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HPS-SOFTWARE  December 2016

HPS-SOFTWARE December 2016

Subject:

Re: problems in reading a local DB

From:

Alessandra Filippi <[log in to unmask]>

Reply-To:

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

Date:

Sun, 11 Dec 2016 14:45:37 +0100

Content-Type:

MULTIPART/MIXED

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (347 lines)

solved!! (I believe)

I also retrieved a dump of the hps_run_db_v2 DB, and point to this in the 
hardcoded fix of RunManager.java (telling to get it from localhost 
instead of hpsdb), while the .prop file always points to local
hps_conditions. Is this consistent?
I'm not sure I fully understand why it works.. but it does :-)

Let me know if you want me to add a few notes to the confluence page 
describing how to run successfully offline, with a local copy of the 
two DBs.
Thanks, cheers
     Alessandra




On Sun, 11 Dec 2016, Alessandra Filippi wrote:

> Hi Maurik, all,
> thanks, with this fix I am able to read my local db.
>
> But, er... as Sho was supposing, I am afraid I am not able to provide the 
> proper db dump. I am retrieving the hps_conditions db, is this correct?
> or do I need a different one?
> To get it, I use the command
>
>> mysqldump -f --lock-tables=false -h hpsdb.jlab.org -u hpsuser -p 
> hps_conditions > hps_conditions_2016_12_11.mysql
>
> if I don't use the -f flag the dump ends almost immediately with this 
> complaint (and the dumpfile is small and clearly incomplete):
>
> mysqldump: Couldn't execute 'show create table 
> `conditions_engrun2015_pass2`': SHOW VIEW command denied to user 
> [log in to unmask] for table 'conditions_engrun2015_pass2' (1142)
>
> If I add the -f flag, it still complains with this and other similar warnings 
> (telling that I cannot view conditions_engrun_pass1_view and 
> svt_alignments_engrun_view), but the dump goes on and the dumpfile is much 
> larger (but this does not mean it contains everything needed, I suppose).
> When I run hps-java, after some happy queries, I get this message:
>
> Exception in thread "main" java.lang.RuntimeException: 
> com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 
> 'hps_conditions.run_summaries' doesn't exist
>
> so clearly I am missing something/doing something wrong with the dump.
> Any idea?
> If it's too complicated and involving privileges I haven't, I would be happy 
> just to retrieve a recent dumpfile from somewhere, if someone can provide me 
> one copy (I have an old one, dating back to 2015, but I guess it's too old - 
> and indeed it does not work properly).
> Thanks for your help.
> cheers
>    Alessandra
>
>
>
>
>
>
>
> On Sat, 10 Dec 2016, Maurik Holtrop wrote:
>
>> Hello Alessandra,
>> You are correct in your assessment that the code does not connect to the 
>> DB. There are 2 locations in the code where the
>> code tries to connect. In one, it does listen to the prop file, in the 
>> other the address is hard coded. In the print outs
>> that you show, the first one … [WARNING]… is the hard coded one not getting 
>> a connection with hpsdb.jlab.org, because you
>> are offline. In your second printout, you are online, so you don’t get any 
>> message from that, and so now it tells you that
>> the other connection that does use the prop file indeed connected to 
>> localhost.
>> 
>> The file that causes the issue is 
>> here: run-database/src/main/java/org/hps/run/database/RunManager.java
>> 
>> Here is the bit of code that I have changed to make it work on our farm
>> 
>> package org.hps.run.database;
>> 
>> import java.sql.Connection;
>> import java.sql.SQLException;
>> import java.util.List;
>> import java.util.logging.Logger;
>> 
>> import org.hps.conditions.database.ConnectionParameters;
>> import org.hps.record.daqconfig.DAQConfig;
>> import org.hps.record.epics.EpicsData;
>> import org.hps.record.scalers.ScalerData;
>> import org.hps.record.svt.SvtConfigData;
>> import org.hps.record.triggerbank.TriggerConfigData;
>> import org.lcsim.conditions.ConditionsEvent;
>> import org.lcsim.conditions.ConditionsListener;
>> 
>> /**
>>  * Manages access to the run database.
>>  *
>>  * @author Jeremy McCormick, SLAC
>>  */
>> public final class RunManager implements ConditionsListener {
>> 
>>     /**
>>      * The default connection parameters for read-only access to the run 
>> database.
>>      */
>>     private static ConnectionParameters DEFAULT_CONNECTION_PARAMETERS = new 
>> ConnectionParameters("hpsuser",
>>             "darkphoton", “hps_run_db", “127.0.0.1");
>> 
>>     /**
>>      * The singleton instance of the RunManager.
>>      */
>>     private static RunManager INSTANCE;
>> 
>>  
>> 
>> 
>> The 127.0.0.1 is the same as “localhost”, usually. Depending on your DB 
>> setup you may need to change the username
>> “hpsuser” or password or database name.
>> 
>> I hope this helps.
>> 
>> Best,
>> Maurik
>> 
>> 
>>
>>       On Dec 10, 2016, at 4:18 AM, Alessandra Filippi <[log in to unmask]> 
>> wrote:
>> 
>> Hi all,
>> so, I guess the issue is that I'm tying to run it completely offline (I 
>> just need to debug the recostruction on a
>> few events, but I cannot be online as I'm away). The command I run is the 
>> following:
>> 
>> java -Dorg.hps.conditions.connection.file=local.prop 
>> -DdisableSvtAlignmentConstants -cp hps-distribution.jar
>> org.hps.evio.EvioToLcio -d HPS-EngRun2015-Nominal-v5-0-fieldmap 
>> -DoutputFile=test -x
>> EngineeringRun2015FullRecon_Pass2_Gbl.lcsim 
>> DATA2015/hps_005772.evio.0-nominalAllevents/hps_005772.evio.0
>> 
>> where hps-distribution.jar is pointing to v3.11 hps-java .jar (freshly 
>> updated). If I run it offline, I just get
>> this:
>> 
>> 2016-12-10 09:58:08 [WARNING] 
>> org.hps.conditions.database.ConnectionParameters createConnection :: Failed 
>> to connect
>> to database jdbc:mysql://hpsdb.jlab.org:3306/ - Communications link failure
>> 
>> The last packet sent successfully to the server was 0 milliseconds ago. The 
>> driver has not received any packets from
>> the server.
>> [..]
>> (repeated for 10 times)
>> 
>> which tells me that it doesn't care at all about my local.prop (even if I 
>> provide the name of a prop file that does
>> not exist).
>> 
>> If I run it with the network, indeed the file is read:
>> 
>> 2016-12-10 09:52:48 [CONFIG] 
>> org.hps.conditions.database.DatabaseConditionsManager 
>> setConnectionProperties ::
>> setting connection properties file local.prop [...]
>> 
>> 2016-12-10 09:59:55 [INFO] 
>> org.hps.conditions.database.DatabaseConditionsManager openConnection :: 
>> opening
>> connection ...
>> connection: jdbc:mysql://localhost:3306/
>> host: localhost
>> port: 3306
>> user: filippi
>> database: hps_conditions
>> 
>> so, if I understand it correctly, as a provisional shortcut I should 
>> hardcode the call to my local db overriding the
>> search over the network of hpsdb.
>> May you tell me where?
>> thanks
>>   Alessandra
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On Fri, 9 Dec 2016, McCormick, Jeremy I. wrote:
>>
>>       Alessandra, can you please send the full print output from your job 
>> and what command line you are
>>       running?
>>
>>       We should start by double checking that at least your prop file is 
>> being picked up for the conditions db
>>       before worrying about what is happening with the run db ...
>>
>>       -----Original Message-----
>>       From: Maurik Holtrop [mailto:[log in to unmask]]
>>       Sent: Friday, December 09, 2016 3:00 PM
>>       To: Omar Moreno
>>       Cc: McCormick, Jeremy I.; Uemura, Sho; Alessandra Filippi; 
>> hps-software
>>       Subject: Re: problems in reading a local DB
>>
>>       Yes, this has been an issue for quite some time, and Jeremy has been 
>> aware of it:
>>       https://jira.slac.stanford.edu/projects/HPSJAVA/issues/HPSJAVA-665?filter=allopenissues
>>       I think we should either obey the prop file everywhere, OR, hard code 
>> it everywhere and not deceive
>>       people with a prop file.
>>
>>       I have had this issue on our backend farm, which simply cannot see 
>> hpsdb.jlab.org, so I went with a
>>       local modification that hard codes the db name everywhere.
>>
>>       Perhaps Jeremy can comment on why this is hard to fix?
>> 
>> 
>>
>>       On Dec 9, 2016, at 5:21 PM, Omar Moreno <[log in to unmask]> wrote:
>>
>>       I think she is trying to run completely offline.
>> 
>>
>>       On Fri, Dec 9, 2016 at 2:07 PM, McCormick, Jeremy I. 
>> <[log in to unmask]> wrote:
>> 
>>
>>       Sho is right -- the run DB URL is currently separate from the 
>> conditions db prop file and hard-coded....
>>
>>       Are you trying to run completely offline?
>>
>>       You should be able to connect to the run db if you have an internet 
>> connection, as it is publically
>>       accessible.
>> 
>>
>>       -----Original Message-----
>>       From: [log in to unmask] 
>> [mailto:[log in to unmask]
>>       <mailto:[log in to unmask]> ] On Behalf Of Sho Uemura
>>       Sent: Friday, December 09, 2016 1:51 PM
>>       To: Alessandra Filippi
>>       Cc: hps-software
>>       Subject: Re: problems in reading a local DB
>>
>>       The instructions don't cover making a local copy of the run DB, which 
>> is a separate database also at
>>       JLab, and uses a different set of connection parameters. I think the 
>> run DB was added sometime
>>       during/after the 2015 run, so you might not have had to deal with it 
>> before.
>>
>>       On Fri, 9 Dec 2016, Alessandra Filippi wrote:
>>
>>       > Hi all,
>>       > I'm trying to use a local copy of the conditions DB to run 2015 
>> data
>>       > reconstruction. I'm following the instructions given in
>>       > 
>> https://confluence.slac.stanford.edu/display/hpsg/Installing+the+Condi
>>       <https://confluence.slac.stanford.edu/display/hpsg/Installing+the+Condi>
>>       > tions+Database+Locally
>>       >
>>       > (I remember that some time ago they were working). However, when I 
>> run
>>       > the reconstruction with the suggested command java
>>       > -Dorg.hps.conditions.connection.file=local.prop -jar
>>       > hps-distribution-bin.jar [args]
>>       >
>>       > it looks like the db redirection to my local file is ignored - the
>>       > default jlab db is always searched for, and there is no complain if 
>> I
>>       > provide a non-existent .prop filename, as if the -D instruction was 
>> neglected.
>>       > Has anything changed (class names, etc) as of lately?
>>       > or is the issue related to my local db copy?
>>       > thanks, cheers
>>       >   Alessandra
>>       >
>>       > 
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