Re: [MSNoise] Problem with database conection.

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/command s/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(a)vaw.baug.ethz.ch&gt; 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 > &lt;oscar.cas.art(a)gmail.com&gt;om>: > > 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(a)vaw.baug.ethz.ch&gt; > > 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 &lt;cevan(a)noa.gr&gt;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(a)gmail.com&gt; 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(a)mailman-as.oma.be >>>> http://mailman-as.oma.be/mailman/listinfo/msnoise >>>> _______________________________________________ >>>> MSNoise mailing list >>>> MSNoise(a)mailman-as.oma.be >>>> http://mailman-as.oma.be/mailman/listinfo/msnoise >>>> >>>> _______________________________________________ >>> MSNoise mailing list >>> MSNoise(a)mailman-as.oma.be >>> http://mailman-as.oma.be/mailman/listinfo/msnoise >>> >>> _______________________________________________ >>> >> MSNoise mailing list >> MSNoise(a)mailman-as.oma.be >> http://mailman-as.oma.be/mailman/listinfo/msnoise >> >> _______________________________________________ > MSNoise mailing list > MSNoise(a)mailman-as.oma.be > http://mailman-as.oma.be/mailman/listinfo/msnoise > > _______________________________________________ > MSNoise mailing list MSNoise(a)mailman-as.oma.be http://mailman-as.oma.be/mailman/listinfo/msnoise