Rafo, can you check in the log file for these jobs what is being loaded for the ‘svt_calibrations’ conditions set and reply with that information?
It should be printed out during the job initialization.
From: [log in to unmask] [mailto:[log in to unmask]] On Behalf Of Rafayel Paremuzyan
Sent: Tuesday, May 23, 2017 4:34 PM
To: Graf, Norman A.; Graham, Mathew Thomas
Cc: Omar Moreno; [log in to unmask]; hps-software
Subject: Re: [Hps-analysis] Test pass1 Status
Hi All,
Ok, outputs from Jun2016 recon, and the one from new recon are different.
Reminder that, I have used same jar file, same detector same steering file.
Attached figures represent comparison of 1st 20K events from file 7796.20
ECal data is almost identical, attached is the cluster_X distribution comparison from two files.
Blue is the June2016 recon file, and red is new recon file.
SVT data is different, it has more 3D hits and more tracks.
Which is probably causing it to run slower.
Since both reconstructions use "Same" jar same steering files, same geometry (v4-4),
Then it is probably something has been changed in the Database.
Probably SVT experts who have modified the database since Jun 2016, can have a look into
to see if there is something that can cause this.
Rafo
On 05/22/2017 03:46 PM, Graf, Norman A. wrote:
Hello Rafo,
I agree that the most concerning issue is the non-reproducibility of the pass0 results.
Norman
From: [log in to unmask]<mailto:[log in to unmask]> [mailto:[log in to unmask]] On Behalf Of Rafayel Paremuzyan
Sent: Monday, May 22, 2017 12:25 PM
To: Graham, Mathew Thomas <[log in to unmask]><mailto:[log in to unmask]>
Cc: Omar Moreno <[log in to unmask]><mailto:[log in to unmask]>; [log in to unmask]<mailto:[log in to unmask]>; hps-software <[log in to unmask]><mailto:[log in to unmask]>
Subject: Re: [Hps-analysis] Test pass1 Status
….ARE the occupancies x2 higher???
This was just a naive assumption, also I assumed the computing time doesn't linearly depend on occupancies,
I was more wondered, that I can not reproduce the code speed that we had 6 months ago.
Rafo
On 05/22/2017 03:19 PM, Graham, Mathew Thomas wrote:
2.3 GeV data recon speed is x2 slower than the 1.05 data recon speed.
This is concerning, but maybe there is a good reason for that, i.e. might be hit occupancies are high etc,
….ARE the occupancies x2 higher???
but the other thing, that seems puzzling, is recon speed for 2.3 GeV data is now more than x2 slower
using the same hps-java version, same detector, same java version, as we did for pass0.
Ok, that’s legit weird.
Rafo
On 05/22/2017 03:10 PM, Graham, Mathew Thomas wrote:
Sorry to ask a dumb question…but I will anyway.
This is a “2.3 GeV vs 1.05 GeV” issue? Or an hps-java version issue?
On May 22, 2017, at 12:05 PM, Omar Moreno <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Jeremy has also profiled the recon before so if Maurik can't do it, I'm sure he can.
On May 22, 2017 11:46 AM, "Rafayel Paremuzyan" <[log in to unmask]<mailto:[log in to unmask]>> wrote:
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]<mailto:[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<http://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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