Disable chunking

[arvados.git] / crunch_scripts / run-command

diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index 1ff985c3379a3dd1330b963b08f586bd61f17068..d9f575ba25875ba5f86377c254ff5af757dc21a0 100755 (executable)
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -12,6 +12,9 @@ import arvados.commands.put as put
 import signal
 import stat
 import copy
+import traceback
+import pprint
+import multiprocessing
 
 os.umask(0077)
 
@@ -25,6 +28,8 @@ os.mkdir("output")
 
 os.chdir("output")
 
+outdir = os.getcwd()
+
 taskp = None
 jobp = arvados.current_job()['script_parameters']
 if len(arvados.current_task()['parameters']) > 0:
@@ -33,16 +38,19 @@ if len(arvados.current_task()['parameters']) > 0:
 links = []
 
 def sub_link(v):
-    r = os.path.basename(v)
-    os.symlink(os.path.join(os.environ['TASK_KEEPMOUNT'], v) , r)
+    r = os.path.join(outdir, os.path.basename(v))
+    os.symlink(v, r)
     links.append(r)
     return r
 
 def sub_tmpdir(v):
     return os.path.join(arvados.current_task().tmpdir, 'tmpdir')
 
+def sub_outdir(v):
+    return outdir
+
 def sub_cores(v):
-     return os.environ['CRUNCH_NODE_SLOTS']
+     return str(multiprocessing.cpu_count())
 
 def sub_jobid(v):
      return os.environ['JOB_UUID']
@@ -50,11 +58,16 @@ def sub_jobid(v):
 def sub_taskid(v):
      return os.environ['TASK_UUID']
 
+def sub_jobsrc(v):
+     return os.environ['CRUNCH_SRC']
+
 subst.default_subs["link "] = sub_link
 subst.default_subs["task.tmpdir"] = sub_tmpdir
+subst.default_subs["task.outdir"] = sub_outdir
+subst.default_subs["job.srcdir"] = sub_jobsrc
 subst.default_subs["node.cores"] = sub_cores
-subst.default_subs["job.id"] = sub_jobid
-subst.default_subs["task.id"] = sub_taskid
+subst.default_subs["job.uuid"] = sub_jobid
+subst.default_subs["task.uuid"] = sub_taskid
 
 rcode = 1
 
@@ -83,7 +96,7 @@ def expand_item(p, c):
             return r
     elif isinstance(c, list):
         return expand_list(p, c)
-    elif isinstance(c, str):
+    elif isinstance(c, str) or isinstance(c, unicode):
         return [subst.do_substitution(p, c)]
 
     return []
@@ -100,7 +113,7 @@ def get_items(p, value):
     prefix = fn[len(os.environ['TASK_KEEPMOUNT'])+1:]
     if mode != None:
         if stat.S_ISDIR(mode):
-            items = ["$(dir %s/%s)" % (prefix, l) for l in os.listdir(fn)]
+            items = ["$(dir %s/%s/)" % (prefix, l) for l in os.listdir(fn)]
         elif stat.S_ISREG(mode):
             with open(fn) as f:
                 items = [line for line in f]
@@ -108,41 +121,49 @@ def get_items(p, value):
     else:
         return None
 
-if "task.foreach" in jobp:
-    if arvados.current_task()['sequence'] == 0:
-        var = jobp["task.foreach"]
-        items = get_items(jobp, jobp[var])
-        if items != None:
-            print("run-command: parallelizing on %s with items %s" % (var, items))
-
-            for i in items:
-                params = copy.copy(jobp)
-                params[var] = i
-                arvados.api().job_tasks().create(body={
-                    'job_uuid': arvados.current_job()['uuid'],
-                    'created_by_job_task_uuid': arvados.current_task()['uuid'],
-                    'sequence': 1,
-                    'parameters': params
-                    }
-                ).execute()
-            arvados.current_task().set_output(None)
-            sys.exit(0)
-        else:
-            sys.exit(1)
-else:
-    p = jobp
+stdoutname = None
+stdoutfile = None
 
 try:
+    if "task.foreach" in jobp:
+        if arvados.current_task()['sequence'] == 0:
+            var = jobp["task.foreach"]
+            items = get_items(jobp, jobp[var])
+            print("run-command: parallelizing on %s with items %s" % (var, items))
+            if items != None:
+                for i in items:
+                    params = copy.copy(jobp)
+                    params[var] = i
+                    arvados.api().job_tasks().create(body={
+                        'job_uuid': arvados.current_job()['uuid'],
+                        'created_by_job_task_uuid': arvados.current_task()['uuid'],
+                        'sequence': 1,
+                        'parameters': params
+                        }
+                    ).execute()
+                arvados.current_task().set_output(None)
+                sys.exit(0)
+            else:
+                sys.exit(1)
+    else:
+        p = jobp
+
     cmd = expand_list(p, p["command"])
 
-    stdoutname = None
-    stdoutfile = None
     if "save.stdout" in p:
         stdoutname = subst.do_substitution(p, p["save.stdout"])
         stdoutfile = open(stdoutname, "wb")
 
     print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
 
+except Exception as e:
+    print("run-command: caught exception:")
+    traceback.print_exc(file=sys.stdout)
+    print("run-command: task parameters was:")
+    pprint.pprint(p)
+    sys.exit(1)
+
+try:
     sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile)
     sig = SigHandler()
 
@@ -161,7 +182,8 @@ try:
         print("run-command: completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
 
 except Exception as e:
-    print("run-command: caught exception: {}".format(e))
+    print("run-command: caught exception:")
+    traceback.print_exc(file=sys.stdout)
 
 # restore default signal handlers.
 signal.signal(signal.SIGINT, signal.SIG_DFL)
@@ -198,7 +220,8 @@ while not done:
         print("run-command: terminating on signal 2")
         sys.exit(2)
     except Exception as e:
-        print("run-command: caught exception: {}".format(e))
+        print("run-command: caught exception:")
+        traceback.print_exc(file=sys.stdout)
         time.sleep(5)
 
 sys.exit(rcode)