[MSNoise] msnoise stack error

Crowder, Emily emily.crowder at abdn.ac.uk
Thu Aug 25 16:25:04 UTC 2016 

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

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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.

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