MSNoise May 2014

msnoise@lists.observatory.be

11 participants
15 discussions

by Oscar Alberto Castro Artola

Hello, I am trying to run *07.plot_dtt.py <http://07.plot_dtt.py>* but there seems to be a problem: *oscar@bayta:~/sweet_noise$ py 07.plot_dtt.py <http://07.plot_dtt.py> * * /home/oscar/anaconda/lib/python2.7/site- packages/numpy/oldnumeric/__init__.py:11: ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy 1.9* * warnings.warn(_msg, ModuleDeprecationWarning)* * /home/oscar/anaconda/lib/python2.7/site-packages/setuptools-2.2- py2.7.egg/pkg_resources.py:991: UserWarning: /home/oscar/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).* * loading 1 days* * Traceback (most recent call last):* * File "07.plot_dtt.py <http://07.plot_dtt.py>", line 115, in <module>* * py1_wmean, py1_wstd = get_wavgwstd(allbut)* * File "07.plot_dtt.py <http://07.plot_dtt.py>", line 59, in get_wavgwstd* * h = grouped.apply(wstd)* * File "/home/oscar/anaconda/lib/python2.7/site- packages/pandas/core/groupby.py", line 424, in apply* * return self._python_apply_general(f)* * File "/home/oscar/anaconda/lib/python2.7/site- packages/pandas/core/groupby.py", line 427, in _python_apply_general* * keys, values, mutated = self.grouper.apply(f, self.obj, self.axis)* * File "/home/oscar/anaconda/lib/python2.7/site- packages/pandas/core/groupby.py", line 883, in apply* * res = f(group)* * File "/home/oscar/anaconda/lib/python2.7/site- packages/pandas/core/groupby.py", line 422, in f* * return func(g, *args, **kwargs)* * File "07.plot_dtt.py <http://07.plot_dtt.py>", line 52, in wstd* * wstd = np.sqrt(np.sum(w * (d - wavg) ** 2) / ((N - 1) * np.sum(w) / N))* * ZeroDivisionError: float division by zero* I do not have much experiencie using python. if anyone has any idea I will appreciate it! Oscar

10 years, 11 months

s03compute_cc number of points issue

by Holly Godfrey

Dear All, I am having difficulty the with s03_compute_cc step. I keep getting the error Traceback (most recent call last): File "s03compute_cc.py", line 284, in <module> tramef_Z[istation] = trame ValueError: operands could not be broadcast together with shapes (1728000) (1727998) I am using input data in SAC format at a sampling rate of 20 Hz. I have checked and checked and checked and all files have 1728000 points in them. In MSNoise I have the resampling rate at 20 Hz, and have also tried it at 10 Hz (where I get ValueError: operands could not be broadcast together with shapes (864000) (863998)). I have tried many different jobs with different stations and days - all give this error. I have used version 1.2.3 without issues on 50 Hz input data (same data as I am using now, just with a lower sampling rate to increase processing speed and decrease file size) and resampling at 25 Hz, but both version 1.2.3 and 1.2.4 don't work for the 20 Hz. I don't understand where the two data points disappear to! Has anyone had this issue? Thanks, -- *Holly Godfrey* Institute of Geophysics, Victoria University of Wellington hollyjoannegodfrey(a)gmail.com

10 years, 11 months

MSNoise CPU-GPU-RAM Processing

by Wardhani, Prima Wira Kusuma

Dear Thomas, Dear All, I want to ask about Scan Archive, Creating New Jobs and CC using MSNoise using CPU-GPU-RAM computing. I processed 49 seismic station, with 2 months data available. For scanning the archive *s01scan_archive.py*, using --init option, and thread option : --init -t 1 : consume 400MB RAM, 17% CPU, 0% GPU : ~24 hours --init -t 2 : consume 1.6GB RAM, 17% CPU, 0% GPU : ~13 hours --init -t 4 : consume 1.6GB RAM, 17% CPU, 0% GPU : ~13 hours the next threads option RAM comsume stuck in 1.6GB, no increase processing using multicore CPU. After finish I tried create new jobs using *s02new_jobs.py* for all station, and it takes 38 minutes for [DEBUG] all station pair for 1 day. I checked the process only consume 1.6GB RAM, 17% CPU, no more than this value. How to optimalize the Processing using RAM-CPU-and GPU? Because it takes along time to process all my Data,, at least it can be optimize using RAM-CPU it will be better. My Computer using 16GB RAM and 4Core(a)3.2GHz, but it only used 1.6GB only.. I tried to insert NumbaPro, but for some reason, it failed,. Can us suggest how to use parallel computing using GPU-CPU-RAM for optimize MSNoise code? Thank you, WARDHANI, Prima Wira Kusuma Master of Earthquake Engineering and Engineering Seismology Universite Joseph Fourier - ISTerre Room 015 prima.dhani06(a)gmail.com +62-81548815815 +33-663964113 がんばります！

10 years, 11 months

NameError: global name 'gps2DistAzimuth' is not defined

by Dimitris Giannopoulos

Dear mailing list, I am facing a problem concerning the cc computation step. Specifically, I have an error message about the coordinates of the stations. I am processing the data of two stations. I have already completed the previous steps without any problem. The following is the error that I have when I execute the "s03compute_cc.py" script: _________________________ Traceback (most recent call last): File "s03compute_cc.py", line 335, in <module> cplAz = azimuth(coordinates, X0, Y0, X1, Y1) File "/localstorage/MSNoise/database_tools.py", line 470, in azimuth dist, azim, bazim = gps2DistAzimuth(y0, x0, y1, x1) NameError: global name 'gps2DistAzimuth' is not defined _____________________________________________ I am going to process R and T components, so the coordinates of the stations are inputted in the station table as it is needed. I think that I did it properly. Did anybody face a similar problem? I also attach a screen-shot of the terminal in order to see when exactly the error appears. Thank you very much in advance. Dimitris

10 years, 11 months

Fwd: Re: Stuck in Compute_cc step

by Thomas Lecocq

Sébastien, (FW to the ML, as this could be useful for many): Le 13/05/2014 16:10, Sébastien Carniato a écrit : > Hi Thomas, > thank you for your quick answer ! > > Indeed, it works when I use only Decimate. I have to check again, but > I think indeed that my data stream are using the same sample rate. You can also check that with the SQLiteManager (group data_availability by "sampling_rate") > I have a bench of other questions : > > *Question 1 : *So now that compute_cc works :), _I would like to know > if the correlations computed are stored_, and in that case where ? I > put the output folder on my desk with the configurator, but nothing > was created so far... If you set "keep_all" to "Y", the 30 minutes CC are stored in the CROSS_CORRELATION folder, named "hh_mm.cc", and these are miniseed files (I know, bad naming, this is going to change in the future). > > *Question 2 :* My data are not continuous. Indeed they are a lot of > days missing, and the maximum length of recording is one day and a > half. _Is it a problem for running MSNoise_ ? Well, MSNoise does correlate M minutes (30 minutes by default) windows, if data is missing, the CC will be corrupted (NaN or infs) and will not be stored. So, normally no problem. BUT, expect results to be quite strange if you have ony like 20% of the day filled with good data. > > *Question 3 :* The only way to get a filter is to create one with the > sqlite manager. Is it normal ? No, there is a bug in the Configurator which doesn't show any empty line. > * > * > *Question 4 : *and the last one : Now when I launch compute_cc, i get > the error : > > 2014-05-13 16:04:21,314 [INFO] *** Starting: Compute CC *** > 2014-05-13 16:04:21,354 [INFO] Will compute ZZ > 2014-05-13 16:04:21,479 [INFO] New CC Job: 2011-01-18 (6 pairs with 3 > stations) > AN.LF1:AN.LF1 > 2014-05-13 16:04:21,595 [DEBUG] Processing pair: AN.LF1 vs AN.LF1 > <msnoise_table_def.Station object at 0x4a06ed0> > <msnoise_table_def.Station object at 0x4a06ed0> > s03compute_cc.py:407: DeprecationWarning: using a non-integer number > instead of an integer will result in an error in the future > trames2hWb[i] = np.zeros(Nfft) > s03compute_cc.py:407: DeprecationWarning: using a non-integer number > instead of an integer will result in an error in the future > trames2hWb[i] = np.zeros(Nfft) > /home/stag01/Bureau/MSNoise-1.2.3/myCorr.py:68: RuntimeWarning: > invalid value encountered in divide > corr /= np.real(normFact) > Traceback (most recent call last): > File "s03compute_cc.py", line 412, in <module> > "%Y-%m-%d", time.gmtime(basetime + itranche * min30 / fe)) > NameError: name 'basetime' is not defined > > Do you know what can be the source of the problem ? Well, first, you should not do Autocorrelation with this version of MSNoise. It'll work normally, but the result is wrong. I'll push a new release very soon that corrects that. But, this problem seems independent. Reading your next mail, it could be related to the file reading part, but it does look strange... Best regards, Thomas

10 years, 11 months

msnoise on hpc cluster

by Wang, Xiao

Hello, I am wondering if MSNoise can run on HPC Cluster. Thanks, Xiao

10 years, 11 months

database_tools.py query failing

by Abbott, Robert E

Thomas, When trying to use s04stack.py, I keep getting the message of "Found 000 updated days" when it is not true. I have tried changing the "–i" interval to no avail (e.g. s04stack.py -m -r -i 100). I think I have traced the problem to the following queries in database_tools.py: if pair == '%': days = session.query(Job).filter(Job.day >= date1).filter(Job.day <= date2).filter(Job.type == type).filter(Job.lastmod >= lastmod).group_by(Job.day).order_by(Job.day).all() else: days = session.query(Job).filter(Job.pair == pair).filter(Job.day >= date1).filter(Job.day <= date2).filter(Job.type == type).filter(Job.lastmod >= lastmod).group_by(Job.day).order_by(Job.day).all() The call from s04stack.py goes to the ELSE conditions, but days == [ ] after the query. If I manually set 'pair = '%' on the line before, then 'days' returns what looks to be correct. As the only difference in the two queries is filtering by Job.pair, maybe that is the problem. I am attaching a screenshot of my jobs table. I manually changed 'lastmod' at one point to yesterday in case the –i switch was not working correctly. I am on Mac OS X. Thanks, Rob +----------------------------+ Robert E. Abbott, Ph.D. Sandia National Laboratories Geophysics Department MS 0750 P.O. Box 5800 Albuquerque, NM 87185-0750 (505) 845-0266 +----------------------------+ +----------------------------+ Robert E. Abbott, Ph.D. Sandia National Laboratories Geophysics Department MS 0750 P.O. Box 5800 Albuquerque, NM 87185-0750 (505) 845-0266 +----------------------------+

10 years, 11 months

Re: [MSNoise] (no subject)

by Thomas Lecocq

Hi Oscar, (cc to the mailing list, it can be very useful to others too) Le 13/05/2014 17:11, Oscar Alberto Castro Artola a écrit : > Hello Thomas, > > I have checked for CCF for 2006-01-01 and is not empty. Everything > seems to be alright! Although I realized that when my filters are too > narrow I get this error: > > *oscar@bayta:~/sweet_noise$ py s05compute_mwcs.py* > 2014-05-13 10:03:03,361 [INFO] We will recompute all MWCS based on the > new REF for TO.BUCU:TO.XALI > 2014-05-13 10:03:03,798 [INFO] We will recompute all MWCS based on the > new REF for TO.PALM:TO.PLLI > 2014-05-13 10:03:04,213 [INFO] We will recompute all MWCS based on the > new REF for TO.PALM:TO.XALI > 2014-05-13 10:03:04,609 [INFO] We will recompute all MWCS based on the > new REF for TO.PLLI:TO.XALI > 2014-05-13 10:03:05,989 [INFO] There are MWCS jobs for some days to > recompute for TO.BUCU:TO.XALI > 2014-05-13 10:03:06,009 [DEBUG] Processing MWCS for: > TO_BUCU_TO_XALI.ZZ.04 - 2006-01-06 - 01 days > /home/oscar/anaconda/lib/python2.7/site-packages/numpy/core/_methods.py:55: > RuntimeWarning: Mean of empty slice. > warnings.warn("Mean of empty slice.", RuntimeWarning) > /home/oscar/anaconda/lib/python2.7/site-packages/numpy/core/_methods.py:77: > RuntimeWarning: Degrees of freedom <= 0 for slice > warnings.warn("Degrees of freedom <= 0 for slice", RuntimeWarning) > Traceback (most recent call last): > File "s05compute_mwcs.py", line 122, in <module> > cur, ref, f.mwcs_low, f.mwcs_high, goal_sampling_rate, -maxlag, > f.mwcs_wlen, f.mwcs_step) > File "/home/oscar/sweet_noise/MWCS.py", line 145, in mwcs > res = sm.regression.linear_model.WLS(phi, v, w**2).fit() > File > "/home/oscar/anaconda/lib/python2.7/site-packages/statsmodels/regression/linear_model.py", > line 381, in __init__ > weights=weights, hasconst=hasconst) > File > "/home/oscar/anaconda/lib/python2.7/site-packages/statsmodels/regression/linear_model.py", > line 79, in __init__ > super(RegressionModel, self).__init__(endog, exog, **kwargs) > File > "/home/oscar/anaconda/lib/python2.7/site-packages/statsmodels/base/model.py", > line 137, in __init__ > self.initialize() > File > "/home/oscar/anaconda/lib/python2.7/site-packages/statsmodels/regression/linear_model.py", > line 88, in initialize > self.rank = rank(self.exog) > File > "/home/oscar/anaconda/lib/python2.7/site-packages/statsmodels/tools/tools.py", > line 381, in rank > D = svdvals(X) > File > "/home/oscar/anaconda/lib/python2.7/site-packages/scipy/linalg/decomp_svd.py", > line 146, in svdvals > check_finite=check_finite) > File > "/home/oscar/anaconda/lib/python2.7/site-packages/scipy/linalg/decomp_svd.py", > line 100, in svd > full_matrices=full_matrices, overwrite_a=overwrite_a) > ValueError: failed to create intent(cache|hide)|optional array-- must > have defined dimensions but got (0,) > > That filter is between 0.04 - 0.046 Hz. 1/ the reason for the first error (filters too narrow) is that you don't have enough data points for doing weighted linear regression. If you use a 10 seconds MWCS_wlen at 20Hz, you have 200 points of data to compute. The FFT is done on the next power of 2 samples, so 256 here. Meaning, you have 256 FFT datapoints between 0 and Nyquist=10Hz, or a frequency step of 0.039 Hz. You filter is 0.006 Hz wide, so, at best, you'll have 1 data point (+ [0,0]) to compute the phase shift, this is not enough. If you want to use such a narrow band, you should either CC at 100 Hz, or edit the s05 file to padd the input data with zeros, in order to have more resolution on the FFT (go up to the second or third next power of 2). > When my filters are broader there is no problem with > /s05compute_mwcs.py/, but when I try to run /s06compute_dtt.py/ I get > this: > > *oscar@bayta:~/sweet_noise$ py s06compute_dtt.py * > */home/oscar/anaconda/lib/python2.7/site-packages/numpy/oldnumeric/__init__.py:11: > ModuleDeprecationWarning: The oldnumeric module will be dropped in > Numpy 1.9* > * warnings.warn(_msg, ModuleDeprecationWarning)* > *2014-05-13 10:07:17,935 [INFO] *** Starting: Compute DT/T **** > */home/oscar/anaconda/lib/python2.7/site-packages/setuptools-2.2-py2.7.egg/pkg_resources.py:991: > UserWarning: /home/oscar/.python-eggs is writable by group/others and > vulnerable to attack when used with get_resource_filename. Consider a > more secure location (set with .set_extraction_path or the > PYTHON_EGG_CACHE environment variable).* > *2014-05-13 10:07:18,139 [DEBUG] Found 731 updated days* > *2014-05-13 10:07:18,203 [INFO] Loading mov=1 days for filter=12* > *2014-05-13 10:07:18,204 [DEBUG] Processing 2005-01-01* > *2014-05-13 10:07:18,216 [DEBUG] Processing 2005-01-02* > *2014-05-13 10:07:18,222 [DEBUG] Processing 2005-01-03* > *2014-05-13 10:07:18,228 [DEBUG] Processing 2005-01-04* > *2014-05-13 10:07:18,235 [DEBUG] Processing 2005-01-05* > *2014-05-13 10:07:18,243 [DEBUG] Processing 2005-01-06* > *2014-05-13 10:07:18,250 [DEBUG] Processing 2005-01-07* > *2014-05-13 10:07:18,257 [DEBUG] Processing 2005-01-08* > *2014-05-13 10:07:18,263 [DEBUG] Processing 2005-01-09* > *2014-05-13 10:07:18,271 [DEBUG] Processing 2005-01-10* > *2014-05-13 10:07:18,278 [DEBUG] Processing 2005-01-11* > *2014-05-13 10:07:18,284 [DEBUG] Processing 2005-01-12* > *Traceback (most recent call last):* > * File "s06compute_dtt.py", line 304, in <module>* > * VecXfilt, prepend=False)* > * File > "/home/oscar/anaconda/lib/python2.7/site-packages/statsmodels/tools/tools.py", > line 289, in add_constant* > * var0 = data.var(0) == 0* > * File > "/home/oscar/anaconda/lib/python2.7/site-packages/numpy/core/_methods.py", > line 111, in _var* > * ret = ret.dtype.type(ret / rcount)* > *AttributeError: 'float' object has no attribute 'dtype'* > 2/ the second error is a bug in numpy 1.8.0, you should try to update numpy to 1.8.1 ! This is not MSNoise :-) Best regards, Thomas

10 years, 11 months

Re: [MSNoise] plotting error

by Kasper van Wijk

Thomas, thanks for the reply. I did find some empty DTT days, and fixed that. Now, I get a different error: /usr/lib64/python2.7/site-packages/pandas/core/common.py:195: DeprecationWarning: numpy boolean negative (the unary `-` operator) is deprecated, use the bitwise_xor (the `^` operator) or the logical_xor function instead. return -res Traceback (most recent call last): File "s07plot_dtt.py", line 130, in <module> plt.fill_between(ALL.index,ALL[dttname]-ALL[errname],ALL[dttname]+ALL[errname],lw=1,color='red',zorder=-1,alpha=0.3) File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py", line 2757, in fill_between interpolate=interpolate, **kwargs) File "/usr/lib64/python2.7/site-packages/matplotlib/axes.py", line 6988, in fill_between x = ma.masked_invalid(self.convert_xunits(x)) File "/usr/lib64/python2.7/site-packages/numpy/ma/core.py", line 2244, in masked_invalid condition = ~(np.isfinite(a)) TypeError: ufunc 'isfinite' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe'' But if I comment out the line that caused this, the process works, and attached is the output. All is quiet under Auckland, I am happy to report. Cheers, Kasper On 12 May 2014 19:02, Thomas Lecocq <thomas.lecocq(a)oma.be> wrote: > Kasper, > > When you changed the mov_stack value, did you re-run MSNoise "from > scratch". The thing is, if jobs have already been done, say, for January > 1 -> January 10, then you modify the mov_stack, and run s04_stack.py a > few days after, Jan1->10 will not be stacked for the 30 day mov_stack. > you have, at least, to run s04stack.py with a "--interval X" (X > 1, > your case probably 20 or 30 max), so the CC jobs in the last 30 days > will be re-considered for stacking. > > As of the plot problem, I've noticed a slight bug in the get_stations() > in the database_tools, but that should only affect the results iif the > stations were input manually in the database and thus not necessarily in > alphabetical order: > (bugfix: > https://github.com/ROBelgium/MSNoise/commit/0dca3cfe101c56f3ed8f6e537412857… > ). > In your case, it looks like the 1-day data is not loaded, could you > confirm the data is present in the folders/files archive ? You could > also print the "day" variable, to know which file is "empty" and causes > the bug. Normally, empty dtt files should not exist... > > Let me know, > > Tom > > > Le 09/05/2014 02:18, Kasper van Wijk a écrit : > > Dear All, > > > > The whole cron.sh was humming a long nicely on our MSNoise network, > until I > > changed from stacking 1,2 and 5 days (initially) to 1,2,3,4,5,30 days. > Now, > > all steps seem to run UNTIL the plot command. Here is the error (after > > putting a print statement on the cause of the problem, df): > > > > (I run as sudo, because root is running the cron.sh overnight:) > > > > [kasper@localhost MSNoise-master]$ sudo python s07plot_dtt.py > > loading 1 days > > Empty DataFrame > > Columns: [A, EA, EM, EM0, M, M0, Pairs] > > Index: [] > > Empty DataFrame > > Columns: [A, EA, EM, EM0, M, M0, Pairs] > > Index: [] > > Traceback (most recent call last): > > File "s07plot_dtt.py", line 102, in <module> > > alldf = alldf.append(df) > > File "/usr/lib64/python2.7/site-packages/pandas/core/frame.py", line > > 4266, in append > > verify_integrity=verify_integrity) > > File "/usr/lib64/python2.7/site-packages/pandas/tools/merge.py", line > > 883, in concat > > return op.get_result() > > File "/usr/lib64/python2.7/site-packages/pandas/tools/merge.py", line > > 964, in get_result > > new_data = self._get_concatenated_data() > > File "/usr/lib64/python2.7/site-packages/pandas/tools/merge.py", line > > 1007, in _get_concatenated_data > > new_data[item] = self._concat_single_item(rdata, item) > > File "/usr/lib64/python2.7/site-packages/pandas/tools/merge.py", line > > 1094, in _concat_single_item > > return com._concat_compat(to_concat, axis=self.axis - 1) > > File "/usr/lib64/python2.7/site-packages/pandas/core/common.py", line > > 1191, in _concat_compat > > axis=axis) > > ValueError: need at least one array to concatenate > > _______________________________________________ > > 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 >

10 years, 11 months

Stuck in Compute_cc step

by Sébastien Carniato

Hello MsNoise users, when trying to launch s03compute_cc.py, I get the error : /appl/anaconda/lib/python2.7/site-packages/numpy-1.8.1-py2.7-linux-x86_64.egg/numpy/oldnumeric/__init__.py:11: ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy 1.9 warnings.warn(_msg, ModuleDeprecationWarning) Traceback (most recent call last): File "s03compute_cc.py", line 70, in <module> from scikits.samplerate import resample File "/home/stag01/Bureau/MSNoise-1.2.3/scikits/samplerate/__init__.py", line 7, in <module> from _samplerate import resample, available_convertors, src_version_str, \ File "/appl/anaconda/lib/python2.7/site-packages/pyximport/pyximport.py", line 431, in load_module language_level=self.language_level) File "/appl/anaconda/lib/python2.7/site-packages/pyximport/pyximport.py", line 210, in load_module mod = imp.load_dynamic(name, so_path) ImportError: Building module scikits.samplerate._samplerate failed: ['ImportError: /home/stag01/.pyxbld/lib.linux-x86_64-2.7/scikits/samplerate/_samplerate.so: undefined symbol: src_get_description\n'] We tried to reinstall scikits, but it happened to be useless... I'm working on linux. Thanks. Sebastien Carniato ENSG Student

10 years, 11 months

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MSNoise May 2014