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From Anirudh Perugu <anirudh.per...@stonybrook.edu>
Subject Settings : number of workers, heap size. jps showing java tasks even after killing application.
Date Sat, 19 Mar 2016 22:56:47 GMT
Hello All,

I am a giraph newbie, so kindly bear with me. I am trying to run BFS on a
graph which has : 28048 edges and 786 nodes.

*Here is my Setup :*
Single Node Cluster, 8GB RAM, 4 Cores, Apache Yarn 2.7.2, Giraph 1.2.0, my
single machine has everything(yarn+giraph) running on it.

*1. How many workers can I have?*
I ask this because my giraph job runs fine with settings :* -w 1 -ca
giraph.SplitMasterWorker=false*

"Testing Results Table"

*no. of workers | maximum no. of containers used | time taken for
completion*
1                          3 (as seen on the UI)                         0
min 50 secs
2                          4
                                                    1 min 18 secs
3                          4
          Long Running Job. I think it times out after 20 minutes.

for 3 workers, this is the log :


*INFO server.PrepRequestProcessor: Got user-level KeeperException when
processing sessionid:0x153910879aa0000 type:create cxid:0x1 zxid:0x2
txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0004/_masterElectionDir
Error:KeeperErrorCode = NoNode for
/_hadoopBsp/giraph_yarn_application_1458425066569_0004/_masterElectionDir *
So, this fails due to a reason I still haven't figured out, can you answer
this ?

Finally, leads me to asking how many workers can I have if I have 4 cores
on my machine? Are # of cores and # of workers related?


*2. How do I use the setting : giraph.yarn.task.heap.mb=x? I set x to 2048
but my job runs indefinitely(hangs up). Works great with default setting of
1024.*


*Job takes forever when x=2048, userlogs say :*
6/03/19 18:05:36 INFO zookeeper.ZooKeeper: Client
environment:java.library.path=/home//Library/Java/Extensions:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java:.
16/03/19 18:05:36 INFO zookeeper.ZooKeeper: Client
environment:java.io.tmpdir=/var/folders/s4/n58qlsh97t11vkmhysts8k680000gn/T/
16/03/19 18:05:36 INFO zookeeper.ZooKeeper: Client
environment:java.compiler=<NA>
16/03/19 18:05:36 INFO zookeeper.ZooKeeper: Client environment:os.name=Mac
OS X
16/03/19 18:05:36 INFO zookeeper.ZooKeeper: Client
environment:os.arch=x86_64
16/03/19 18:05:36 INFO zookeeper.ZooKeeper: Client
environment:os.version=10.11.3
16/03/19 18:05:36 INFO zookeeper.ZooKeeper: Client environment:user.name
=Anirudh
16/03/19 18:05:36 INFO zookeeper.ZooKeeper: Client
environment:user.home=/Users/Anirudh
16/03/19 18:05:36 INFO zookeeper.ZooKeeper: Client
environment:user.dir=/private/tmp/hadoop-Anirudh/nm-local-dir/usercache/Anirudh/appcache/application_1458425066569_0001/container_1458425066569_0001_01_000002
16/03/19 18:05:36 INFO zookeeper.ZooKeeper: Initiating client connection,
connectString=172.24.18.199:22181 sessionTimeout=60000
watcher=org.apache.giraph.master.BspServiceMaster@4097cac
16/03/19 18:05:36 INFO zookeeper.ClientCnxn: Opening socket connection to
server 172.24.18.199/172.24.18.199:22181. Will not attempt to authenticate
using SASL (unknown error)
16/03/19 18:05:36 INFO server.NIOServerCnxnFactory: Accepted socket
connection from /172.24.18.199:61815
16/03/19 18:05:36 INFO zookeeper.ClientCnxn: Socket connection established
to 172.24.18.199/172.24.18.199:22181, initiating session
16/03/19 18:05:36 INFO server.ZooKeeperServer: Client attempting to
establish new session at /172.24.18.199:61815
16/03/19 18:05:36 INFO persistence.FileTxnLog: Creating new log file: log.1
16/03/19 18:05:36 INFO server.ZooKeeperServer: Established session
0x15390e97a2a0000 with negotiated timeout 600000 for client /
172.24.18.199:61815
16/03/19 18:05:36 INFO zookeeper.ClientCnxn: Session establishment complete
on server 172.24.18.199/172.24.18.199:22181, sessionid = 0x15390e97a2a0000,
negotiated timeout = 600000
16/03/19 18:05:36 INFO bsp.BspService: process: Asynchronous connection
complete.
16/03/19 18:05:36 INFO yarn.GiraphYarnTask: [STATUS: task-0]
MASTER_ZOOKEEPER_ONLY starting...
16/03/19 18:05:36 INFO graph.GraphTaskManager: map: No need to do anything
when not a worker
16/03/19 18:05:36 INFO graph.GraphTaskManager: cleanup: Starting for
MASTER_ZOOKEEPER_ONLY
16/03/19 18:05:36 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x1 zxid:0x2 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_masterElectionDir
Error:KeeperErrorCode = NoNode for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_masterElectionDir
16/03/19 18:05:36 INFO master.BspServiceMaster: becomeMaster: First child
is
'/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_masterElectionDir/172.24.18.199_00000000000'
and my bid is
'/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_masterElectionDir/172.24.18.199_00000000000'
16/03/19 18:05:36 INFO netty.NettyServer: NettyServer: Using execution
group with 8 threads for requestFrameDecoder.
16/03/19 18:05:36 INFO Configuration.deprecation: mapred.map.tasks is
deprecated. Instead, use mapreduce.job.maps
16/03/19 18:05:36 INFO netty.NettyServer: start: Started server
communication server: /172.24.18.199:30000 with up to 16 threads on bind
attempt 0 with sendBufferSize = 32768 receiveBufferSize = 524288
16/03/19 18:05:36 INFO netty.NettyClient: NettyClient: Using execution
handler with 8 threads after request-encoder.
16/03/19 18:05:36 INFO master.BspServiceMaster: becomeMaster: I am now the
master!
16/03/19 18:05:36 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0xe zxid:0x9 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0
Error:KeeperErrorCode = NoNode for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0
16/03/19 18:05:36 INFO bsp.BspService: process: applicationAttemptChanged
signaled
16/03/19 18:05:36 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x16 zxid:0xc txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1
Error:KeeperErrorCode = NoNode for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1
16/03/19 18:05:36 WARN bsp.BspService: process: Unknown and unprocessed
event
(path=/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir,
type=NodeChildrenChanged, state=SyncConnected)
16/03/19 18:05:36 INFO yarn.GiraphYarnTask: [STATUS: task-0]
MASTER_ZOOKEEPER_ONLY checkWorkers: Only found 0 responses of 1 needed to
start superstep -1
16/03/19 18:06:06 INFO master.BspServiceMaster: checkWorkers: Only found 0
responses of 1 needed to start superstep -1.  Reporting every 30000 msecs,
569971 more msecs left before giving up.
16/03/19 18:06:06 INFO master.BspServiceMaster:
logMissingWorkersOnSuperstep: No response from partition 1 (could be master)
16/03/19 18:06:06 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x22 zxid:0x10 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerHealthyDir
Error:KeeperErrorCode = NodeExists for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerHealthyDir
16/03/19 18:06:06 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x23 zxid:0x11 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerUnhealthyDir
Error:KeeperErrorCode = NodeExists for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerUnhealthyDir
16/03/19 18:06:06 INFO yarn.GiraphYarnTask: [STATUS: task-0]
MASTER_ZOOKEEPER_ONLY checkWorkers: Only found 0 responses of 1 needed to
start superstep -1
16/03/19 18:06:36 INFO master.BspServiceMaster: checkWorkers: Only found 0
responses of 1 needed to start superstep -1.  Reporting every 30000 msecs,
539950 more msecs left before giving up.
16/03/19 18:06:36 INFO master.BspServiceMaster:
logMissingWorkersOnSuperstep: No response from partition 1 (could be master)
16/03/19 18:06:36 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x26 zxid:0x12 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerHealthyDir
Error:KeeperErrorCode = NodeExists for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerHealthyDir
16/03/19 18:06:36 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x27 zxid:0x13 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerUnhealthyDir
Error:KeeperErrorCode = NodeExists for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerUnhealthyDir
16/03/19 18:06:36 INFO yarn.GiraphYarnTask: [STATUS: task-0]
MASTER_ZOOKEEPER_ONLY checkWorkers: Only found 0 responses of 1 needed to
start superstep -1
16/03/19 18:07:06 INFO master.BspServiceMaster: checkWorkers: Only found 0
responses of 1 needed to start superstep -1.  Reporting every 30000 msecs,
509938 more msecs left before giving up.
16/03/19 18:07:06 INFO master.BspServiceMaster:
logMissingWorkersOnSuperstep: No response from partition 1 (could be master)
16/03/19 18:07:06 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x2a zxid:0x14 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerHealthyDir
Error:KeeperErrorCode = NodeExists for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerHealthyDir
16/03/19 18:07:06 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x2b zxid:0x15 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerUnhealthyDir
Error:KeeperErrorCode = NodeExists for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerUnhealthyDir
16/03/19 18:07:06 INFO yarn.GiraphYarnTask: [STATUS: task-0]
MASTER_ZOOKEEPER_ONLY checkWorkers: Only found 0 responses of 1 needed to
start superstep -1
16/03/19 18:07:36 INFO master.BspServiceMaster: checkWorkers: Only found 0
responses of 1 needed to start superstep -1.  Reporting every 30000 msecs,
479927 more msecs left before giving up.
16/03/19 18:07:36 INFO master.BspServiceMaster:
logMissingWorkersOnSuperstep: No response from partition 1 (could be master)
16/03/19 18:07:36 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x2e zxid:0x16 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerHealthyDir
Error:KeeperErrorCode = NodeExists for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerHealthyDir
16/03/19 18:07:36 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x2f zxid:0x17 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerUnhealthyDir
Error:KeeperErrorCode = NodeExists for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerUnhealthyDir
16/03/19 18:07:36 INFO yarn.GiraphYarnTask: [STATUS: task-0]
MASTER_ZOOKEEPER_ONLY checkWorkers: Only found 0 responses of 1 needed to
start superstep -1
16/03/19 18:08:06 INFO master.BspServiceMaster: checkWorkers: Only found 0
responses of 1 needed to start superstep -1.  Reporting every 30000 msecs,
449916 more msecs left before giving up.
16/03/19 18:08:06 INFO master.BspServiceMaster:
logMissingWorkersOnSuperstep: No response from partition 1 (could be master)
16/03/19 18:08:06 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x32 zxid:0x18 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerHealthyDir
Error:KeeperErrorCode = NodeExists for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerHealthyDir
16/03/19 18:08:06 INFO server.PrepRequestProcessor: Got user-level
KeeperException when processing sessionid:0x15390e97a2a0000 type:create
cxid:0x33 zxid:0x19 txntype:-1 reqpath:n/a Error
Path:/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerUnhealthyDir
Error:KeeperErrorCode = NodeExists for
/_hadoopBsp/giraph_yarn_application_1458425066569_0001/_applicationAttemptsDir/0/_superstepDir/-1/_workerUnhealthyDir
16/03/19 18:08:06 INFO yarn.GiraphYarnTask: [STATUS: task-0]
MASTER_ZOOKEEPER_ONLY checkWorkers: Only found 0 responses of 1 needed to
start superstep -1
16/03/19 18:08:36 INFO master.BspServiceMaster: checkWorkers: Only found 0
responses of 1 needed to start superstep -1.  Reporting every 30000 msecs,
419894 more msecs left before giving up.
----------------------------------------End of
Logs--------------------------------------------------------

Does this mean that it required 1 worker to start the -1th superstep but
did not find any or is it something else?
- If that is the case, I can confirm that I have a node (the only) which is
healthy.

Finally, how do I give more memory to the giraph job?


*3. When I kill a long running job by either killing the application on GUI
or by pressing control+c, why does my jps still show these :*
anirudh:hadoop-2.7.2 Anirudh$ jps


*9009 GiraphYarnTask8962 GiraphApplicationMaster*9267 Jps
8725 NameNode
8855 NodeManager
8764 DataNode
8815 ResourceManager

Aren't they supposed to be killed as well? I ask this because if I run a
new job at this time, the job is forever in ACCEPTED state. Only after
those are killed, a fresh job does go to completion (my observation).

Alright then, I am hoping for a reply which will address these issues.

Thanks
Anirudh

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