[MSNoise] msnoise stack error
Crowder, Emily
emily.crowder at abdn.ac.uk
Fri Aug 26 10:21:59 UTC 2016
Hi Tom,
There seems to be a problem with that too...
root at COPS-023603-L:/home/rpgsbs/r01ec15/Documents/BASS_DATA/sorted# sudo service mysqld restart
Failed to restart mysqld.service: Unit mysqld.service not found.
Emily
~~~~~~~~~~~~~~~~~~~~~~~~~
Emily Crowder MSc BSc
PhD Student
School of Geosciences
University of Aberdeen
Aberdeen AB24 3UE
Scotland
Em: emily.crowder at abdn.ac.uk
~~~~~~~~~~~~~~~~~~~~~~~~~
________________________________
From: msnoise-bounces at mailman-as.oma.be <msnoise-bounces at mailman-as.oma.be> on behalf of Thomas Lecocq <thomas.lecocq at oma.be>
Sent: 26 August 2016 07:52:08
To: msnoise at mailman-as.oma.be
Subject: Re: [MSNoise] msnoise stack error
Emily,
I think you should restart mysqld (with a d) ?
Tom
Le 25/08/2016 à 18:25, Crowder, Emily a écrit :
> Hi Tom,
>
>
> Thanks for the advice. I think the problems might be there because I upgraded my Ubuntu to 16.04. I tried adding it to the 'my.cnf' file, I'll copy that file below:
>
>
> #
>
> # The MySQL database server configuration file.
>
> #
>
> # You can copy this to one of:
>
> # - "/etc/mysql/my.cnf" to set global options,
>
> # - "~/.my.cnf" to set user-specific options.
>
> #
>
> # One can use all long options that the program supports.
>
> # Run program with --help to get a list of available options and with
>
> # --print-defaults to see which it would actually understand and use.
>
> #
>
> # For explanations see
>
> # http://dev.mysql.com/doc/mysql/en/server-system-variables.html
>
>
> #
>
> # * IMPORTANT: Additional settings that can override those from this file!
>
> # The files must end with '.cnf', otherwise they'll be ignored.
>
> #
>
>
> !includedir /etc/mysql/conf.d/
>
> !includedir /etc/mysql/mysql.conf.d/
>
>
> sql_mode=TRADITIONAL
>
>
>
> Is that the correct way to add it? Because when I try to do 'sudo service mysql start' (after stopping it) I get the following error:
>
>
> Job for mysql.service failed because the control process exited with error code. See "systemctl status mysql.service" and "journalctl -xe" for details.
>
>
>
> Emily
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Emily Crowder MSc BSc
> PhD Student
> School of Geosciences
> University of Aberdeen
> Aberdeen AB24 3UE
> Scotland
> Em: emily.crowder at abdn.ac.uk
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~
>
> ________________________________
> From: msnoise-bounces at mailman-as.oma.be <msnoise-bounces at mailman-as.oma.be> on behalf of Thomas Lecocq <thomas.lecocq at oma.be>
> Sent: 25 August 2016 15:15:17
> To: msnoise at mailman-as.oma.be
> Subject: Re: [MSNoise] msnoise stack error
>
> Hi Emily,
>
> This is an issue with the latest MySQL release(s), you have to edit the
> file my.cnf on your system and edit/add the sql_mode parameter:
>
> sql_mode=TRADITIONAL
>
>
> my.cnf is the general MySQL configuration file, usually located in one
> of these:
>
> * /etc/my.cnf
> * /etc/mysql/my.cnf
> * $MYSQL_HOME/my.cnf
> * [datadir]/my.cnf
> * ~/.my.cnf
>
> you'll need to restart mysqld after the change (sudo service mysqld restart)
>
> HTH
>
> Tom
>
>
>
> Le 25/08/2016 à 16:07, Crowder, Emily a écrit :
>> Hello,
>>
>>
>> I have successfully run 'msnoise compute_cc' for my data so that I now have a file of 1 day long cross-correlations. I would now like to stack them for the whole time period (~2 years). However, when I try to run 'msnoise stack -r' it fails and I get an error message. I have pasted this below. Would you be able to shed some light onto it? How can I resolve this?
>>
>>
>> Thanks in advance,
>>
>>
>> Emily
>>
>>
>> root at COPS-023603-L:/home/rpgsbs/r01ec15/Documents/BASS_DATA/sorted# msnoise stack -r
>>
>> Lets STACK !
>>
>> 2016-08-25 15:02:55 [DEBUG] Starting the ref stack
>>
>> []
>>
>> 2016-08-25 15:02:55 [DEBUG] Processing BA_BA01:BA_BA02-TT-1
>>
>> Traceback (most recent call last):
>>
>> File "/root/anaconda2/bin/msnoise", line 11, in <module>
>>
>> sys.exit(run())
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/msnoise/scripts/msnoise.py", line 614, in run
>>
>> cli(obj={})
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/click/core.py", line 716, in __call__
>>
>> return self.main(*args, **kwargs)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/click/core.py", line 696, in main
>>
>> rv = self.invoke(ctx)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
>>
>> return _process_result(sub_ctx.command.invoke(sub_ctx))
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/click/core.py", line 889, in invoke
>>
>> return ctx.invoke(self.callback, **ctx.params)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/click/core.py", line 534, in invoke
>>
>> return callback(*args, **kwargs)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/msnoise/scripts/msnoise.py", line 301, in stack
>>
>> main('ref', interval)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/msnoise/s04stack.py", line 203, in main
>>
>> updated_days = updated_days_for_dates(db, start, end, pair.replace('_', '.'), jobtype='CC', interval=datetime.timedelta(days=interval),returndays=True)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/msnoise/api.py", line 1189, in updated_days_for_dates
>>
>> days = session.query(Job).filter(Job.pair == pair).filter(Job.day >= date1).filter(Job.day <= date2).filter(Job.jobtype == jobtype).filter(Job.lastmod >= lastmod).group_by(Job.day).order_by(Job.day).all()
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2613, in all
>>
>> return list(self)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2761, in __iter__
>>
>> return self._execute_and_instances(context)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2776, in _execute_and_instances
>>
>> result = conn.execute(querycontext.statement, self._params)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 914, in execute
>>
>> return meth(self, multiparams, params)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
>>
>> return connection._execute_clauseelement(self, multiparams, params)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement
>>
>> compiled_sql, distilled_params
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context
>>
>> context)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1341, in _handle_dbapi_exception
>>
>> exc_info
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause
>>
>> reraise(type(exception), exception, tb=exc_tb, cause=cause)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context
>>
>> context)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute
>>
>> cursor.execute(statement, parameters)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/pymysql/cursors.py", line 161, in execute
>>
>> result = self._query(query)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/pymysql/cursors.py", line 317, in _query
>>
>> conn.query(q)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/pymysql/connections.py", line 837, in query
>>
>> self._affected_rows = self._read_query_result(unbuffered=unbuffered)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/pymysql/connections.py", line 1021, in _read_query_result
>>
>> result.read()
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/pymysql/connections.py", line 1304, in read
>>
>> first_packet = self.connection._read_packet()
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/pymysql/connections.py", line 983, in _read_packet
>>
>> packet.check_error()
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/pymysql/connections.py", line 395, in check_error
>>
>> err.raise_mysql_exception(self._data)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/pymysql/err.py", line 120, in raise_mysql_exception
>>
>> _check_mysql_exception(errinfo)
>>
>> File "/root/anaconda2/lib/python2.7/site-packages/pymysql/err.py", line 115, in _check_mysql_exception
>>
>> raise InternalError(errno, errorvalue)
>>
>> sqlalchemy.exc.InternalError: (pymysql.err.InternalError) (1055, u"Expression #1 of SELECT list is not in GROUP BY clause and contains nonaggregated column 'msnoise.jobs.ref' which is not functionally dependent on columns in GROUP BY clause; this is incompatible with sql_mode=only_full_group_by") [SQL: u'SELECT jobs.ref AS jobs_ref, jobs.day AS jobs_day, jobs.pair AS jobs_pair, jobs.jobtype AS jobs_jobtype, jobs.flag AS jobs_flag, jobs.lastmod AS jobs_lastmod \nFROM jobs \nWHERE jobs.pair = %(pair_1)s AND jobs.day >= %(day_1)s AND jobs.day <= %(day_2)s AND jobs.jobtype = %(jobtype_1)s AND jobs.lastmod >= %(lastmod_1)s GROUP BY jobs.day ORDER BY jobs.day'] [parameters: {u'day_2': datetime.date(2013, 4, 29), u'lastmod_1': datetime.datetime(2016, 8, 24, 15, 2, 55, 233936), u'day_1': datetime.date(2011, 5, 22), u'jobtype_1': 'CC', u'pair_1': 'BA.BA01:BA.BA02'}]
>>
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> Emily Crowder MSc BSc
>> PhD Student
>> School of Geosciences
>> University of Aberdeen
>> Aberdeen AB24 3UE
>> Scotland
>> Em: emily.crowder at abdn.ac.uk
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>>
>> The University of Aberdeen is a charity registered in Scotland, No SC013683.
>> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
>> _______________________________________________
>> MSNoise mailing list
>> MSNoise at mailman-as.oma.be
>> http://mailman-as.oma.be/mailman/listinfo/msnoise
> _______________________________________________
> MSNoise mailing list
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>
>
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
> _______________________________________________
> MSNoise mailing list
> MSNoise at mailman-as.oma.be
> http://mailman-as.oma.be/mailman/listinfo/msnoise
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