How To’s - Recipes¶
Run MSNoise only to have Power Spectral Densities and Spectrograms:¶
This recipe is a kind of “let’s check noise content rapidly”:
msnoise db init --tech 1 msnoise config set startdate=2019-01-01 msnoise config set enddate=2019-02-01 msnoise config set response_path=/path/to/response_files msnoise scan_archive --path /path/to/archive --recursively msnoise populate --fromDA msnoise db update_loc_chan msnoise new_jobs --init --nocc msnoise admin # check the qc_* parameters msnoise qc compute_psd msnoise qc plot_psd YA.UV05.00.HHZ
Run the simplest MSNoise run ever¶
This recipe is a kind of “let’s check this data rapidly”:
msnoise db init --tech 1 msnoise config set startdate=2019-01-01 msnoise config set enddate=2019-02-01 msnoise config set overlap=0.5 msnoise config set mov_stack=1,5,10 msnoise scan_archive --path /path/to/archive --recursively msnoise populate --fromDA msnoise db update_loc_chan msnoise new_jobs --init msnoise admin # add 1 filter in the Filter table # or msnoise db execute "insert into filters (ref, low, mwcs_low, high, mwcs_high, rms_threshold, mwcs_wlen, mwcs_step, used) values (1, 0.1, 0.1, 1.0, 1.0, 0.0, 12.0, 4.0, 1)" msnoise compute_cc msnoise stack -r msnoise reset STACK msnoise stack -m msnoise compute_mwcs msnoise compute_dtt msnoise plot dvv
Run MSNoise using lots of cores on a HPC¶
Avoid Database I/O by using the
With MSNoise 1.6, most of the API calls have been cleaned from calling the
database, for example the
def stack() called a SELECT on the database for
each call, which is useless as configuration parameters are not supposed to
change during the execution of the code. This modification allows running
MSNoise on an HPC infrastructure with a remote central MySQL database.
The new configuration parameter
hpc is used for flagging if MSNoise is
running High Performance. If True, the jobs processed at each step are marked
Done when finished, but the next jobtype according to the workflow is not
created. This removes a lot of select/update/insert actions on the database
and makes the whole much faster (one INSERT instead of tons of
Commands and actions with
hpc = N :
msnoise new_jobs: creates the CC jobs
msnoise compute_cc: processes the CC jobs and creates the STACK jobs
msnoise stack -m: processes the STACK jobs and creates the MWCS jobs
Commands and actions with
hpc = Y :
msnoise new_jobs: creates the CC jobs
msnoise compute_cc: processes the CC jobs
msnoise new_jobs --hpc CC:STACK: creates the STACK jobs based on the CC jobs marked “D”one
msnoise stack -m: processes the STACK jobs
msnoise new_jobs --hpc STACK:MWCS: creates the MWCS jobs based on the STACK jobs marked “D”one
Set up the HPC¶
To avoid having to rewrite MSNoise for using techniques relying on MPI or other parallel computing tools, I decided to go “simple”, and this actually works. The only limitation of the following is that you need to have a strong MySQL server machine that accepts hundreds or thousands of connections. In my case, the MySQL server is running on a computing blade, and its my.cnf is configured to allow 1000 users/connections, and to listen on all its IPs.
The easiest set up (maybe not your sysadmin’s preferred, please check), is to
install miniconda on your home directory and make miniconda’s python executable your default python (I add the paths to .profile).
Then install the requirements and finally MSNoise.
As usual, create a project folder and
msnoise db initthere, choose MySQL and provide the hostname of the machine running the MySQL server.
At that point, your project is ready. I usually request an interactive node on
the HPC for doing the
msnoise populate and
`msnoise scan_archive. Our
jobs scheduler is PBS, so this command
qsub -I -l walltime=02:00:00 -l select=1:ncpus=16:mem=1g
requests an Interactive node with 16 cpus, 1GB ram, for 2 hours. Once connected,
check that the python version is correct (or source .profile again). Because
we requested 16 cores, we can
msnoise -t 16 scan_archive --init.
Depending on the server configuration, you can maybe run the
on the login node, and access it via its hostname:5000 in your browser. If not,
the easiest way to set up the config is running
msnoise config set <parameter>=<value> from the console. To add filters,
do it either:
in the Admin
using MySQL workbench connected to your MySQL server
using such commands
msnoise db execute "insert into filters (ref, low, mwcs_low, high, mwcs_high, rms_threshold, mwcs_wlen, mwcs_step, used) values (1, 0.1, 0.1, 1.0, 1.0, 0.0, 12.0, 4.0, 1)"
msnoise db dump, edit the filter table in CSV format, then
msnoise db import filters --force
Once done, the project is set up and should run. Again, test if all goes OK in an interactive node.
To run on N cores in parallel, we have the advantage that, e.g. for CC jobs, the day-jobs are independent. We can thus request an “Array” of single cores, which is usually quite easy to get on HPCs (most users run heavily parallel codes and request large number of “connected” cores, while we can run “shared”).
The job file in my PBS case looks like this for computing the CC:
#!/bin/bash #PBS -N MSNoise_PDF_CC #PBS -l walltime=01:00:00 #PBS -l select=1:ncpus=1:mem=1g #PBS -l place=shared #PBS -J 1-400 cd /scratch-a/thomas/2019_PDF source /space/hpc-home/thomas/.profile msnoise compute_cc2
This requests 400 cores with 1GB of RAM. The content of my .profile file contains:
# added by Miniconda3 installer export PATH="/home/thomas/miniconda3/bin:$PATH" export MPLBACKEND="Agg"
The last line is important as nodes are usually “head-less” and matplotlib and packages relating to it would fail if they expect a gui-capable system.
For submitting this job, run
qsub qc.job. The process usually routes stdout
and stderr to files in the current directory, make sure to check them if jobs
seem to have failed. If all goes well, calling
msnoise info -j repeatedly
from the login or interactive node’s console should show the evolution of Todo,
In Progress and Done jobs.
HPC experts are welcome to suggest, comment, etc… It’s a quick’n’dirty solution, but it works for me!
When starting to use MSNoise, one will most probably need to re-run different parts of the Workflow more than one time. By default, MSNoise is designed to only process “what’s new”, which is antagonistic to what is wanted. Hereafter, we present cases that will cover most of the re-run techniques:
When adding a new filter¶
If new filter are added to the filters list in the Configurator, one has to reprocess all CC jobs, but not for filters already existing. The recipe is:
Add a new filter, be sure to mark ‘used’=1
Set all other filters ‘used’ value to 0
Redefine the flag of the CC jobs, from ‘D’one to ‘T’odo with the following:
msnoise reset CC --all
Run next commands if needed (stack, mwcs, dtt)
Set back the other filters ‘used’ value to 1
The compute_cc will only compute the CC’s for the new filter(s) and output the results in the STACKS/ folder, in a sub-folder named by a formatted integer from the filter ID. For example: STACKS/01 for ‘filter id’=1, STACKS/02 for ‘filter id’=2, etc.
When changing the REF¶
When changing the REF (
ref_end), the REF stack has to be
msnoise reset STACK --all msnoise stack -r
The REF will then be re-output, and you probably should reset the MWCS jobs to recompute daily correlations against this new ref:
msnoise reset MWCS --all msnoise compute_mwcs
When changing the MWCS parameters¶
If the MWCS parameters are changed in the database, all MWCS jobs need to be reprocessed:
msnoise reset MWCS --all msnoise compute_mwcs
shoud do the trick.
When changing the dt/t parameters¶
msnoise reset DTT --all msnoise compute_dtt
Recompute only the specific days¶
You want to recompute CC jobs after a certain date only, for whatever reason:
msnoise reset CC --rule="day>='2019-01-01'"
SQL experts can also use the
msnoise db execute command (with caution!):
msnoise db execute "update jobs set flag='T' where jobtype='CC' and day>='2019-01-01'"
If you want to only reprocess one day:
msnoise reset CC --rule="day='2019-01-15'"
Define one’s own data structure of the waveform archive¶
The data_structure.py file contains the known data archive formats. If another
data format needs to be defined, it will be done in the
in the current project folder:
Check the “Populate Station Table” step in the workflow/002_populate.
How to have MSNoise work with 2+ data structures at the same time¶
In this case, the easiest solution is to scan the archive(s) with the “Lazy Mode”:
msnoise scan_archive --path /path/to/archive1/ --recursively msnoise scan_archive --path /path/to/archive2/ --recursively
Remember to either manually fill in the station table, or
msnoise populate --fromDA
How to duplicate/dump the MSNoise configuration¶
To export all tables of the current database, run
msnoise db dump
This will create as many CSV files as there are tables in the database.
Then, on a new location, init a new msnoise project and import the tables one by one:
msnoise db init msnoise db import config --force msnoise db import stations --force msnoise db import filters --force msnoise db import data_availability --force msnoise db import jobs --force
Check if my response file works¶
To check if your response file can be used by msnoise, you simply should check that it is readable with ObsPy and contains the response information. In a python shell, do the following:
from obspy.core import UTCDateTime, read_inventory, read st = read("/path/to/a/file/for/station/XX.BBB") inv = read_inventory("/path/to/the/response/for/station/XX.BBB) print(inv) response = inv.get_response(st.id, st.stats.starttime) print(response)
alternatively, if you have configured the path to the response files
response_path) correctly you can also call the msnoise api:
from msnoise.api import connect, preload_instrument_responses st = read("/path/to/a/file/for/station/XX.BBB") db = connect() inv = preload_instrument_responses(db, return_format="inventory") response = inv.get_response(st.id, st.stats.starttime) print(response)
Testing the Dependencies¶
Once installed, you should be able to import the python packages in a python console. MSNoise comes with a little script called bugreport.py that can be useful to check if you have all the required packages (+ some extras).
The usage is such:
$ msnoise bugreport -h usage: msnoise bugreport [-h] [-s] [-m] [-e] [-a] Helps determining what didn\'t work optional arguments: -h, --help show this help message and exit -s, --sys Outputs System info -m, --modules Outputs Python Modules Presence/Version -e, --env Outputs System Environment Variables -a, --all Outputs all of the above
On my Windows machine, the execution of
$ msnoise bugreport -s -m
************* Computer Report ************* ----------------+SYSTEM+------------------- Windows PC1577-as 10 10.0.17134 AMD64 Intel64 Family 6 Model 158 Stepping 9, GenuineIntel ----------------+PYTHON+------------------- Python:3.7.3 | packaged by conda-forge | (default, Jul 1 2019, 22:01:29) [MSC v.1900 64 bit (AMD64)] This script is at d:\pythonforsource\msnoise_stack\msnoise\msnoise\bugreport.py ---------------+MODULES+------------------- Required: [X] setuptools: 41.2.0 [X] numpy: 1.15.4 [X] scipy: 1.3.0 [X] pandas: 0.25.0 [X] matplotlib: 3.1.1 [X] sqlalchemy: 1.3.8 [X] obspy: 1.1.0 [X] click: 7.0 [X] pymysql: 0.9.3 [X] flask: 1.1.1 [X] flask_admin: 1.5.3 [X] markdown: 3.1.1 [X] wtforms: 2.2.1 [X] folium: 0.10.0 [X] jinja2: 2.10.1 Only necessary if you plan to build the doc locally: [X] sphinx: 2.2.0 [X] sphinx_bootstrap_theme: 0.7.1 Graphical Backends: (at least one is required) [ ] wx: not found [ ] pyqt: not found [ ] PyQt4: not found [X] PyQt5: present (no version) [ ] PySide: not found Not required, just checking: [X] json: 2.0.9 [X] psutil: 5.6.3 [ ] reportlab: not found [ ] configobj: not found [X] pkg_resources: present (no version) [ ] paramiko: not found [X] ctypes: 1.1.0 [X] pyparsing: 2.4.2 [X] distutils: 3.7.3 [X] IPython: 7.7.0 [ ] vtk: not found [ ] enable: not found [ ] traitsui: not found [ ] traits: not found [ ] scikits.samplerate: not found
The [X] marks the presence of the module. In the case above, PyQt4 is missing, but that’s not a problem because PyQt5 is present. The “not-required” packages are checked for information, those packages can be useful for reporting / hacking / rendering the data.