[MSNoise] MSNoise Digest, Vol 47, Issue 2

Yawar Hussain yawar.pgn at gmail.com
Mon Apr 9 18:47:15 UTC 2018


Yes, I restarted.

How can I fix it?


Regards,
Yawar Hussain
Ph.D. Student, Geotechnical Engineering
University of Brasilia, Brazil.

On Thu, Apr 5, 2018 at 9:00 AM, <msnoise-request at mailman-as.oma.be> wrote:

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> Today's Topics:
>
>    1. Stack_error (Yawar Hussain)
>    2. Re: Stack_error (Thomas Lecocq)
>    3. Mean dvv output (Colton Lynner)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 4 Apr 2018 10:37:23 -0300
> From: Yawar Hussain <yawar.pgn at gmail.com>
> To: msnoise at mailman-as.oma.be
> Subject: [MSNoise] Stack_error
> Message-ID:
>         <CAP7arHTi9mZ6s8KzUVzJkNB-mSSV0AYPj7FSg6DsfVMWBaAySg@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
>
> I run stack command and received following errors.
> Please, have a look.
> I tried to fix it by editing 'my.cnf' file as 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/
> [global]
> sql_mode = TRADITIONAL
>
>
>
> Stack error!
>
>
> yawar at yawar-Vostro-5470:~/anaconda3/bin$ msnoise stack -r -m -i 10
> Lets STACK !
> 2018-04-03 10:59:04 [DEBUG] Starting the ref stack
> []
> 2018-04-03 10:59:04 [DEBUG] Processing DF01_BHE:DF01_BHE-ZZ-1
> Traceback (most recent call last):
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> line 1139, in _execute_context
>     context)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/default.py",
> line 450, in do_execute
>     cursor.execute(statement, parameters)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/cursors.py",
> line 166, in execute
>     result = self._query(query)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/cursors.py",
> line 322, in _query
>     conn.query(q)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> line 835, in query
>     self._affected_rows = self._read_query_result(unbuffered=unbuffered)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> line 1019, in _read_query_result
>     result.read()
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> line 1302, in read
>     first_packet = self.connection._read_packet()
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> line 981, in _read_packet
>     packet.check_error()
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> line 393, in check_error
>     err.raise_mysql_exception(self._data)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/pymysql/err.py",
> line 107, in raise_mysql_exception
>     raise errorclass(errno, errval)
> pymysql.err.InternalError: (1055, "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")
>
> The above exception was the direct cause of the following exception:
>
> Traceback (most recent call last):
>   File "/home/yawar/anaconda3/bin/msnoise", line 11, in <module>
>     sys.exit(run())
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> msnoise/scripts/msnoise.py",
> line 614, in run
>     cli(obj={})
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/click/core.py",
> line 716, in __call__
>     return self.main(*args, **kwargs)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/click/core.py",
> line 696, in main
>     rv = self.invoke(ctx)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/click/core.py",
> line 1060, in invoke
>     return _process_result(sub_ctx.command.invoke(sub_ctx))
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/click/core.py",
> line 889, in invoke
>     return ctx.invoke(self.callback, **ctx.params)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/click/core.py",
> line 534, in invoke
>     return callback(*args, **kwargs)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> msnoise/scripts/msnoise.py",
> line 301, in stack
>     main('ref', interval)
>   File "/home/yawar/anaconda3/lib/python3.5/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 "/home/yawar/anaconda3/lib/python3.5/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 "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/orm/query.py",
> line 2613, in all
>     return list(self)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/orm/query.py",
> line 2761, in __iter__
>     return self._execute_and_instances(context)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/orm/query.py",
> line 2776, in _execute_and_instances
>     result = conn.execute(querycontext.statement, self._params)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> line 914, in execute
>     return meth(self, multiparams, params)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/sql/elements.py",
> line 323, in _execute_on_connection
>     return connection._execute_clauseelement(self, multiparams, params)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> line 1010, in _execute_clauseelement
>     compiled_sql, distilled_params
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> line 1146, in _execute_context
>     context)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> line 1341, in _handle_dbapi_exception
>     exc_info
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/util/compat.py",
> line 202, in raise_from_cause
>     reraise(type(exception), exception, tb=exc_tb, cause=cause)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/util/compat.py",
> line 185, in reraise
>     raise value.with_traceback(tb)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> line 1139, in _execute_context
>     context)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/default.py",
> line 450, in do_execute
>     cursor.execute(statement, parameters)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/cursors.py",
> line 166, in execute
>     result = self._query(query)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/cursors.py",
> line 322, in _query
>     conn.query(q)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> line 835, in query
>     self._affected_rows = self._read_query_result(unbuffered=unbuffered)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> line 1019, in _read_query_result
>     result.read()
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> line 1302, in read
>     first_packet = self.connection._read_packet()
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> line 981, in _read_packet
>     packet.check_error()
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> line 393, in check_error
>     err.raise_mysql_exception(self._data)
>   File "/home/yawar/anaconda3/lib/python3.5/site-packages/pymysql/err.py",
> line 107, in raise_mysql_exception
>     raise errorclass(errno, errval)
> sqlalchemy.exc.InternalError: (pymysql.err.InternalError) (1055,
> "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: '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: {'lastmod_1':
> datetime.datetime(2018, 3, 24, 10, 59, 4, 395159), 'jobtype_1': 'CC',
> 'day_2': datetime.date(2018, 1, 1), 'pair_1': 'DF01.BHE:DF01.BHE', 'day_1':
> datetime.date(1970, 1, 1)}]
>
>
> Regards,
> Yawar Hussain
> Ph.D. Student, Geotechnical Engineering
> University of Brasilia, Brazil.
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 4 Apr 2018 17:15:04 +0200
> From: Thomas Lecocq <Thomas.Lecocq at seismology.be>
> To: msnoise at mailman-as.oma.be
> Subject: Re: [MSNoise] Stack_error
> Message-ID: <71175284-be10-c592-dc74-0db7ab6286c8 at seismology.be>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hi,
>
> I assume your other errors are solved, that's good news.
>
> For MySQL, did you restart the mysql or mysqld service after adapting
> my.cnf ?
>
> Best regards,
>
> Thomas
>
>
> On 04/04/2018 15:37, Yawar Hussain wrote:
> > Hello,
> >
> > I run stack command and received following errors.
> > Please, have a look.
> > I tried to fix it by editing 'my.cnf' file as 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/
> > [global]
> > sql_mode = TRADITIONAL
> >
> >
> >
> > Stack error!
> >
> >
> > yawar at yawar-Vostro-5470:~/anaconda3/bin$ msnoise stack -r -m -i 10
> > Lets STACK !
> > 2018-04-03 10:59:04 [DEBUG] Starting the ref stack
> > []
> > 2018-04-03 10:59:04 [DEBUG] Processing DF01_BHE:DF01_BHE-ZZ-1
> > Traceback (most recent call last):
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> > line 1139, in _execute_context
> >      context)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/default.py",
> > line 450, in do_execute
> >      cursor.execute(statement, parameters)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/cursors.py",
> > line 166, in execute
> >      result = self._query(query)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/cursors.py",
> > line 322, in _query
> >      conn.query(q)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> > line 835, in query
> >      self._affected_rows = self._read_query_result(
> unbuffered=unbuffered)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> > line 1019, in _read_query_result
> >      result.read()
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> > line 1302, in read
> >      first_packet = self.connection._read_packet()
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> > line 981, in _read_packet
> >      packet.check_error()
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> > line 393, in check_error
> >      err.raise_mysql_exception(self._data)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/err.py",
> > line 107, in raise_mysql_exception
> >      raise errorclass(errno, errval)
> > pymysql.err.InternalError: (1055, "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")
> >
> > The above exception was the direct cause of the following exception:
> >
> > Traceback (most recent call last):
> >    File "/home/yawar/anaconda3/bin/msnoise", line 11, in <module>
> >      sys.exit(run())
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> msnoise/scripts/msnoise.py",
> > line 614, in run
> >      cli(obj={})
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/click/
> core.py",
> > line 716, in __call__
> >      return self.main(*args, **kwargs)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/click/
> core.py",
> > line 696, in main
> >      rv = self.invoke(ctx)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/click/
> core.py",
> > line 1060, in invoke
> >      return _process_result(sub_ctx.command.invoke(sub_ctx))
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/click/
> core.py",
> > line 889, in invoke
> >      return ctx.invoke(self.callback, **ctx.params)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/click/
> core.py",
> > line 534, in invoke
> >      return callback(*args, **kwargs)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> msnoise/scripts/msnoise.py",
> > line 301, in stack
> >      main('ref', interval)
> >    File "/home/yawar/anaconda3/lib/python3.5/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 "/home/yawar/anaconda3/lib/python3.5/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 "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/orm/query.py",
> > line 2613, in all
> >      return list(self)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/orm/query.py",
> > line 2761, in __iter__
> >      return self._execute_and_instances(context)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/orm/query.py",
> > line 2776, in _execute_and_instances
> >      result = conn.execute(querycontext.statement, self._params)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> > line 914, in execute
> >      return meth(self, multiparams, params)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/sql/elements.py",
> > line 323, in _execute_on_connection
> >      return connection._execute_clauseelement(self, multiparams, params)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> > line 1010, in _execute_clauseelement
> >      compiled_sql, distilled_params
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> > line 1146, in _execute_context
> >      context)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> > line 1341, in _handle_dbapi_exception
> >      exc_info
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/util/compat.py",
> > line 202, in raise_from_cause
> >      reraise(type(exception), exception, tb=exc_tb, cause=cause)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/util/compat.py",
> > line 185, in reraise
> >      raise value.with_traceback(tb)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/base.py",
> > line 1139, in _execute_context
> >      context)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> sqlalchemy/engine/default.py",
> > line 450, in do_execute
> >      cursor.execute(statement, parameters)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/cursors.py",
> > line 166, in execute
> >      result = self._query(query)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/cursors.py",
> > line 322, in _query
> >      conn.query(q)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> > line 835, in query
> >      self._affected_rows = self._read_query_result(
> unbuffered=unbuffered)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> > line 1019, in _read_query_result
> >      result.read()
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> > line 1302, in read
> >      first_packet = self.connection._read_packet()
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> > line 981, in _read_packet
> >      packet.check_error()
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/connections.py",
> > line 393, in check_error
> >      err.raise_mysql_exception(self._data)
> >    File "/home/yawar/anaconda3/lib/python3.5/site-packages/
> pymysql/err.py",
> > line 107, in raise_mysql_exception
> >      raise errorclass(errno, errval)
> > sqlalchemy.exc.InternalError: (pymysql.err.InternalError) (1055,
> > "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: '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: {'lastmod_1':
> > datetime.datetime(2018, 3, 24, 10, 59, 4, 395159), 'jobtype_1': 'CC',
> > 'day_2': datetime.date(2018, 1, 1), 'pair_1': 'DF01.BHE:DF01.BHE',
> 'day_1':
> > datetime.date(1970, 1, 1)}]
> >
> >
> > Regards,
> > Yawar Hussain
> > Ph.D. Student, Geotechnical Engineering
> > University of Brasilia, Brazil.
> > _______________________________________________
> > MSNoise mailing list
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> --
> Dr. Thomas Lecocq
> Geologist - Seismologist
>
> Seismology - Gravimetry
> Royal Observatory of Belgium
>
>             *
>         * * * * *
>          * * * *
>         ---------
> http://www.seismology.be
> http://msnoise.org
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>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 4 Apr 2018 14:47:22 -0700
> From: Colton Lynner <colton.lynner at gmail.com>
> To: msnoise at mailman-as.oma.be
> Subject: [MSNoise] Mean dvv output
> Message-ID: <65BA42B1-BB75-484F-AC31-1F5B244C2DE7 at gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hello,
>
> I have a couple questions about MSNoise.
>
> 1) Is there a way to output the mean values calculated from the DVV plots?
> I have found that if you use the -p option with the ALL pair, it produces a
> csv file of the ALL line values. The ALL and mean lines are slightly
> different for some frequencies, and I would like to be able to output both.
> Also, the documentation mentions the ALL pair, but can you offer more
> explanation on how that is calculated? Is it an average (stack?) of all
> traces? I am trying to work out why the ALL and the mean may be different.
>
> 2) Is there a plot tool to make the delay time variation plots that are
> shown in the documentation and in the SRL paper (Figure 4)?
>
> Thanks,
> Colton
>
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> End of MSNoise Digest, Vol 47, Issue 2
> **************************************
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