Re: [MSNoise] Problem with database conection.

wrote: Oscar, just try: pip uninstall msnoise and then pip install msnoise Cheers, Tom On 15/06/2017 18:10, Oscar Alberto Castro Artola wrote: 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/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/cur >>>>> sors.py", >>>>> >>>>> line >>>> >>>> 158, in execute* >>>>> * result = self._query(query)* >>>>> * File >>>>> "/usr/local/anaconda/lib/python2.7/site-packages/pymysql/cur >>>>> sors.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 > > --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus _______________________________________________ MSNoise mailing list MSNoise(a)mailman-as.oma.be http://mailman-as.oma.be/mailman/listinfo/msnoise _______________________________________________