Disable chunking

[arvados.git] / crunch_scripts / run-command

diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index 4708bd8aba235a32c95c464407266ce1f271c231..d9f575ba25875ba5f86377c254ff5af757dc21a0 100755 (executable)
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -13,6 +13,8 @@ import signal
 import stat
 import copy
 import traceback
+import pprint
+import multiprocessing
 
 os.umask(0077)
 
@@ -26,6 +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:
@@ -34,16 +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']
@@ -51,11 +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
 
@@ -84,7 +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 []
@@ -101,7 +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]
@@ -147,7 +159,8 @@ try:
 except Exception as e:
     print("run-command: caught exception:")
     traceback.print_exc(file=sys.stdout)
-    print("run-command: parameters is %s" % p)
+    print("run-command: task parameters was:")
+    pprint.pprint(p)
     sys.exit(1)
 
 try: