[MSNoise] Problem with database conection.

Thomas Lecocq Thomas.Lecocq at seismology.be
Thu Jun 15 16:43:59 UTC 2017 

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/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
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>>>>> http://mailman-as.oma.be/mailman/listinfo/msnoise
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