') # hack for tgz
     if static and Path(base).is_file():
+        print("Skipping cached input %s"%base)
         return
-    ret = subprocess.call( ["gsutil", "cp", bucket + '/' + name, base] )
+    ret = gsutil( ["cp", bucket + '/' + name, base] )
     if ret: return ret
     if base[-4:] == '.tgz':
         ret = subprocess.call("tar xzf {0} && echo >{0}".format(base), shell=True)
@@ -68,14 +75,15 @@ def copyin(name, bucket = bucket, static=False):
 
 def moveout(name, bucket = bucket):
     if name[-1] == '/': # move whole directory
-        return subprocess.call( ["gsutil", "mv", name+"*", bucket + '/' + name] )
+        return gsutil( ["-m", "cp", name+"*", bucket + '/' + name] )
     loc = PurePosixPath(name).name
-    return subprocess.call( ["gsutil", "mv", loc, bucket + '/' + name] )
+    return gsutil( ["mv", loc, bucket + '/' + name] )
 
 def cleanup(job):
     for inp in job['inp'] + job['out']:
-        if inp[:-4] == ".tgz": continue
-        subprocess.call( ["rm", "-fr", inp.format(**job)] )
+        loc = PurePosixPath(inp.format(**job)).name
+        if loc[-4:] == ".tgz": continue
+        subprocess.call( ["rm", "-fr", loc] )
 
 def run_job(job, item):
     for p,x in zip(job['params'], item.split()):
@@ -103,10 +111,25 @@ def requeue(assigned, host, db):
             if item is None:
                 break
             r.smove(assigned, 'ready', item)
+            print("%s %s re-queued %s."%(stamp(), assigned, item))
         else:
             raise IndexError("More than 10 items assigned to %s!"%assigned)
     run_redis(run, host, db)
 
+# Apparently, we need to get some things sorted first.
+def setup(rank):
+    print("%s Rank %s starting."%(stamp(),rank))
+    if Path(rank).exists():
+        subprocess.call( ["rm", "-fr", rank] )
+    os.mkdir(rank)
+    os.chdir(rank)
+    os.mkdir("gsutil")
+    import resource
+    s,h = resource.getrlimit(resource.RLIMIT_NPROC)
+    resource.setrlimit(resource.RLIMIT_NPROC, (h,h))
+    s,h = resource.getrlimit(resource.RLIMIT_NOFILE)
+    resource.setrlimit(resource.RLIMIT_NOFILE, (h,h))
+
 # usually run as:
 #   loadem.py localhost $SLURM_JOB_ID $SLURM_ARRAY_TASK_ID
 def main(argv):
@@ -125,11 +148,7 @@ def main(argv):
     except KeyError:
         pass
 
-    print("%s Rank %s starting."%(stamp(),rank))
-    if Path(rank).exists():
-        subprocess.call( ["rm", "-fr", rank] )
-    os.mkdir(rank)
-    os.chdir(rank)
+    setup(rank)
 
     job = rules[jobname]
     db = int(job['db']) # assoc. redis db
@@ -174,8 +193,6 @@ def main(argv):
             consecutive_errors = 0
 
         n += 1
-        if testone:
-            break
 
     run_redis(lambda r: r.srem('hosts', assigned), host, db)
     print("%s Rank %s completed (%d items processed, "

mk_done.sh

-# create the 'done' file listing completed decishards
-find /gpfs/alpine/world-shared/bif128/docked/ -name 'p*.tgz' | sed -n -e 's/.*\/p\([0-9]*\)\.\([0-9]*\)\.tgz/\1 \2/p' >done

requeue.py

@@ -8,20 +8,37 @@ def get_rdb(host, db):
     import redis
     return redis.Redis(host=host, port=6379, password="Z1908840168_2_T1", db=db)
 
-def main(argv):
-    assert len(argv) == 3, "Usage: %s <server name> <db>"
-    r = get_rdb(argv[1], int(argv[2]))
-
-    todo = r.scard('errors')
+def redo_key(r, key):
     k = 0
     while True:
-        sh = r.spop('errors')
+        sh = r.spop(key)
         if sh is None:
             break
         k += r.sadd('ready', sh)
+    return k
+
+def main(argv):
+    assigned = False
+    if len(argv) >= 2 and argv[1] == "-a":
+        assigned = True
+        del argv[1]
+    assert len(argv) == 3, "Usage: %s [-a] <server name> <db>"
+    r = get_rdb(argv[1], int(argv[2]))
+
+    todo = r.scard('errors')
+    k = redo_key(r, 'errors')
 
     print("%d/%d items requeued"%(k,todo))
 
+    if not assigned:
+        return 0
+
+    k = 0
+    for srv in r.smembers('hosts'):
+        k += redo_key(r, srv)
+        r.srem('hosts', srv)
+    print("%d in-progress elements requeued"%(k))
+
 if __name__=="__main__":
     import sys
     main(sys.argv)

rules.yaml

@@ -9,15 +9,17 @@ dock:
        - ligs/{n}.pq
    script: |
       export OMP_NUM_THREADS=2
-      version="dwork v1.0"
-      log() {{ echo $(date +"%F %H:%M:%S.%N") "($version) {r}_docked/{n} $*" }}
-      log started
-      ls *{r}*.fld >filelist
+      ls {r}.maps.fld >filelist
       /apps/launchad/create_inp.py {n}.pq >>filelist
       rm {n}.pq
-      log completed file list
-      autodock_gpu_64wi -filelist filelist -nrun 20 -autostop 1 -nev 3000000 >/dev/null
+      AD=`which autodock_gpu_64wi`
+      #AD=/apps/launchad/autodock-Aug28
+      $AD -filelist filelist \
+        -nrun 20 -autostop 1 -nev 3000000 >/dev/null
       /apps/launchad/package_out.py filelist {n}.pq
+      rm -f *_*.pdbqt
+      rm -f *.xml
+      rm -f *.dlg
 
 # Re-score ligand/receptor conf.
 rescore:
@@ -42,3 +44,22 @@ breakup:
        mkdir -p ligs
        /apps/launchad/breakup.py -n 512 $((1+{n}*512)) docked.{n}.parquet ligs/%s.pq
 
+dock_test:
+   queue: dock
+   db: 4
+   params: [r, n]
+   out: [ "{r}_docked/{n}.pq" ]
+   inp:
+       - targets/{r}.tgz # note: untarring is automatic
+       - ligs/{n}.pq
+   script: |
+      export OMP_NUM_THREADS=2
+      ls {r}.maps.fld >filelist
+      /apps/launchad/create_inp.py {n}.pq >>filelist
+      rm {n}.pq
+      autodock_gpu_64wi -filelist filelist \
+        -nrun 20 -autostop 1 -nev 3000000 >/dev/null
+      /apps/launchad/package_out.py filelist {n}.pq
+      rm -f *_*.pdbqt
+      rm -f *.xml
+      rm -f *.dlg