add

genps

@@ -8,13 +8,19 @@
 
  var_list=(sfc_ps sfcship_ps sondes_ps)
 
+<<<<<<< HEAD
 #gridfile=regrid/lonlat_sfc-letkf-nbc.nc
+=======
+>>>>>>> 1e65deecb93b2e797e71d7c27ba0128b055d9edd
  gridfile=regrid/lonlat_sfc-letkf.nc
  if [ ! -f ${gridfile} ]
  then
    cd regrid
    rm -f fv3latlon.nc
+<<<<<<< HEAD
   #interp.sh ${case_dir}/sfc-letkf/analysis.2/increment/
+=======
+>>>>>>> 1e65deecb93b2e797e71d7c27ba0128b055d9edd
    interp.sh ${case_dir}/sfc-letkf/analysis/increment/
    cd ..
    mv regrid/fv3latlon.nc ${gridfile}

main_timing.py

@@ -0,0 +1,341 @@
+#########################################################################
+#$Id: bld.py 28 2021-01-21 15:10:31Z whuang $
+#$Revision: 28 $
+#$HeadURL: file:///Users/whuang/.wei_svn_repository/trunk/jedi-build-tools/bld.py $
+#$Date: 2021-01-21 08:10:31 -0700 (Thu, 21 Jan 2021) $
+#$Author: whuang $
+#########################################################################
+
+import getopt
+import os, sys
+import subprocess
+import time
+import datetime
+
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+
+def cmdout(command):
+    result = run(command, stdout=PIPE, stderr=PIPE, universal_newlines=True, shell=True)
+    ostr = result.stdout
+    return ostr.strip()
+
+""" Profiler """
+class Profiler:
+  """ Constructor """
+  def __init__(self, debug=0, corelist=[], casename=None, output=0,
+               nodelist=[], workdir=None, linear=0):
+
+    """ Initialize class attributes """
+    self.debug = debug
+    self.workdir = workdir
+    self.corelist = corelist
+    self.nodelist = nodelist
+    self.casename = casename
+    self.output = output
+    self.linear = linear
+
+    self.shortest_time = 0.1
+
+    if(workdir is None):
+      print('workdir not defined. Exit.')
+      sys.exit(-1)
+
+    if(len(corelist) < 1):
+      print('corelist not defined. Exit.')
+      sys.exit(-1)
+
+    if(len(nodelist) < 1):
+      print('nodelist not defined. Exit.')
+      sys.exit(-1)
+
+    self.colorlist = ['red', 'green', 'cyan', 'blue', 'magenta',
+                      'firebrick', 'lime', 'teal']
+    self.linestyle = ['solid', 'solid', 'solid', 'solid', 'solid',
+                      'dashed', 'dashed', 'dashed']
+    self.function_list = ['Timers::Total',
+                          'GETKFSolver::computeHofX',
+                          'GETKFSolver::measurementUpdate',
+                          'sum(oops::Increment)',
+                          'sum(oops::State)',
+                          'sum(oops::UnstructuredInterpolator)',
+                          'sum(oops::Parameters)',
+                          'sum(oops::Geometry']
+    self.fullfunction_list = ['util::Timers::Total',
+                              'oops::GETKFSolver::computeHofX',
+			      'oops::GETKFSolver::measurementUpdate',
+			      'oops::Increment',
+			      'oops::State',
+			      'oops::UnstructuredInterpolator',
+			      'oops::Parameters',
+			      'oops::Geometry']
+    self.statstime = []
+    for i in range(len(self.fullfunction_list)):
+      tmax = {}
+      for n in range(len(self.nodelist)):
+        tmax[n] = 0.0
+      self.statstime.append(tmax)
+
+  def set_linear(self, linear=1):
+    self.linear = linear
+
+  def set_output(self, output=1):
+    self.output = output
+
+  def process(self):
+    for n in range(len(self.nodelist)):
+      rundir = '%s/%s/run_80.40t%dn_%dp' %(self.workdir, self.casename,
+                self.nodelist[n], self.corelist[n])
+      flnm = '%s/stdoutNerr/stdout.00000000' %(rundir)
+      if(self.debug):
+        print('Processing node: %d, as file: %s' %(self.nodelist[n], flnm))
+      if(os.path.exists(flnm)):
+        pass
+      else:
+        print('Filename ' + flnm + ' does not exit. Stop')
+        sys.exit(-1)
+
+      with open(flnm) as fp:
+        lines = fp.readlines()
+       #line = fp.readline()
+        num_lines = len(lines)
+       #print('Total number of lines: ', num_lines)
+
+        nl = 0
+        while(nl < num_lines):
+          if(lines[nl].find('Parallel Timing Statistics') > 0):
+           #if(self.debug):
+           #  print('lines[%d]: %s' %(nl, lines[nl]))
+            self.parallel_time_stats(n, lines, nl)
+            break
+          nl += 1
+
+  def parallel_time_stats(self, n, lines, nl):
+    going = 1
+    ns = nl + 3
+    while(going):
+      line = lines[ns].strip()
+      ns += 1
+      if(line.find('Parallel Timing Statistics') > 0):
+        going = 0
+        break
+
+     #print('Line ' + str(ns) + ': ' + line)
+
+      item = line.split(': ')
+     #print(item)
+      nlist = item[0].strip().split(' ')
+      name = nlist[1]
+
+      tstr = item[1].strip()
+      while(tstr.find('  ') > 0):
+        tstr = tstr.replace('  ', ' ')
+      nlist = tstr.split(' ')
+      tmin = float(nlist[0])
+      tmax = float(nlist[1])
+      tavg = float(nlist[2])
+
+      self.updatestats(n, name, tmax)
+
+  def updatestats(self, n, name, tmax):
+    for i in range(len(self.fullfunction_list)):
+      if(name.find(self.fullfunction_list[i]) >= 0):
+        self.statstime[i][n] = tmax
+        return
+
+  def plot(self):
+    try:
+      plt.close('all')
+      plt.clf()
+      plt.cla()
+    except Exception:
+      pass
+
+    title = '%s Timing' %(self.casename)
+
+    nl = len(self.nodelist)
+    x = np.zeros((nl), dtype=float)
+    y = np.zeros((nl), dtype=float)
+    z = np.zeros((nl), dtype=float)
+    xlabels = []
+    for k in range(nl):
+      x[k] = self.nodelist[k]
+      lbl = '%d' %(self.nodelist[k])
+      xlabels.append(lbl)
+
+    pmin = 1.0/128.0
+    pmax = 256.0
+    ylabels = []
+    yp = []
+    pcur = pmin/2.0
+    while(pcur < pmax):
+      pcur *= 4.0
+      lbl = '%6.2f' %(pcur)
+      ylabels.append(lbl)
+      yp.append(pcur)
+      print('yp = ', yp)
+
+    fig = plt.figure()
+    ax = plt.subplot()
+
+    if(self.linear):
+      plt.xscale('linear')
+    else:
+     #plt.xscale('log', base=2)
+     #plt.yscale('log', base=10)
+      plt.xscale('log', basex=2)
+      plt.yscale('log', basey=2)
+      plt.xticks(x, xlabels)
+     #plt.xticks(x, xlabels, rotation ='vertical')
+      plt.yticks(yp, ylabels)
+
+    pmin = 1.0e20
+    pmax = 0.0
+
+    txtname = 'main_timing_%s.csv' %(self.casename)
+    OPF = open(txtname, 'w')
+    header = '%40s' %('Function Name')
+    for k in range(nl):
+      header = '%s, %12d' %(header, self.nodelist[k])
+    OPF.write(header+'\n')
+
+    for i in range(len(self.function_list)):
+      print('self.function_list[%d] = %s' %(i, self.function_list[i]))
+      print('self.statstime[i] = ', self.statstime[i])
+      txtinfo = '%40s' %(self.function_list[i])
+      npnts = 0
+      for k in range(nl):
+        y[k] = 0.001*self.statstime[i][k]/60.0
+        if(pmin > y[k]):
+          pmin = y[k]
+        if(pmax < y[k]):
+          pmax = y[k]
+        txtinfo = '%s, %12.2f' %(txtinfo, y[k])
+        if(y[k] > self.shortest_time):
+          npnts += 1
+      OPF.write(txtinfo+'\n')
+      print('x = ', x[0:npnts])
+      print('y = ', y[0:npnts])
+      print('self.colorlist[%d] = %s' %(i, self.colorlist[i]))
+      print('self.linestyle[%d] = %s' %(i, self.linestyle[i]))
+      if(npnts > 1):
+        ax.plot(x[0:npnts], y[0:npnts], color=self.colorlist[i], linewidth=2,
+                linestyle=self.linestyle[i], alpha=0.9)
+    OPF.close()
+
+    if(self.linear == 0):
+      for i in range(len(self.fullfunction_list)):
+        npnts = 0
+        for k in range(nl):
+          fact = 1.0/np.log2(2*self.nodelist[k])
+          z[k] = 0.001*self.statstime[i][0]*fact/60.0
+          if(z[k] > self.shortest_time):
+            npnts += 1
+       #https://matplotlib.org/stable/gallery/lines_bars_and_markers/linestyles.html
+        if(npnts > 1):
+          ax.plot(x[0:npnts], z[0:npnts], color='black', linewidth=1, alpha=0.5, linestyle='dotted')
+
+    plt.grid()
+
+   #Same limits for everybody!
+    print('pmin: %f, pmax: %f' %(pmin, pmax))
+
+   #if(pmin < self.shortest_time):
+   #  pmin = self.shortest_time
+   #if(pmax < 10000.0):
+   #  pmax = 10000.0
+
+    pmin = 1.0/128.0
+    pmax = 256.0
+
+    plt.xlim(x[0], x[-1])
+    plt.ylim(pmin, pmax)
+
+   #general title
+   #title = '%s Timing (in minutes), min: %8.2f, max: %8.2f' %(self.casename, pmin, pmax)
+    title = '%s Timing (in minutes)' %(self.casename)
+   #plt.suptitle(title, fontsize=13, fontweight=0, color='black', style='italic', y=1.02)
+    plt.suptitle(title, fontsize=16, fontweight=1, color='black')
+
+   #Create a big subplot
+    bs = fig.add_subplot(111, frameon=False)
+   #plt.subplots_adjust(bottom=0.2, right=0.70, top=0.8)
+   #plt.subplots_adjust(bottom=0.2, right=0.675, top=0.8)
+    plt.subplots_adjust(bottom=0.2, right=0.65, top=0.8)
+   #plt.subplots_adjust(bottom=0.2, right=0.5, top=0.8)
+
+   #hide tick and tick label of the big axes
+    plt.tick_params(labelcolor='none', top='off', bottom='off', left='off', right='off')
+
+    bs.set_xlabel('Node', labelpad=10) # Use argument `labelpad` to move label downwards.
+    bs.set_ylabel('Time (minutes)', labelpad=20)
+
+   #Create the legend
+    fig.legend(ax, labels=self.function_list,
+           loc="center right",   # Position of legend
+           fontsize=6,
+           borderpad=1.2,
+           handlelength=1.5
+           )
+
+#          borderpad=1.2,
+#          labelspacing=1.2,
+#          handlelength=1.5
+
+   #Adjust the scaling factor to fit your legend text completely outside the plot
+   #(smaller value results in more space being made for the legend)
+
+    if(self.linear):
+      imgname = 'lin_%s_main_timing.png' %(self.casename)
+    else:
+      imgname = 'log_%s_main_timing.png' %(self.casename)
+
+    if(self.output):
+      plt.savefig(imgname)
+    else:
+      plt.show()
+
+#--------------------------------------------------------------------------------
+if __name__== '__main__':
+  debug = 1
+  casename = 'sondes'
+ #workdir = '/work2/noaa/gsienkf/weihuang/jedi/case_study'
+  workdir = '/scratch2/BMC/gsienkf/Wei.Huang/tools/vis_tools'
+  corelist = [36, 78, 156, 312]
+ #corelist = [36, 72, 144, 288]
+  nodelist = [1, 2, 4, 8]
+  output = 0
+  linear = 1
+
+  opts, args = getopt.getopt(sys.argv[1:], '', ['debug=', 'workdir=',
+                             'corelist=', 'nodelist=', 'casename='])
+
+  for o, a in opts:
+    if o in ('--debug'):
+      debug = int(a)
+    elif o in ('--workdir'):
+      workdir = a
+    elif o in ('--corelist'):
+      corelist = a
+    elif o in ('--nodelist'):
+      nodelist = a
+    elif o in ('--casename'):
+      casename = a
+    elif o in ('--output'):
+      output = a
+    elif o in ('--linear'):
+      linear = int(a)
+    else:
+      assert False, 'unhandled option'
+
+  pr = Profiler(debug=debug, corelist=corelist, nodelist=nodelist, output=output,
+                workdir=workdir, casename=casename, linear=linear)
+  pr.process()
+  for linear in [1, 0]:
+    pr.set_linear(linear=linear)
+    for output in [0, 1]:
+   #for output in [1]:
+      pr.set_output(output=output)
+      pr.plot()
+

make-panel.py

@@ -43,7 +43,8 @@ def genit(self):
 
    #iterate over axes
     for i, ax in enumerate(axes):
-      imageprefix = '%s_%s_increment_lev' %(casename, varname)
+     #imageprefix = '%s_%s_increment_lev' %(casename, varname)
+      imageprefix = '%s_lev' %(casename)
       imgname = img[i].replace('FAKENAME', imageprefix)
       im = image.imread(imgname)
       ax.axis('off')