You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 10 Next »

Can't open lockfile

This message was received:

Event type: L1Proc.unLockRun
Event timestamp: 2017-10-30 21:57:42.474089
Spacecraft ID: -1
Target: None
Trigger name: L1-processing
Cluster size: 1
Message text: Can't open lockfile cd /r0531060188.lock.
 

Status in data monitoring pages:

The process was listed as terminated and has this java error:

org.srs.jobcontrol.JobControlException: Remote Exception performing operation
	at org.srs.jobcontrol.JobControlClient.checkException(JobControlClient.java:219)
	at org.srs.jobcontrol.JobControlClient.submit(JobControlClient.java:77)
	at org.srs.pipeline.server.process.batch.BatchProcessExecutor.run(BatchProcessExecutor.java:202)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.net.SocketTimeoutException: Read timed out
	at java.net.SocketInputStream.socketRead0(Native Method)
	at java.net.SocketInputStream.read(SocketInputStream.java:152)
	at java.net.SocketInputStream.read(SocketInputStream.java:122)
	at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)
	at java.io.BufferedInputStream.read(BufferedInputStream.java:254)
	at java.io.DataInputStream.readByte(DataInputStream.java:265)
	at sun.rmi.transport.StreamRemoteCall.executeCall(StreamRemoteCall.java:214)
	at sun.rmi.server.UnicastRef.invoke(UnicastRef.java:161)
	at java.rmi.server.RemoteObjectInvocationHandler.invokeRemoteMethod(RemoteObjectInvocationHandler.java:194)
	at java.rmi.server.RemoteObjectInvocationHandler.invoke(RemoteObjectInvocationHandler.java:148)
	at com.sun.proxy.$Proxy7.submit(Unknown Source)
	at org.srs.jobcontrol.JobControlClient.submit(JobControlClient.java:74)
	... 4 more

 

Solution:

Seems to be an NFS error.  I can't write to that directory as myself or the glast account.  Need to check on propre account/permissions

 

Handling Stuck Jobs

A stuck job usually shows up in a bjobs list as having consumed no CPU or memory, and in an UNKWN state and has been sitting around for a long time (depends on job, need more data).

The procedure is to log on as glastraw an bkill them.  As Warren explained:

You can't roll back a running job. You have to bkill them and wit for the reaper to notice that they're dead. The pipeline will automatically retry them once for L1 (0 is the default, you can ask for up to 3). If the jobs you killed were retries, then you'll have to roll them back. I've never seen a job in unknown state recover by itself.

 

Checking Host Status

Use bhosts to check the host status (although you might want to grep with the host name as the list is long).

 

Running a command directly on a Host

From Warren:

You can just immediately run a command on any batch host with lsrun. Obviously this should be used sparingly. uptime is a good cheap thing that will show you if the host is responsive and what the load is. Or check to see if a particular filesystem is causing trouble, or if some command works.

 

Failure to execute java script

(Need to update this title to exact phrase.  The system doesn't keep old messages and I forgot to write it down)

When a script gets terminated and viewing messages includes the error message "failure when executing java...(Need to get exact text next time it happens)".  This is typically an indication of a bad variable in the environment/database that the process is running it.  This bad value is typically set by the upstream process having run in some strange manner and mangling the variable.  In every case so far that I've seen, the upstream process ran twice simultaneously on two different hosts and so the two processes were overwriting each other.  This is fairly easy to identify as the output log contains all the execution output (except possibly the environment output) twice and there are two different LSF summary blocks at the end of the log.

The solution is to simply roll back the upstream process so it gets a clean execution.

 

Failure in checkRun

Check run failed and I thought at first it was a case of bad data as the process ran simultaneously on two different hosts.  However a simple rollback did not solve the problem as there was a lock left from running the mergeCalChunks upstream process.  This lock was left because of an infrastructure glitch preventing proper access to the xroot data disks.  Rerunning that process removed the lock file but checkRun still didn't work, complaining about the existence of a dontCleanUp file.  This file was actually left from the bad mergeCalChunks run.  Before deleting it we need to check that the files listed there actually exist.  This command:

for ff in $(egrep '^root' <path to>/dontCleanUp) ; do xrd.pl --where stat $ff ; done

will poll the xroot server for information on the files listed in the dontCleanUp file.

If they are all there, we are good to go and can remove the dontCleanUp file and rollback the checkRun process.  If not, we need to look further upstream in the data processing chain.

Note: the xrd.pl in the above command is found at /afs/slac.stanford.edu/g/glast/applications/xrootd/PROD/bin/xrd.pl

 

Job fails to start (stays in PEND status)

The particular event that triggered this scenario was the two deliveries of run 543796948.  The first delivery (180315009) had several recon jobs that ended up on a dead host and had to be killed.  While they were hung, the rest of the events in the run arrived in delivery 180315010 and the findChunks task was in a pending state waiting for its pre-exec command (/afs/slac/g/glast/isoc/flightOps/rhel6_gcc44/ISOC_PROD/bin/isoc run /afs/slac.stanford.edu/g/glast/ground/PipelineConfig/Level1/5.6/lockFile.py) to give it the go ahead.  After the hung recon tasks were killed, the reaper properly restarted them and the run completed and properly cleaned up after itself.  However, the findChunks task never started up.  LSF normally retries the pre-exec command regularly (every 2.5 minutes in this case - how to we check?) but had not run it in over 2 hours (again how to we check? is there a max retries?).

When this happens:

1) First try stopping and restarting the job (bstop and bresume).  This will often kickstart things and get them going again

2) If that doesn't work, just bkill the process and let the reaper resubmit it (Which is what we had to do in this case).

 

Handling a host with lots of hung jobs

This is only a partial description of handling this.  This comes up when there are a large number of jobs in an UNKWN state all on the same host.  Often, looking at the status of the host (bhosts <hostname>) will tell you it is unavailable, in which case you're probably safe.  If it is still open and accepting jobs, however, you want to prevent it from getting new batch jobs as they will just hang as well.  From Warren your options are:

Close the host.

sudo badmin -C "Witty comment" <hostname>

Which requires sudo permission which you probably don't have yet and they'll want to limit to some machine we own and we should find a box that's not my workstation to use for that.

 

Fill it up with dummy jobs.

for ii in $(seq 8) ; do bsub -q glastdataq -sp 90 -m <hostname> sleep 86400

# in bash, as glastraw

 

So probably really only one realistic option at the moment.

 

Also you should probably notify unix-admin.

 

Files missing from NFS file server

This one came up the incident reference by this thread in the opsprob mailing list: https://www-glast.stanford.edu/protected/mail/opsprob/11338.html

Basically several jobs were hung, when they were killed, they still didn't work and rolling things back made it worse.  In the end, we needed to copy the files back from xroot to NFS and restart the process.  Some questions, comments, and answers from the thread (some of these still need answers):

1) How do we know that? Is it just because the logs complain that they are not there? How do we check for their existence?

2) Where do they live to copy them from?

3) I'm assuming they need to get copied to directory that it can't find them in (root://glast-rdr.slac.stanford.edu//glast/Scratch/l1Stage/runs/542/r0542185591/e00000000000002729588/event/ in this case). Or do they go somewhere else?

4) How do we perform the copy?

See #10 below

5) I'm guessing we'll need to move/rename the existing chunkList file so a new one can be created at this point? Is this correct? (BTW the notes say we should have a section on chunkList files that no one has written yet)

6) Where do we roll back at to get everything going again? Just a general rollback on the command line? Or is there a specific task that can be rolled back to kick everything off properly again?

7) The .evt files reference by the chunkList file (in /nfs/farm/g/glast/u28/stage/180308007/r0542185591/) don't exist.

They've been moved to xroot. It really would be better if they were copied, I [Warren] don't remember why I get discouraged every time I try to make that change.

8) The directory in xroot (root://glast-rdr.slac.stanford.edu//glast/Scratch/l1Stage/runs/542/r0542185591/e00000000000002729588/event/) only contains a single evt file: r0542185591_e00000000000002729588_v246043240_event.evt.  The failed jobs are complaining about other files which are missing.

Each was moved to it's own directory.

9) In the /nfs/farm/g/glast/u41/L1/deliveries/1803 directory, there is no entry for this delivery (180308007).  The entries for 180308006 and 180308008 are there though.  Found it.  It's in the /nfs/farm/g/glast/u28/stage directory.  I looks like that gets moved over to deliveries once it's done.

10) Still can't seem to find the original evt files.

Each has a directory corresponding to the chunk number. The second-to-last component in the path you give above.

I use a command like this to generate a script to move them back to NFS:

"awk '/^\/afs.*xrdcp/{print  $1, $2, $3, $5, $4}' /nfs/farm/g/glast/u41/L1/logs/PROD/L1Proc/5.5/doRun/findChunks/160xxxxxx/515xxx/011/485xxxxxx/001xxx/694/archive/198092024/logFile.txt

Final thoughts from Warren on this particular issue:

There are some things here I don't understand, LSF is definitely screwing up and maybe the ippeline too, but:

Among the jobs that were launched after 2:30 and failed was findChunks, which had moved some of the evt files. The automatic retry moved the rest. Then some of the digi and fastMon jobs couldn't find their inputs. This was a little trickier than the usual "move them back" scenario, because their locations in xroot had to be gathered from 2 log files. So I did that and rolled back findChunks and it all looks OK to me now.

 

Throttling the Pipeline

If you ever need to limit the amount of work being done on the pipeline (like we wanted to with the LAT restart in April 2018), you can manually create throttle locks to limit the number of simultaneous runs that can be worked on at a time.  Right now the pipeline is set to allow up to 6 runs to be worked on at once.  If you want to limit that, simply create lock files in the /nfs/farm/g/glast/u41/L1/throttle directory of the form 0.lock, 1.lock, ... up to 5.lock.  The contents can be anything you want.  It is just the presence of the file that stops things from running.  Each lock file created will reduce the number of simultaneous runs by one.  Creating all six will stop the pipeline from processing anything.

 

Changing the Reaper Settings

There are some variables found on the JMX page of the pipeline that control the operation of the reaper (the process that looks for dead process, cleans them up, and restarts them).

The first is the ReaperFrequencySeconds in the Control section at the top.  This parameter controls how often the reaper actually runs.  Currently set to 60 (once per minute).

The other parameter is set on a per submission source basis.  This is the ReaperDelayMinutes parameter and is found in each of the later sections on that page.  This controls how long a process has to be dead for before the reaper kills it.  It is typically set to 60 or 120 minutes.  NOTE (from Warren): I'm not convinced that ReaperDelayMinutes actually does anything. Restarting the pipeline set both of them back to default.

 

 

  • No labels