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-requ...@mailman-as.oma.be> wrote: > Send MSNoise mailing list submissions to > msnoise@mailman-as.oma.be > > To subscribe or unsubscribe via the World Wide Web, visit > http://mailman-as.oma.be/mailman/listinfo/msnoise > or, via email, send a message with subject or body 'help' to > msnoise-requ...@mailman-as.oma.be > > You can reach the person managing the list at > msnoise-ow...@mailman-as.oma.be > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MSNoise digest..." > > > 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....@gmail.com> > To: msnoise@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@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.lec...@seismology.be> > To: msnoise@mailman-as.oma.be > Subject: Re: [MSNoise] Stack_error > Message-ID: <71175284-be10-c592-dc74-0db7ab628...@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@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 > > MSNoise@mailman-as.oma.be > > http://mailman-as.oma.be/mailman/listinfo/msnoise > > -- > Dr. Thomas Lecocq > Geologist - Seismologist > > Seismology - Gravimetry > Royal Observatory of Belgium > > * > * * * * * > * * * * > --------- > http://www.seismology.be > http://msnoise.org > http://twitter.com/#!/Seismologie_be > https://www.facebook.com/seismologie.be > > > > ------------------------------ > > Message: 3 > Date: Wed, 4 Apr 2018 14:47:22 -0700 > From: Colton Lynner <colton.lyn...@gmail.com> > To: msnoise@mailman-as.oma.be > Subject: [MSNoise] Mean dvv output > Message-ID: <65ba42b1-bb75-484f-ac31-1f5b244c2...@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 > > ------------------------------ > > _______________________________________________ > MSNoise mailing list > MSNoise@mailman-as.oma.be > http://mailman-as.oma.be/mailman/listinfo/msnoise > > > End of MSNoise Digest, Vol 47, Issue 2 > ************************************** > _______________________________________________ MSNoise mailing list MSNoise@mailman-as.oma.be http://mailman-as.oma.be/mailman/listinfo/msnoise