Updating the dag scripts

README.md

@@ -6,3 +6,22 @@ Some example setup files for using UMD computing.
 * Example HT condor job files 
 
 This is new material
+
+
+# Copy the code from github. This way assumes you have your public ssh key on github
+git clone [email protected]:mjlarson/umd_computing_examples.git 
+
+# List any changed or new files
+git status
+
+# List where these files came from on github
+git remote -v
+
+# Tell git that you plan to copy the updates of these files to the repository
+git add <filename>
+
+# updates to the local repo
+git commit
+
+# update on the server
+git push

condor/dagman/build_dag.py

@@ -1,24 +1,37 @@
 #!/usr/bin/env python
 
-#Let's make a dag.
-# ./build_dag.py > newdag.dag
-# then hand it to condor
-import numpy as np
-
-jobbase = 'stacked_sens_test'
-script = '/data/condor_builds/users/blaufuss/umd_computing_examples/jupyter/stacked_sensitivity_refactor.py'
-
-counter = 0
-
-time_windows = np.logspace(1,6,6)
-spectra = np.linspace(-3.5,-1,11)
-
-for twin in time_windows:
-    for spec_ind in spectra:
-        #twin = 100
-        #spec_ind = -2.0
-        command = f'python {script} {twin} {spec_ind} {counter}'
-        job_id = f'{jobbase}_{counter}'
-        print(f'JOB {job_id} /data/condor_builds/users/blaufuss/umd_computing_examples/condor/dagman/submit.sub')
-        print(f'VARS {job_id} JOBNAME="{job_id}" command="{command}"')
-        counter += 1
+# test_script.py [-h] -o OUTFILE [-p PLOTFILE] [-n NVALUES] [--gaussian]
+# Want to run 100 files with 10000 values each with gaussian
+# + 100 files with 10000 values each with uniform
+
+executable = "/data/condor_builds/users/mlarson/umd_workshop/umd_computing_examples/condor/dagman/test_script.py"
+sub_name = "/data/condor_builds/users/mlarson/umd_workshop/umd_computing_examples/condor/dagman/submit.sub"
+logdir = "/data/condor_builds/users/mlarson/umd_workshop/umd_computing_examples/condor/dagman/logs/"
+outfile_dir = "/data/condor_builds/users/mlarson/umd_workshop/umd_computing_examples/condor/dagman/output/"
+
+dagman = ""
+
+for gaussian in [True, False]:
+    for i in range(100):
+        if gaussian: job_name = "gaussian_"
+        else: job_name = "uniform_"
+
+        job_name += str(i)
+        dagman += f"JOB {job_name} {sub_name}\n"
+        dagman += f"VARS {job_name} "
+        dagman += f"executable=\"{executable}\" "
+        dagman += f"args=\""
+        dagman += f" -o {outfile_dir}{job_name}.npy "
+        dagman += f" -p {outfile_dir}{job_name}.pdf "
+        dagman += f" -n 10000 "
+        if gaussian:
+            dagman += " --gaussian"
+        dagman += "\""
+
+        dagman += f" logfile=\"{logdir}{job_name}.log\""
+
+        dagman += "\n"
+
+
+with open("my_dagman.dag", "w") as f:
+    f.write(dagman)

condor/dagman/submit.sub

@@ -13,30 +13,30 @@
 #        /data/i3store0/ OR /data/i3scratch0/
 ################################################################
 
-## Jobs requiring more than 1GB of memory or 1CPU can add:
-#request_cpus = <num_cpus>
-#request_memory = 5
-#<mem_in_MB> (default 1GB in umd, 2GB in wisc)
-#request_disk = <disk_in_KB>
-
 # Run the environment script from icetray before anything else
-#executable = /data/condor_builds/users/blaufuss/combo/stable/build/env-shell.sh
-executable = /cvmfs/icecube.opensciencegrid.org/py3-v4.1.0/Ubuntu_18.04_x86_64/metaprojects/combo/V01-00-00/env-shell.sh
+executable = $(executable)
+Arguments = "$(args)"
+
 # Where the log, out, err files will live
-basedir     = /data/condor_builds/users/blaufuss/umd_computing_examples/condor/dagman/
-output      = $(basedir)$(Jobname).$(Cluster).out
-error       = $(basedir)$(Jobname).$(Cluster).err
-should_transfer_files = YES
+output      = $(logfile)
+error       = $(logfile)
+
+should_transfer_files = NO
 
 # Only 1 log file for all jobs
-log = /data/condor_builds/users/blaufuss/umd_computing_examples/condor/dagman/$(Jobname).log
+# "log" holds the information about how Condor is assigning the job
+log = $(logfile)
+
+## Jobs requiring more than 1GB of memory or 1CPU can add:
+request_cpus = 1
+request_memory = 2GB
+request_disk = 1GB
 
 # Other condor stuff
 notification   = never
 getenv         = true
 universe       = vanilla
 
 # Submit !
-Arguments = $(command)
 queue
 

condor/dagman/test_script.py

@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+
+import os
+import pickle
+import argparse
+import matplotlib
+matplotlib.use('Agg')
+
+from matplotlib import pyplot as plt
+import numpy as np
+from scipy.stats import norm
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-o", "--outfile", type=str, required=True,
+                    help = "Name of the output file (ending in .npy")
+parser.add_argument("-p", "--plotfile", type=str, default=None,
+                    help = "If given, create a histogram of the values and save it here.")
+parser.add_argument("-n", "--nvalues", type=int,
+                    default = 10000,
+                    help = "The number of random values to create")
+parser.add_argument("--gaussian", default=False, action="store_true",
+                    help = "If given, produce values from a Gaussian instead of"
+                           " from a uniform distribution")
+args = parser.parse_args()
+
+
+# Going to generate some basic test data
+if args.gaussian:
+    my_random_values = norm.rvs(loc=0, scale=1, size=args.nvalues)
+else:
+    my_random_values = np.random.uniform(low=-1, high=1, size=args.nvalues)
+
+# Save the files
+np.save(args.outfile, my_random_values)
+
+# Are we making a plot?
+if args.plotfile is not None:
+    fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(8, 5))
+
+    ax.hist(my_random_values,
+            bins = np.linspace(-1, 1, 101),
+            histtype='step',
+            linewidth=3,
+            color='k',
+            label = "My values!")
+
+    # Add a legend
+    ax.legend(loc='upper right', framealpha=1, fontsize=12)
+
+    # Make it look nice
+    ax.grid(alpha=0.25)
+    ax.set_xlim(xmin=-1, xmax=1)
+    ax.set_xlabel("Random values", fontsize=16)
+    ax.set_ylabel("Number of values in each bin", fontsize=16)
+
+    # Make the numbers on the axis larger
+    ax.tick_params(labelsize=12)
+
+    # Move things around to fix any spacing issues
+    fig.tight_layout()
+
+    # And save
+    plt.savefig(args.plotfile)
+

condor/dagman/test_single.sub

@@ -0,0 +1,22 @@
+# Unix submit description file
+# sleep.sub -- simple sleep job
+universe		= vanilla
+getenv			= True
+
+executable              = test_script.py
+
+log                     = Busy.log
+output                  = Busy.$(Process).out
+error                   = Busy.$(Process).error
+
+should_transfer_files   = Yes
+when_to_transfer_output = ON_EXIT
+
+arguments		= "-o test1.npy --gaussian"
+queue
+
+arguments		= "-o test2.npy --gaussian"
+queue
+
+arguments		= "-o test3.npy"
+queue