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HPS-SOFTWARE  May 2017

HPS-SOFTWARE May 2017

Subject:

Re: Test pass1 Status

From:

Rafayel Paremuzyan <[log in to unmask]>

Reply-To:

Software for the Heavy Photon Search Experiment <[log in to unmask]>

Date:

Mon, 22 May 2017 14:46:20 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (501 lines)

Hi Alessandra and all,

Yes clearly I see that pattern as well,
going to the faster machine (pumpkin1), as Maurik suggested,
recon speed increased, but 2016 recon was about x2 slower than the 2015 
recon speed.
I also tried to with -Xms=4000m -Xmx=4000m options, and without that 
options,
but I didn't notice noticeable speed improvement.

Another thing that is *concering* is I run
same jar on batch farms, centos6. and centos7, and
can't get same speed as we got during the pass0.
Note, jar is the same,  detector is the same, run number and file number 
is the same.
Difference is the time when it started to tun (Oct 19 2016 vs May 21 2017)

If someone is interested to look at job log files
The log file that I run yesterday: 
/lustre/expphy/work/hallb/hps/data/physrun2016/tpass1/logs/hps_008054.27_pass0XML.err
The log file that run on Oct 19 2016 for pass0 
/lustre/expphy/work/hallb/hps/data/physrun2016/pass0/logs/hps_008054.27_R3.9.err

I have never done profiling with java.
I know Maurik is in workshop, he might not have time to do this,
if someone else is set up doing this, it will probably be useful.

Also, I noticed /group/hps is full

Has anyone recently put some data there?

Rafo


On 05/22/2017 04:04 AM, Alessandra Filippi wrote:
> Hi Maurik, Rafo and all,
> I think that the different Java VM could impact on the absolute speed 
> comparing different machines and jar versions compiled in different 
> times... but I am running the same jar (hps-java 3.10, compiled afresh 
> at slac on rhel6-64, jvm 1.7.0) on 2015 and 2016 data, and the factor 
> ~2 of speed decrease for newer data is striking (whichever geometry 
> version).
> About garbage collection, I don't use any flag in compilation, so it 
> acts in default mode in both cases.
>
> Are 2016 data affected by more noisy hits that could extend the 
> reconstruction time over testing all different strategies, to your 
> knowledge?
> cheers
>     Alessandra
>
>
>
>
>
>
> On Sun, 21 May 2017, Maurik Holtrop wrote:
>
>> Hello Rafo,
>> One thing that probably is different between the last time we ran 
>> with the 3.8 jar and now
>> is a different version of the Java VM. It could well be that the 
>> newer version of Java is
>> not faster. Also, it is tricky to compare Endeavour with the Jlab 
>> farm computers. They are
>> probably not equivalent in speed. At UNH, Pumpkin has the more modern 
>> processors, whereas
>> Endeavour is now ~5 years old.
>>
>> Best,
>> Maurik
>>
>>       On May 21, 2017, at 6:54 AM, Rafayel Paremuzyan 
>> <[log in to unmask]> wrote:
>>
>> Hi Alessandra, Norman, all
>>
>> thank you for replay and your tests.
>>
>> I tested both 2015 and 2016 data using v4-4 detector on UNH computers.
>> I have use 3.8 JAR (the jar for 2015 pass6). 3.9 JAR (the jar for 
>> 2016 pass0 recon),
>> and the NEW jar v051717 (the newest jar tag is v051717)
>>
>> Ok, I also noticed that recon of 2015 data is faster that 2016 data.
>> Also seems the new jar is 20% slower than the 3.9 jar for 2016 data, 
>> and about 60%
>> slower for 2015 data.
>> now recon speed is about 2.55 EV/S for 2015 data, This is too slow
>> it cause more than 40h for a single file.
>>
>> Ths is summary of code speeds with different jar files
>> V4-4 Detector, UNH (endeavour), 5K events are reconstructed
>>
>> Events per second
>> Events per second
>> Events per second
>>
>> 3.8JAR (2015 recon jar)
>> 3.9JAR, 2016 pass0 recon jar
>> v051717JAR, jar vor tpass1
>> 2015 Data 5772, file 20
>> 5.07
>> 5.19
>> 3.157
>> 2016 Data file 25
>>
>> 3.11
>> 2.53
>>
>> *However* I looked into job Wall times for pass0 recon.
>> The recon speed is more than 7.4 Events/sec, which is about x3 faster 
>> than with the
>> new JAR.
>>
>> I again checked *same 3.9 jar*, which is slower again.
>> I don't know why now the code speed is so low!
>>
>>
>> Norman, I have tried the "-DdisableSvtAlignmentConstants", but it 
>> didn't work
>>
>> =================The command===============
>> java -XX:+UseSerialGC -cp hps-distribution-3.11-v051717-bin.jar
>> org.hps.evio.EvioToLcio -x 
>> /org/hps/steering/recon/PhysicsRun2016FullRecon.lcsim -r
>> -d HPS-PhysicsRun2016-v5-3-fieldmap_globalAlign -R 7796 
>> -DoutputFile=out_7796_0
>> -DdisableSvtAlignmentConstants hps_007796.evio.25 -n 10000
>>
>> ============The error backtrache============
>> 2017-05-21 00:45:39 [CONFIG] org.hps.evio.EvioToLcio parse :: using 
>> steering
>> resource /org/hps/steering/recon/PhysicsRun2016FullRecon.lcsim
>> 2017-05-21 00:45:39 [CONFIG] org.hps.evio.EvioToLcio parse :: set max 
>> events to
>> 10000
>> 2017-05-21 00:45:48 [INFO] org.hps.rundb.RunManager <init> :: 
>> ConnectionParameters {
>> database: hps_run_db_v2, hostname: hpsdb.jlab.org, password: 
>> darkphoton, port: 3306,
>> user: hpsuser }
>> 2017-05-21 00:45:48 [CONFIG] org.lcsim.job.JobControlManager 
>> addVariableDefinition
>> :: outputFile = out_7796_0
>> 2017-05-21 00:45:48 [CONFIG] org.hps.evio.EvioToLcio parse :: set 
>> steering variable:
>> outputFile=out_7796_0
>> 2017-05-21 00:45:48 [SEVERE] org.hps.evio.EvioToLcio parse :: bad 
>> variable format:
>> disableSvtAlignmentConstants
>> java.lang.IllegalArgumentException: Bad variable format:
>> disableSvtAlignmentConstants
>>         at org.hps.evio.EvioToLcio.parse(EvioToLcio.java:393)
>>         at org.hps.evio.EvioToLcio.main(EvioToLcio.java:97)
>>
>> Exception in thread "main" java.lang.IllegalArgumentException: Bad 
>> variable format:
>> disableSvtAlignmentConstants
>>         at org.hps.evio.EvioToLcio.parse(EvioToLcio.java:393)
>>         at org.hps.evio.EvioToLcio.main(EvioToLcio.java:97)
>>
>> Rafo
>>
>>
>>
>>
>>
>>
>> On 05/20/2017 06:17 AM, Alessandra Filippi wrote:
>>       Hi Rafo, all,
>>       I also noticed that the reconstruction for 2016 data is about 
>> twice as
>>       slow as compared to 2015 (whichever geometry and reconstruction
>>       version).
>>       This happens when I run the aligned geometry as well as the 
>> "current"
>>       one (v5.0), and the geometry taken from the db as well (the 
>> result is
>>       the same as v5.0). I did not make any test with v4.4, though - 
>> actually
>>       as far as svt alignment is concerned it should be the same as 
>> v5.0. Can
>>       you please try and make the same short test with the newest jar 
>> with
>>       v4.4?
>>       This happens to me both with hps-java 5.10 and 5.11 (not the most
>>       updated one).
>>
>>       I would be surprised if it could be something connected to the
>>       alignment, unless for some reason new positions and harder tracks
>>       trigger some long loops in the reconstruction. But this happens 
>> (to me)
>>       also with the
>>       standard geometry, so a check with the one used with pass0 
>> (that should
>>       however be equivalent to v5.0) could at least help to rule out, 
>> or blame
>>       on, the alignment step.
>>       Thanks, cheers
>>           Alessandra
>>
>>
>>       ps. make also sure that the correct fieldmap is called in all the
>>       compact files - you never know!
>>
>>
>>
>>       On Fri, 19 May 2017, Rafayel Paremuzyan wrote:
>>
>>             Hi All,
>>
>>             During the testing the recon for test pass1,
>>             I noticed the recon time is more than x2 longer wrt pass0
>>             recon time.
>>
>>             To demonstrate it
>>             I submit 3 simple jobs with 10K events to reconstruct, with
>>             new pass1 xml
>>             file (this has the new jar v051717, and the new detector
>>             HPS-PhysicsRun2016-v5-3-fieldmap_globalAlign),
>>             and the old pass0 xml file (pass0 jar release 3.9, and the
>>             detector
>>             HPS-PhysicsRun2016-Nominal-v4-4-fieldmap)
>>
>>             Below is a printout from the jobs with a new JAR, v051717,
>>             the average time
>>             for 1000 events is more than 7 minutes
>>             ===================== LOG from the v051717 JAR
>>             ==============================
>>             2017-05-19 09:36:51 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10614074 with sequence 0
>>             2017-05-19 09:43:13 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10615074 with sequence 1000
>>             2017-05-19 09:49:18 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10616074 with sequence 2000
>>             2017-05-19 09:55:54 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10617074 with sequence 3000
>>             2017-05-19 10:02:55 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10618074 with sequence 4000
>>             2017-05-19 10:09:57 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10619074 with sequence 5000
>>             2017-05-19 10:16:13 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10620074 with sequence 6000
>>             2017-05-19 10:25:20 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10621074 with sequence 7000
>>             2017-05-19 10:32:56 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10622074 with sequence 8000
>>             2017-05-19 10:36:19 [WARNING]
>>             org.hps.recon.tracking.TrackerReconDriver
>>             process :: Discarding track with bad HelicalTrackHit
>>             (correction distance
>>             0.000000, chisq penalty 0.000000)
>>             2017-05-19 10:42:03 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10623074 with sequence 9000
>>             2017-05-19 10:47:44 [INFO] org.hps.evio.EvioToLcio run ::
>>             maxEvents 10000
>>             was reached
>>             2017-05-19 10:47:44 [INFO] org.lcsim.job.EventMarkerDriver
>>             endOfData ::
>>             10000 events processed in job.
>>             2017-05-19 10:47:44 [INFO] org.hps.evio.EvioToLcio run ::
>>             Job finished
>>             successfully!
>>
>>
>>             And below is the Job log info from the pass0 jar. The
>>             average time for 1000
>>             events is less than 3 minutes
>>             ===================== LOG from the 3.9 release JAR
>>             ==============================
>>             2017-05-19 13:19:46 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10614074 with sequence 0
>>             2017-05-19 13:23:36 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10615074 with sequence 1000
>>             2017-05-19 13:27:03 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10616074 with sequence 2000
>>             2017-05-19 13:30:40 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10617074 with sequence 3000
>>             2017-05-19 13:34:20 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10618074 with sequence 4000
>>             2017-05-19 13:38:11 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10619074 with sequence 5000
>>             2017-05-19 13:41:43 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10620074 with sequence 6000
>>             2017-05-19 13:45:54 [WARNING]
>>             org.hps.recon.tracking.TrackerReconDriver
>>             process :: Discarding track with bad HelicalTrackHit
>>             (correction distance
>>             0.000000, chisq penalty 0.000000)
>>             2017-05-19 13:46:05 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10621074 with sequence 7000
>>             2017-05-19 13:50:08 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10622074 with sequence 8000
>>             2017-05-19 13:55:03 [INFO] org.lcsim.job.EventMarkerDriver
>>             process :: Event
>>             10623074 with sequence 9000
>>             2017-05-19 13:58:27 [INFO] org.hps.evio.EvioToLcio run ::
>>             maxEvents 10000
>>             was reached
>>             2017-05-19 13:58:27 [INFO] org.lcsim.job.EventMarkerDriver
>>             endOfData ::
>>             10000 events processed in job.
>>             2017-05-19 13:58:27 [INFO] org.hps.evio.EvioToLcio run ::
>>             Job finished
>>             successfully!
>>
>>             I also tried to do reconstruction by myself interactively,
>>             but I am getting
>>             error below,
>>
>>             The command
>>             /apps/scicomp/java/jdk1.7/bin/java -XX:+UseSerialGC -cp
>>             hps-distribution-3.9-bin.jar org.hps.evio.EvioToLcio -x
>> /org/hps/steering/recon/PhysicsRun2016FullRecon.lcsim -r -d
>>             HPS-PhysicsRun2016-v5-3-fieldmap_globalAlign -R 7796
>>             -DoutputFile=out_7796_0
>>             hps_007796.evio.0 -n 10000
>>
>>             The Error traceback
>>             017-05-19 14:58:44 [CONFIG] org.hps.evio.EvioToLcio parse ::
>>             using steering
>>             resource
>> /org/hps/steering/recon/PhysicsRun2016FullRecon.lcsim
>>             2017-05-19 14:58:44 [CONFIG] org.hps.evio.EvioToLcio parse
>>             :: set max events
>>             to 10000
>>             2017-05-19 14:58:45 [CONFIG]
>>             org.lcsim.job.JobControlManager
>>             addVariableDefinition :: outputFile = out_7796_0
>>             2017-05-19 14:58:45 [CONFIG] org.hps.evio.EvioToLcio parse
>>             :: set steering
>>             variable: outputFile=out_7796_0
>>             2017-05-19 14:58:45 [CONFIG] org.lcsim.job.JobControlManager
>>             initializeLoop
>>             :: initializing LCSim loop
>>             2017-05-19 14:58:45 [CONFIG] org.lcsim.job.JobControlManager
>>             initializeLoop
>>             :: Event marker printing disabled.
>>             2017-05-19 14:58:45 [INFO]
>> org.hps.conditions.database.DatabaseConditionsManager
>>             resetInstance ::
>>             DatabaseConditionsManager instance is reset
>>             Exception in thread "main" java.lang.UnsatisfiedLinkError:
>> /u/apps/scicomp/java/jdk1.7.0_75/jre/lib/i386/xawt/libmawt.so:
>>             libXext.so.6:
>>             cannot open shared object file: No such file or directory
>>                     at java.lang.ClassLoader$NativeLibrary.load(Native
>>             Method)
>>                     at
>> java.lang.ClassLoader.loadLibrary1(ClassLoader.java:1965)
>>                     at
>> java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1890)
>>                     at
>> java.lang.ClassLoader.loadLibrary(ClassLoader.java:1851)
>>                     at java.lang.Runtime.load0(Runtime.java:795)
>>                     at java.lang.System.load(System.java:1062)
>>                     at java.lang.ClassLoader$NativeLibrary.load(Native
>>             Method)
>>                     at
>> java.lang.ClassLoader.loadLibrary1(ClassLoader.java:1965)
>>                     at
>> java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1890)
>>                     at
>> java.lang.ClassLoader.loadLibrary(ClassLoader.java:1872)
>>                     at java.lang.Runtime.loadLibrary0(Runtime.java:849)
>>                     at java.lang.System.loadLibrary(System.java:1088)
>>                     at
>> sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:67)
>>                     at
>> sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:47)
>>                     at
>>             java.security.AccessController.doPrivileged(Native Method)
>>                     at
>>             java.awt.Toolkit.loadLibraries(Toolkit.java:1653)
>>                     at java.awt.Toolkit.<clinit>(Toolkit.java:1682)
>>                     at java.awt.Component.<clinit>(Component.java:595)
>>                     at org.lcsim.util.aida.AIDA.<init>(AIDA.java:68)
>>                     at
>> org.lcsim.util.aida.AIDA.defaultInstance(AIDA.java:53)
>>                     at
>> org.hps.evio.RfFitterDriver.<init>(RfFitterDriver.java:31)
>>                     at
>> sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
>>             Method)
>>         atsun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAcce
>>             ssorImpl.java:57)
>>         atsun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstru
>>             ctorAccessorImpl.java:45)
>>                     at
>> java.lang.reflect.Constructor.newInstance(Constructor.java:526)
>>                     at java.lang.Class.newInstance(Class.java:379)
>>                     at
>> org.lcsim.job.JobControlManager.setupDrivers(JobControlManager.java:1199) 
>>
>>                     at
>> org.hps.job.JobManager.setupDrivers(JobManager.java:82)
>>                     at
>> org.lcsim.job.JobControlManager.setup(JobControlManager.java:1052)
>>                     at
>> org.lcsim.job.JobControlManager.setup(JobControlManager.java:1110)
>>                     at
>>             org.hps.evio.EvioToLcio.parse(EvioToLcio.java:407)
>>                     at org.hps.evio.EvioToLcio.main(EvioToLcio.java:97)
>>
>>
>>
>>             I see this library libXext.so.6: in /usr/lib64, but not in
>>             /usr/lib,
>>             when I put /usr/lib64 in my LD_LIBRARY_PATH, then it
>>             complaines again (see
>>             below)
>>
>>             Exception in thread "main" java.lang.UnsatisfiedLinkError:
>> /u/apps/scicomp/java/jdk1.7.0_75/jre/lib/i386/xawt/libmawt.so:
>>             libXext.so.6:
>>             wrong ELF class: ELFCLASS64
>>
>>             I would appreciate, if I get some help on running the
>>             reconstruction
>>             interactively, then I could look more closely into logs
>>             of the old, and new JAR files.
>>
>>             Rafo
>>
>>
>> ____________________________________________________________________________ 
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