-
Notifications
You must be signed in to change notification settings - Fork 358
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'gwastro:master' into master
- Loading branch information
Showing
109 changed files
with
1,554 additions
and
988 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,56 @@ | ||
name: run small inference workflow using pegasus + condor | ||
|
||
on: [push, pull_request] | ||
|
||
jobs: | ||
build: | ||
runs-on: ubuntu-20.04 | ||
steps: | ||
- uses: actions/checkout@v1 | ||
- name: Set up Python | ||
uses: actions/setup-python@v1 | ||
with: | ||
python-version: 3.8 | ||
- name: install condor | ||
run: | | ||
wget -qO - https://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add - | ||
echo "deb http://research.cs.wisc.edu/htcondor/ubuntu/8.9/focal focal contrib" | sudo tee -a /etc/apt/sources.list | ||
echo "deb-src http://research.cs.wisc.edu/htcondor/ubuntu/8.9/focal focal contrib" | sudo tee -a /etc/apt/sources.list | ||
sudo apt-get update | ||
sudo apt-get install minihtcondor | ||
sudo systemctl start condor | ||
sudo systemctl enable condor | ||
- name: install pegasus | ||
run: | | ||
wget https://download.pegasus.isi.edu/pegasus/ubuntu/dists/bionic/main/binary-amd64/pegasus_5.0.1-1+ubuntu18_amd64.deb | ||
sudo apt install ./pegasus_5.0.1-1+ubuntu18_amd64.deb | ||
- run: sudo apt-get install *fftw3* intel-mkl* | ||
- name: Install pycbc | ||
run: | | ||
python -m pip install --upgrade pip setuptools | ||
pip install -r requirements.txt | ||
pip install . | ||
- name: retrieving data | ||
run: bash -e examples/inference/single/get.sh | ||
- name: generating, submitting and running workflow | ||
run: | | ||
cp examples/inference/single/single.ini ./ | ||
cp examples/workflow/inference/small_test/*.ini ./ | ||
bash -e examples/workflow/inference/small_test/gen.sh | ||
condor_status | ||
cd gw_output | ||
bash -e ../examples/search/submit.sh | ||
./status | ||
python ../examples/search/check_job.py | ||
find submitdir/work/ -type f -name '*.tar.gz' -delete | ||
- name: store log files | ||
if: always() | ||
uses: actions/upload-artifact@v2 | ||
with: | ||
name: logs | ||
path: gw_output/submitdir/work | ||
- name: store result page | ||
uses: actions/upload-artifact@v2 | ||
with: | ||
name: results | ||
path: html |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -17,38 +17,33 @@ | |
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. | ||
|
||
""" | ||
Programe for concatenating the output of the geometric aligned bank dagman. | ||
Program for concatenating the output of the geometric aligned bank dagman. | ||
This will gather all the meta-output files and create a valid template bank | ||
xml file. | ||
""" | ||
import logging | ||
import fileinput | ||
import glob | ||
import argparse | ||
import numpy | ||
import pycbc.version | ||
import h5py | ||
from glue.ligolw import ligolw | ||
from glue.ligolw import lsctables | ||
from glue.ligolw import utils | ||
from ligo.lw import utils | ||
from pycbc import tmpltbank | ||
from numpy import loadtxt | ||
import pycbc | ||
import pycbc.psd | ||
import pycbc.strain | ||
import pycbc.version | ||
import pycbc.tmpltbank | ||
from pycbc.waveform import get_waveform_filter_length_in_time | ||
from pycbc.io.ligolw import LIGOLWContentHandler | ||
|
||
|
||
__author__ = "Ian Harry <[email protected]>" | ||
__version__ = pycbc.version.git_verbose_msg | ||
__date__ = pycbc.version.date | ||
__program__ = "pycbc_aligned_bank_cat" | ||
|
||
# Read command line options | ||
usage = """usage: %prog [options]""" | ||
_desc = __doc__[1:] | ||
parser = argparse.ArgumentParser(description=_desc, | ||
parser = argparse.ArgumentParser(description=__doc__, | ||
formatter_class=tmpltbank.IndentedHelpFormatterWithNL) | ||
|
||
parser.add_argument("--version", action="version", version=__version__) | ||
|
@@ -163,12 +158,9 @@ temp_bank = numpy.array([mass1,mass2,spin1z,spin2z]).T | |
# needed for any reason, this code would have to be able to recalculate the | ||
# moments (or read them in) and use the correct value of f0 and pn-order | ||
if options.metadata_file: | ||
class LIGOLWContentHandler(ligolw.LIGOLWContentHandler): | ||
pass | ||
lsctables.use_in(LIGOLWContentHandler) | ||
outdoc = utils.load_filename(options.metadata_file,\ | ||
gz = options.metadata_file.endswith("gz"), | ||
contenthandler=LIGOLWContentHandler) | ||
outdoc = utils.load_filename(options.metadata_file, | ||
compress='auto', | ||
contenthandler=LIGOLWContentHandler) | ||
else: | ||
outdoc = None | ||
if options.output_file.endswith(('.xml','.xml.gz','.xmlgz')): | ||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -23,29 +23,28 @@ metric approximation to the parameter space. | |
|
||
from __future__ import division | ||
|
||
import argparse | ||
import logging | ||
import numpy | ||
import h5py | ||
from ligo.lw import table, lsctables, utils as ligolw_utils | ||
import pycbc | ||
import pycbc.version | ||
from pycbc import tmpltbank, psd, strain | ||
from pycbc.io.ligolw import LIGOLWContentHandler | ||
import matplotlib | ||
matplotlib.use('Agg') | ||
import pylab | ||
|
||
|
||
__author__ = "Ian Harry <[email protected]>" | ||
__version__ = pycbc.version.git_verbose_msg | ||
__date__ = pycbc.version.date | ||
__program__ = "pycbc_bank_verification" | ||
|
||
import argparse | ||
import os, sys | ||
import copy | ||
import logging | ||
import numpy | ||
import h5py | ||
from glue.ligolw import ligolw, table, lsctables, utils as ligolw_utils | ||
from pycbc import tmpltbank, psd, strain, pnutils | ||
import matplotlib | ||
matplotlib.use('Agg') | ||
import pylab | ||
|
||
# Read command line option | ||
_desc = __doc__[1:] | ||
parser = argparse.ArgumentParser(description=_desc, | ||
parser = argparse.ArgumentParser(description=__doc__, | ||
formatter_class=tmpltbank.IndentedHelpFormatterWithNL) | ||
|
||
# Begin with code specific options | ||
|
@@ -195,12 +194,6 @@ logging.info("Reading template bank.") | |
|
||
|
||
if opts.input_bank.endswith(('.xml','.xml.gz','.xmlgz')): | ||
# dummy class needed for loading LIGOLW files | ||
class LIGOLWContentHandler(ligolw.LIGOLWContentHandler): | ||
pass | ||
|
||
lsctables.use_in(LIGOLWContentHandler) | ||
|
||
indoc = ligolw_utils.load_filename(opts.input_bank, | ||
contenthandler=LIGOLWContentHandler) | ||
template_list = table.get_table(indoc, | ||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.