[MSNoise] Problem with database conection.
Oscar Alberto Castro Artola
oscar.cas.art at gmail.com
Thu Jun 15 16:10:32 UTC 2017
Dear Lukas,
I have tried: *pip install msnoise -U,* but I get this error. Do you know
what the problem is?
*Collecting msnoise*
*Collecting setuptools (from msnoise)*
* Using cached setuptools-36.0.1-py2.py3-none-any.whl*
*Collecting pymysql (from msnoise)*
* Using cached PyMySQL-0.7.11-py2.py3-none-any.whl*
*Collecting numpy>=1.0 (from msnoise)*
* Downloading numpy-1.13.0-cp27-cp27mu-manylinux1_x86_64.whl (16.6MB)*
* 100% |████████████████████████████████| 16.6MB 10kB/s *
*Collecting matplotlib (from msnoise)*
* Using cached matplotlib-2.0.2-cp27-cp27mu-manylinux1_x86_64.whl*
*Requirement already up-to-date: scipy in
/usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
*Collecting jinja2 (from msnoise)*
* Using cached Jinja2-2.9.6-py2.py3-none-any.whl*
*Requirement already up-to-date: wtforms in
/usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
*Collecting pandas (from msnoise)*
* Using cached pandas-0.20.2-cp27-cp27mu-manylinux1_x86_64.whl*
*Collecting flask (from msnoise)*
* Using cached Flask-0.12.2-py2.py3-none-any.whl*
*Collecting sqlalchemy (from msnoise)*
*Collecting folium (from msnoise)*
* Using cached folium-0.3.0-py2-none-any.whl*
*Collecting click (from msnoise)*
* Using cached click-6.7-py2.py3-none-any.whl*
*Collecting flask-admin (from msnoise)*
*Collecting obspy (from msnoise)*
*Collecting flask-wtf (from msnoise)*
* Using cached Flask_WTF-0.14.2-py2.py3-none-any.whl*
*Collecting markdown (from msnoise)*
*Requirement already up-to-date: python-dateutil in
/usr/local/anaconda/lib/python2.7/site-packages (from matplotlib->msnoise)*
*Requirement already up-to-date: subprocess32 in
/usr/local/anaconda/lib/python2.7/site-packages (from matplotlib->msnoise)*
*Requirement already up-to-date: cycler>=0.10 in
/usr/local/anaconda/lib/python2.7/site-packages/cycler-0.10.0-py2.7.egg
(from matplotlib->msnoise)*
*Requirement already up-to-date: six>=1.10 in
/usr/local/anaconda/lib/python2.7/site-packages (from matplotlib->msnoise)*
*Requirement already up-to-date: pytz in
/usr/local/anaconda/lib/python2.7/site-packages (from matplotlib->msnoise)*
*Requirement already up-to-date: functools32 in
/usr/local/anaconda/lib/python2.7/site-packages (from matplotlib->msnoise)*
*Requirement already up-to-date: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6
in /usr/local/anaconda/lib/python2.7/site-packages (from
matplotlib->msnoise)*
*Collecting MarkupSafe>=0.23 (from jinja2->msnoise)*
*Collecting Werkzeug>=0.7 (from flask->msnoise)*
* Using cached Werkzeug-0.12.2-py2.py3-none-any.whl*
*Requirement already up-to-date: itsdangerous>=0.21 in
/usr/local/anaconda/lib/python2.7/site-packages (from flask->msnoise)*
*Collecting branca (from folium->msnoise)*
* Using cached branca-0.2.0-py2-none-any.whl*
*Requirement already up-to-date: future>=0.12.4 in
/usr/local/anaconda/lib/python2.7/site-packages (from obspy->msnoise)*
*Collecting requests (from obspy->msnoise)*
* Downloading requests-2.18.1-py2.py3-none-any.whl (88kB)*
* 100% |████████████████████████████████| 92kB 4.0MB/s *
*Requirement already up-to-date: decorator in
/usr/local/anaconda/lib/python2.7/site-packages (from obspy->msnoise)*
*Collecting lxml (from obspy->msnoise)*
* Using cached lxml-3.8.0-cp27-cp27mu-manylinux1_x86_64.whl*
*Collecting chardet<3.1.0,>=3.0.2 (from requests->obspy->msnoise)*
* Downloading chardet-3.0.4-py2.py3-none-any.whl (133kB)*
* 100% |████████████████████████████████| 143kB 2.5MB/s *
*Requirement already up-to-date: certifi>=2017.4.17 in
/usr/local/anaconda/lib/python2.7/site-packages (from
requests->obspy->msnoise)*
*Collecting idna<2.6,>=2.5 (from requests->obspy->msnoise)*
* Using cached idna-2.5-py2.py3-none-any.whl*
*Collecting urllib3<1.22,>=1.21.1 (from requests->obspy->msnoise)*
* Using cached urllib3-1.21.1-py2.py3-none-any.whl*
*Installing collected packages: setuptools, pymysql, numpy, matplotlib,
MarkupSafe, jinja2, pandas, click, Werkzeug, flask, sqlalchemy, branca,
folium, flask-admin, chardet, idna, urllib3, requests, lxml, obspy,
flask-wtf, markdown, msnoise*
* Found existing installation: setuptools 33.1.1.post20170320*
* Uninstalling setuptools-33.1.1.post20170320:*
*Exception:*
*Traceback (most recent call last):*
* File
"/usr/local/anaconda/lib/python2.7/site-packages/pip/basecommand.py", line
215, in main*
* status = self.run(options, args)*
* File
"/usr/local/anaconda/lib/python2.7/site-packages/pip/commands/install.py",
line 342, in run*
* prefix=options.prefix_path,*
* File
"/usr/local/anaconda/lib/python2.7/site-packages/pip/req/req_set.py", line
778, in install*
* requirement.uninstall(auto_confirm=True)*
* File
"/usr/local/anaconda/lib/python2.7/site-packages/pip/req/req_install.py",
line 754, in uninstall*
* paths_to_remove.remove(auto_confirm)*
* File
"/usr/local/anaconda/lib/python2.7/site-packages/pip/req/req_uninstall.py",
line 115, in remove*
* renames(path, new_path)*
* File
"/usr/local/anaconda/lib/python2.7/site-packages/pip/utils/__init__.py",
line 267, in renames*
* shutil.move(old, new)*
* File "/usr/local/anaconda/lib/python2.7/shutil.py", line 303, in move*
* os.unlink(src)*
*OSError: [Errno 13] Permission denied:
'/usr/local/anaconda/bin/easy_install'*
Thank you very much for your time!
Greetings,
Oscar
On Tue, Jun 6, 2017 at 1:42 AM, Lukas Preiswerk <preiswerk at vaw.baug.ethz.ch>
wrote:
> Oscar,
>
> I think “pip install msnoise -U” should do the trick (-U is for —upgrade).
>
> Lukas
>
>
>
>
>
>
>
> 2017-06-02 18:55 GMT+02:00 Oscar Alberto Castro Artola
> <oscar.cas.art at gmail.com>:
> > Dear Christos and Lukas,
> >
> > first of all thanks for you help! I really apreciate it!
> >
> > Christos: I have a server with 40 cores, so I think the *-t 20* flag is
> > working fine!
> >
> > Lukas: I tried to do a *pip install msnoise*, but I don't think it is
> > actually upgrading MSNoise, the output is:
> >
> > *Requirement already satisfied: msnoise in
> > /usr/local/anaconda/lib/python2.7/site-packages*
> > *Requirement already satisfied: setuptools in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: numpy>=1.0 in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: scipy in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: pandas in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: matplotlib in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: statsmodels in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: sqlalchemy in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: obspy in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: click in
> > /usr/local/anaconda/lib/python2.7/site-packages/click-4.0-py2.7.egg
> (from
> > msnoise)*
> > *Requirement already satisfied: pymysql in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: flask in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: flask-admin in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: multiprocessing_logging in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: markdown in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: folium in
> > /usr/local/anaconda/lib/python2.7/site-packages (from msnoise)*
> > *Requirement already satisfied: six>=1.10 in
> > /usr/local/anaconda/lib/python2.7/site-packages (from
> matplotlib->msnoise)*
> > *Requirement already satisfied: python-dateutil in
> > /usr/local/anaconda/lib/python2.7/site-packages (from
> matplotlib->msnoise)*
> > *Requirement already satisfied: functools32 in
> > /usr/local/anaconda/lib/python2.7/site-packages (from
> matplotlib->msnoise)*
> > *Requirement already satisfied: subprocess32 in
> > /usr/local/anaconda/lib/python2.7/site-packages (from
> matplotlib->msnoise)*
> > *Requirement already satisfied: pytz in
> > /usr/local/anaconda/lib/python2.7/site-packages (from
> matplotlib->msnoise)*
> > *Requirement already satisfied: cycler>=0.10 in
> > /usr/local/anaconda/lib/python2.7/site-packages/cycler-0.10.0-py2.7.egg
> > (from matplotlib->msnoise)*
> > *Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6
> in
> > /usr/local/anaconda/lib/python2.7/site-packages (from
> matplotlib->msnoise)*
> > *Requirement already satisfied: future>=0.12.4 in
> > /usr/local/anaconda/lib/python2.7/site-packages (from obspy->msnoise)*
> > *Requirement already satisfied: lxml in
> > /usr/local/anaconda/lib/python2.7/site-packages (from obspy->msnoise)*
> > *Requirement already satisfied: decorator in
> > /usr/local/anaconda/lib/python2.7/site-packages (from obspy->msnoise)*
> > *Requirement already satisfied: requests in
> > /usr/local/anaconda/lib/python2.7/site-packages (from obspy->msnoise)*
> > *Requirement already satisfied: wtforms in
> > /usr/local/anaconda/lib/python2.7/site-packages (from
> flask-admin->msnoise)*
> > *Requirement already satisfied: Jinja2 in
> > /usr/local/anaconda/lib/python2.7/site-packages (from folium->msnoise)*
> >
> > This is the second time I do *msnoise -t 20 compute_mwcs*, last time it
> > worked fine but I needed to change *dtt_lag* to "dynamic". So when I
> tried
> > to rerun* msnoise -t 20 compute_mwcs* with the new parameter this error
> > message appears. What I've done is run the process in the morning, all
> day
> > it works fine, but the next morning I always find that error message.
> >
> > Thanks again!
> >
> > Oscar
> >
> > On Fri, Jun 2, 2017 at 8:39 AM, Lukas Preiswerk <
> preiswerk at vaw.baug.ethz.ch>
> > wrote:
> >
> >> Hi Oscar
> >>
> >> The problem is that “MySQL server has gone away”, so it can’t update
> >> the database after finishing the MWCS job. We fixed this in the newest
> >> version, so you should indeed update.
> >>
> >> I think that updating is done by “pip install msnoise”, and then for
> >> each project “msnoise upgrade_db” (see the release notes
> >> http://msnoise.org/doc/releasenotes/msnoise-1.5.html ). Tom can
> >> clarify if this method I just described is actually the way to go…
> >>
> >> Best, Lukas
> >>
> >>
> >>
> >> 2017-06-02 15:20 GMT+02:00 Christos Evangelidis <cevan at noa.gr>:
> >> > Dear Oscar,
> >> >
> >> > Can you really run 20 instances of the code (-t 20) ? I find the -t 20
> >> > rather high, but your machine might support it..
> >> >
> >> > Regards,
> >> >
> >> > Christos
> >> >
> >> > Στις 1 Ιουν 2017 6:01 μμ, ο χρήστης "Oscar Alberto Castro Artola" <
> >> > oscar.cas.art at gmail.com> έγραψε:
> >> >
> >> > Hello,
> >> >
> >> > I have 10 years of data for 13 stations, I have computed the CCF and
> now
> >> it
> >> > is turn to compute the MWCS. When I do *msnoise -t 20 compute_mwcs
> *this
> >> > error appears:
> >> >
> >> > *Process Process-4:*
> >> > *Traceback (most recent call last):*
> >> > * File "/usr/local/anaconda/lib/python2.7/multiprocessing/
> process.py",
> >> > line 258, in _bootstrap*
> >> > * self.run()*
> >> > * File "/usr/local/anaconda/lib/python2.7/multiprocessing/
> process.py",
> >> > line 114, in run*
> >> > * self._target(*self._args, **self._kwargs)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/msnoise/
> >> > s05compute_mwcs.py",
> >> > line 150, in main*
> >> > * update_job(db, day, pair, jobtype='DTT', flag='D')*
> >> > * File "/usr/local/anaconda/lib/python2.7/site-packages/
> >> msnoise/api.py",
> >> > line 615, in update_job*
> >> > * job = session.query(Job).filter(Job.day == day).filter(Job.pair
> ==
> >> > pair).filter(Job.jobtype == jobtype).first()*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> sqlalchemy/orm/query.py",
> >> > line 2755, in first*
> >> > * ret = list(self[0:1])*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> sqlalchemy/orm/query.py",
> >> > line 2547, in __getitem__*
> >> > * return list(res)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> sqlalchemy/orm/query.py",
> >> > line 2855, in __iter__*
> >> > * return self._execute_and_instances(context)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> sqlalchemy/orm/query.py",
> >> > line 2878, in _execute_and_instances*
> >> > * result = conn.execute(querycontext.statement, self._params)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> sqlalchemy/engine/base.py",
> >> > line 945, in execute*
> >> > * return meth(self, multiparams, params)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/sqlalchemy/
> >> > sql/elements.py",
> >> > line 263, in _execute_on_connection*
> >> > * return connection._execute_clauseelement(self, multiparams,
> >> params)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> sqlalchemy/engine/base.py",
> >> > line 1053, in _execute_clauseelement*
> >> > * compiled_sql, distilled_params*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> sqlalchemy/engine/base.py",
> >> > line 1189, in _execute_context*
> >> > * context)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> sqlalchemy/engine/base.py",
> >> > line 1402, in _handle_dbapi_exception*
> >> > * exc_info*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> sqlalchemy/util/compat.py",
> >> > line 203, in raise_from_cause*
> >> > * reraise(type(exception), exception, tb=exc_tb, cause=cause)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> sqlalchemy/engine/base.py",
> >> > line 1182, in _execute_context*
> >> > * context)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/sqlalchemy/
> >> > engine/default.py",
> >> > line 470, in do_execute*
> >> > * cursor.execute(statement, parameters)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/pymysql/cursors.py",
> >> line
> >> > 158, in execute*
> >> > * result = self._query(query)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/pymysql/cursors.py",
> >> line
> >> > 308, in _query*
> >> > * conn.query(q)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> pymysql/connections.py",
> >> > line 819, in query*
> >> > * self._execute_command(COMMAND.COM_QUERY, sql)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> pymysql/connections.py",
> >> > line 1037, in _execute_command*
> >> > * self._write_bytes(packet)*
> >> > * File
> >> > "/usr/local/anaconda/lib/python2.7/site-packages/
> >> pymysql/connections.py",
> >> > line 989, in _write_bytes*
> >> > * raise err.OperationalError(2006, "MySQL server has gone away
> (%r)" %
> >> > (e,))*
> >> > *OperationalError: (pymysql.err.OperationalError) (2006, "MySQL server
> >> has
> >> > gone away (error(32, 'Broken pipe'))") [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.day = %(day_1)s AND jobs.pair = %(pair_1)s AND jobs.jobtype =
> >> > %(jobtype_1)s \n LIMIT %(param_1)s'] [parameters: {u'param_1': 1,
> >> u'day_1':
> >> > '2009-02-16', u'jobtype_1': 'DTT', u'pair_1': 'IG.ARIG:IG.MOIG'}]*
> >> >
> >> > At the beginning everything works fine, but because it takes a long
> time
> >> to
> >> > make the computation (around 5 days), every time that I come back to
> see
> >> > the results this happens. I am working with MSNoise 1.4 and I don't
> know
> >> > how to upgrade to MSNoise 1.5.
> >> >
> >> > Does anyone know how to fix this?
> >> >
> >> > Thanks in advance!
> >> >
> >> > Oscar
> >> > _______________________________________________
> >> > MSNoise mailing list
> >> > MSNoise at mailman-as.oma.be
> >> > http://mailman-as.oma.be/mailman/listinfo/msnoise
> >> > _______________________________________________
> >> > MSNoise mailing list
> >> > MSNoise at mailman-as.oma.be
> >> > http://mailman-as.oma.be/mailman/listinfo/msnoise
> >> _______________________________________________
> >> MSNoise mailing list
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> >> http://mailman-as.oma.be/mailman/listinfo/msnoise
> >>
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