15 Jun
2017
15 Jun
'17
6:43 p.m.
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(a)vaw.baug.ethz.ch>
wrote:
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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(a)gmail.com>om>:
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http://mailman-as.oma.be/mailman/listinfo/msnoise 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>
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(a)noa.gr>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> 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
> _______________________________________________
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