Add parallel processing capability for satellite comparisons

2026-01-09 10:47:54 -05:00 · 2021-05-07 13:31:52 -04:00
parent 3f464dbd20
commit 88ab336ec7
4 changed files with 459 additions and 212 deletions
--- a/kaipy/kaiTools.py
+++ b/kaipy/kaiTools.py
@@ -1,5 +1,7 @@
 import numpy as np
 import datetime
+import os
+import glob
 from astropy.time import Time
 from xml.dom import minidom

@@ -11,8 +13,10 @@ def MJD2UT(mjd):

 	return utall

-def genSCXML(scid="sctrack_A",ebfile="msphere",h5traj="sctrack_A.h5"):
+def genSCXML(fdir,ftag,
+	scid="sctrack_A",h5traj="sctrack_A.h5"):

+	(fname,isMPI,Ri,Rj,Rk) = getRunInfo(fdir,ftag)
 	root = minidom.Document()
 	xml = root.createElement('Chimp')
 	root.appendChild(xml)
@@ -22,8 +26,16 @@ def genSCXML(scid="sctrack_A",ebfile="msphere",h5traj="sctrack_A.h5"):
 	fieldsChild = root.createElement("fields")
 	fieldsChild.setAttribute("doMHD","T")
 	fieldsChild.setAttribute("grType","LFM")
-	fieldsChild.setAttribute("ebfile",ebfile)
+	fieldsChild.setAttribute("ebfile",ftag)
+	if isMPI:
+		fieldsChild.setAttribute("isMPI","T")
 	xml.appendChild(fieldsChild)
+	if isMPI:
+		parallelChild = root.createElement("parallel")
+		parallelChild.setAttribute("Ri","%d"%Ri)
+		parallelChild.setAttribute("Rj","%d"%Rj)
+		parallelChild.setAttribute("Rk","%d"%Rk)
+		xml.appendChild(parallelChild)
 	unitsChild = root.createElement("units")
 	unitsChild.setAttribute("uid","EARTH")
 	xml.appendChild(unitsChild)
@@ -34,4 +46,236 @@ def genSCXML(scid="sctrack_A",ebfile="msphere",h5traj="sctrack_A.h5"):

 	return root

+def getRunInfo(fdir,ftag):
+	idStr = "_0000_0000_0000.gam.h5"
+	isMPI = False
+	Ri = 0
+	Rj = 0
+	Rk = 0
+	fOld = os.path.join(fdir,ftag+'.h5')
+	fNew = os.path.join(fdir,ftag+'.gam.h5')
+	try:
+		if (os.path.exists(fOld)):
+			return fOld,isMPI,Ri,Rj,Rk
+		if (os.path.exists(fNew)):
+			return fNew,isMPI,Ri,Rj,Rk
+		fIns = glob.glob(os.path.join(fdir,ftag)+'_*'+idStr)
+		if (len(fIns) > 1):
+			raise ValueError('Should not find more that one parallel file')
+		if (len(fIns) == 0):
+			raise ValueError('No MPI database found')
+		else:
+			isMPI = True
+			fName = fIns[0]
+			Ns = [int(s) for s in fName.split('_') if s.isdigit()]
+			Ri = Ns[-5]
+			Rj = Ns[-4]
+			Rk = Ns[-3]
+			return fName,isMPI,Ri,Rj,Rk
+	except ValueError as ve:
+			print(ve)
+			sys.exit()
+
+def getScIds():
+	scDic = {}
+	scDic['GOES11'] = {'ephemId':'GOES11_K0_MAG',
+						'ephemData':'SC_pos_sm',
+						'ephemCoordSys':'SM',
+						'denId':None,
+						'denData':None,
+						'presId': None,
+						'presData': None,
+						'velId': None,
+						'velData':None,
+						'velCoordSys':None,
+						'magId': 'GOES11_K0_MAG',
+						'magData': 'B_GSM_c',
+						'magCoordSys': 'GSM'
+						}
+	scDic['GOES12'] = {'ephemId':'GOES12_K0_MAG',
+						'ephemData':'SC_pos_sm',
+						'ephemCoordSys':'SM',
+						'denId':None,
+						'denData':None,
+						'presId': None,
+						'presData': None,
+						'velId': None,
+						'velData':None,
+						'velCoordSys':None,
+						'magId': 'GOES12_K0_MAG',
+						'magData': 'B_GSM_c',
+						'magCoordSys': 'GSM'
+						}
+	scDic['GEOTAIL'] = {'ephemId':'GE_K0_MGF',
+						'ephemData':'POS',
+						'ephemCoordSys':'GSE',
+						'denId':'GE_H0_CPI',
+						'denData':'SW_P_Den',
+						'presId': None,
+						'presData': None,
+						'velId': 'GE_H0_CPI',
+						'velData':'SW_Vc',
+						'velCoordSys':'GSE',
+						'magId': 'GE_K0_MGF',
+						'magData': 'IB_vector',
+						'magCoordSys': 'GSE'
+						}
+	scDic['RBSPA'] = {'ephemId':'RBSP-A_MAGNETOMETER_1SEC-GSM_EMFISIS-L3',
+						'ephemData':'coordinates',
+						'ephemCoordSys':'GSM',
+						'denId':'RBSPA_REL04_ECT-HOPE-MOM-L3',
+						'denData':'Dens_p_30',
+						'presId': None,
+						'presData': None,
+						'velId': None,
+						'velData':None,
+						'velCoordSys':None,
+						'magId': 'RBSP-A_MAGNETOMETER_1SEC-GSM_EMFISIS-L3',
+						'magData': 'B_vec_xyz_gse__C1_CP_FGM_SPIN',
+						'magCoordSys': 'GSE'
+						}
+	scDic['RBSPB'] = {'ephemId':'RBSP-B_MAGNETOMETER_1SEC-GSM_EMFISIS-L3',
+						'ephemData':'coordinates',
+						'ephemCoordSys':'GSM',
+						'denId':'RBSPB_REL04_ECT-HOPE-MOM-L3',
+						'denData':'Dens_p_30',
+						'presId': None,
+						'presData': None,
+						'velId': None,
+						'velData':None,
+						'velCoordSys':None,
+						'magId': 'RBSP-B_MAGNETOMETER_1SEC-GSM_EMFISIS-L3',
+						'magData': 'B_vec_xyz_gse__C1_CP_FGM_SPIN',
+						'magCoordSys': 'GSE'
+						}
+	scDic['CLUSTER1'] = {'ephemId':'C1_CP_FGM_SPIN',
+						'ephemData':'sc_pos_xyz_gse__C1_CP_FGM_SPIN',
+						'ephemCoordSys':'GSE',
+						'denId':'C1_PP_CIS',
+						'denData':'N_p__C1_PP_CIS',
+						'presId': None,
+						'presData': None,
+						'velId': 'C1_PP_CIS',
+						'velData':'V_p_xyz_gse__C1_PP_CIS',
+						'velCoordSys':'GSE',
+						'magId': 'C1_CP_FGM_SPIN',
+						'magData': 'B_vec_xyz_gse__C1_CP_FGM_SPIN',
+						'magCoordSys': 'GSE'
+						}
+	scDic['CLUSTER2'] = {'ephemId':'C2_CP_FGM_SPIN',
+						'ephemData':'sc_pos_xyz_gse__C2_CP_FGM_SPIN',
+						'ephemCoordSys':'GSE',
+						'denId':'C2_PP_CIS',
+						'denData':'N_p__C2_PP_CIS',
+						'presId': None,
+						'presData': None,
+						'velId': 'C2_PP_CIS',
+						'velData':'V_p_xyz_gse__C2_PP_CIS',
+						'velCoordSys':'GSE',
+						'magId': 'C2_CP_FGM_SPIN',
+						'magData': 'B_vec_xyz_gse__C2_CP_FGM_SPIN',
+						'magCoordSys': 'GSE'
+						}
+	scDic['CLUSTER3'] = {'ephemId':'C3_CP_FGM_SPIN',
+						'ephemData':'sc_pos_xyz_gse__C3_CP_FGM_SPIN',
+						'ephemCoordSys':'GSE',
+						'denId':'C3_PP_CIS',
+						'denData':'N_p__C3_PP_CIS',
+						'presId': None,
+						'presData': None,
+						'velId': 'C3_PP_CIS',
+						'velData':'V_p_xyz_gse__C3_PP_CIS',
+						'velCoordSys':'GSE',
+						'magId': 'C3_CP_FGM_SPIN',
+						'magData': 'B_vec_xyz_gse__C3_CP_FGM_SPIN',
+						'magCoordSys': 'GSE'
+						}
+	scDic['CLUSTER4'] = {'ephemId':'C4_CP_FGM_SPIN',
+						'ephemData':'sc_pos_xyz_gse__C4_CP_FGM_SPIN',
+						'ephemCoordSys':'GSE',
+						'denId':'C4_PP_CIS',
+						'denData':'N_p__C4_PP_CIS',
+						'presId': None,
+						'presData': None,
+						'velId': 'C4_PP_CIS',
+						'velData':'V_p_xyz_gse__C4_PP_CIS',
+						'velCoordSys':'GSE',
+						'magId': 'C4_CP_FGM_SPIN',
+						'magData': 'B_vec_xyz_gse__C4_CP_FGM_SPIN',
+						'magCoordSys': 'GSE'
+						}
+	scDic['THEMISA'] = {'ephemId':'THA_L1_STATE',
+						'ephemData':'tha_pos_gsmV',
+						'ephemCoordSys':'GSM',
+						'denId':'THA_L2_MOM',
+						'denData':'tha_peim_density',
+						'presId': 'THA_L2_MOM',
+						'presData': 'tha_peim_ptot',
+						'velId': 'THA_L2_MOM',
+						'velData':'tha_peim_velocity_gsm',
+						'velCoordSys':'GSM',
+						'magId': 'THA_L2_MOM',
+						'magData': 'tha_peim_mag',
+						'magCoordSys': 'GSM'
+						}
+	scDic['MMS1'] = {'ephemId':'MMS1_FGM_SRVY_L2',
+						'ephemData':'mms1_fgm_r_gsm_srvy_l2',
+						'ephemCoordSys':'GSM',
+						'denId':'MMS1_FPI_FAST_L2_DIS-MOMS',
+						'denData':'mms1_dis_numberdensity_fast',
+						'presId': 'MMS1_FPI_FAST_L2_DIS-MOMS',
+						'presData': 'mms1_dis_pres_bg_fast',
+						'velId': 'MMS1_FPI_FAST_L2_DIS-MOMS',
+						'velData':'mms1_dis_bulkv_gse_fast',
+						'velCoordSys':'GSE',
+						'magId': 'MMS1_FGM_SRVY_L2',
+						'magData': 'mms1_fgm_b_gsm_srvy_l2',
+						'magCoordSys': 'GSM'
+						}
+	scDic['MMS2'] = {'ephemId':'MMS2_FGM_SRVY_L2',
+						'ephemData':'mms2_fgm_r_gsm_srvy_l2',
+						'ephemCoordSys':'GSM',
+						'denId':'MMS2_FPI_FAST_L2_DIS-MOMS',
+						'denData':'mms2_dis_numberdensity_fast',
+						'presId': 'MMS2_FPI_FAST_L2_DIS-MOMS',
+						'presData': 'mms2_dis_pres_bg_fast',
+						'velId': 'MMS2_FPI_FAST_L2_DIS-MOMS',
+						'velData':'mms2_dis_bulkv_gse_fast',
+						'velCoordSys':'GSE',
+						'magId': 'MMS2_FGM_SRVY_L2',
+						'magData': 'mms2_fgm_b_gsm_srvy_l2',
+						'magCoordSys': 'GSM'
+						}
+	scDic['MMS3'] = {'ephemId':'MMS3_FGM_SRVY_L2',
+						'ephemData':'mms3_fgm_r_gsm_srvy_l2',
+						'ephemCoordSys':'GSM',
+						'denId':'MMS3_FPI_FAST_L2_DIS-MOMS',
+						'denData':'mms3_dis_numberdensity_fast',
+						'presId': 'MMS3_FPI_FAST_L2_DIS-MOMS',
+						'presData': 'mms3_dis_pres_bg_fast',
+						'velId': 'MMS3_FPI_FAST_L2_DIS-MOMS',
+						'velData':'mms3_dis_bulkv_gse_fast',
+						'velCoordSys':'GSE',
+						'magId': 'MMS3_FGM_SRVY_L2',
+						'magData': 'mms3_fgm_b_gsm_srvy_l2',
+						'magCoordSys': 'GSM'
+						}
+	scDic['MMS4'] = {'ephemId':'MMS4_FGM_SRVY_L2',
+						'ephemData':'mms4_fgm_r_gsm_srvy_l2',
+						'ephemCoordSys':'GSM',
+						'denId':'MMS4_FPI_FAST_L2_DIS-MOMS',
+						'denData':'mms4_dis_numberdensity_fast',
+						'presId': 'MMS4_FPI_FAST_L2_DIS-MOMS',
+						'presData': 'mms1_dis_pres_bg_fast',
+						'velId': 'MMS4_FPI_FAST_L2_DIS-MOMS',
+						'velData':'mms4_dis_bulkv_gse_fast',
+						'velCoordSys':'GSE',
+						'magId': 'MMS1_FGM_SRVY_L2',
+						'magData': 'mms4_fgm_b_gsm_srvy_l2',
+						'magCoordSys': 'GSM'
+						}
+
+	return scDic
+
+

--- a/places/cheyenne/satExample.pbs
+++ b/places/cheyenne/satExample.pbs
@@ -0,0 +1,20 @@
+#!/bin/tcsh
+#PBS -A P28100045
+#PBS -N PSATCOMP
+#PBS -j oe
+#PBS -q casper
+#PBS -l walltime=4:00:00
+#PBS -l select=1:ncpus=18
+
+source ~/.tcshrc
+echo $DIR
+cd $DIR
+module purge
+module restore kaiju
+ncar_pylib casper_kaiju_pylib
+
+date
+echo "Running parallel analysis"
+msphParallelSatComp.py
+date
+
--- a/scripts/msphParallelSatComp.py
+++ b/scripts/msphParallelSatComp.py
@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+
+#standard python
+import sys
+import os
+import datetime
+import subprocess
+from xml.dom import minidom
+import argparse
+from argparse import RawTextHelpFormatter
+
+
+#import spacepy and cdasws
+import spacepy
+from spacepy.coordinates import Coords
+from spacepy.time import Ticktock
+import spacepy.datamodel as dm
+from cdasws import CdasWs
+
+
+#import numpy and matplotlib
+import numpy as np
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+import matplotlib.gridspec as gridspec
+
+
+#Kaipy and related
+from   astropy.time import Time
+import h5py
+import kaipy.kaiH5 as kaiH5
+import kaipy.kaiViz as kv
+import kaipy.kaiTools as kaiTools
+
+if __name__ == '__main__':
+    MainS = """Extracts information from satellite trajectory for various
+    spacecraft.  Space craft data is pulled from CDAWeb.  Output CDF files
+    contain data pulled from CDAWeb along with data extracted from GAMERA.
+    Image files of satellite comparisons are also produced.
+    """
+
+
+    parser = argparse.ArgumentParser(description=MainS,
+        formatter_class=RawTextHelpFormatter)
+    parser.add_argument('-id',type=str,metavar='runid',default='msphere',
+        help='RunID of data (default: %(default)s)')
+    parser.add_argument('-path',type=str,metavar='path',default='.',
+        help='Path to directory containing REMIX files (default: %(default)s)')
+    parser.add_argument('-cmd',type=str,metavar='command',default=None,
+        help='Full path to sctrack.x command')
+    parser.add_argument('--keep',action='store_true',
+        help='Keep intermediate files')
+
+    args = parser.parse_args()
+
+    fdir = args.path
+    ftag = args.id
+    cmd = args.cmd
+    keep = args.keep
+
+    if fdir == '.':
+        fdir = os.getcwd()
+
+    if None == cmd:
+        my_env = os.environ.copy()
+        cmd = os.path.join(os.getenv('KAIJUDIR'),'build','bin','sctrack.x')
+    if not (os.path.isfile(cmd) and os.access(cmd, os.X_OK)):
+        print(cmd,'either not found or not executable')
+        sys.exit()
+
+    satCmd = os.path.join(os.getenv('KAIJUDIR'),'scripts',
+        'msphSatComp.py')
+    if not (os.path.isfile(satCmd) and os.access(satCmd, os.X_OK)):
+        print(satCmd,'either not found or not executable')
+        sys.exit()
+    scIds = kaiTools.getScIds()
+
+    process = []
+
+    for scId in scIds:
+        cmdList = [satCmd,'-id',ftag,'-path',fdir,'-cmd',cmd,'-satId',scId]
+        if keep:
+            cmdList.append('--keep')
+        print(cmdList)
+        process.append(subprocess.Popen(cmdList,
+            stdout=subprocess.PIPE, stderr=subprocess.PIPE))
+    for proc in process:
+        proc.communicate()
+    print('All done!')
--- a/scripts/msphSatComp.py
+++ b/scripts/msphSatComp.py
@@ -33,137 +33,6 @@ import kaipy.kaiViz as kv
 import kaipy.kaiTools as kaiTools


-def getScIds():
-	scDic = {}
-	scDic['GOES11'] = {'ephemId':'GOES11_K0_MAG',
-						'ephemData':'SC_pos_sm',
-						'ephemCoordSys':'SM',
-						'denId':None,
-						'denData':None,
-						'presId': None,
-						'presData': None,
-						'velId': None,
-						'velData':None,
-						'velCoordSys':None,
-						'magId': 'GOES11_K0_MAG',
-						'magData': 'B_GSM_c',
-						'magCoordSys': 'GSM'
-						}
-	scDic['GOES12'] = {'ephemId':'GOES12_K0_MAG',
-						'ephemData':'SC_pos_sm',
-						'ephemCoordSys':'SM',
-						'denId':None,
-						'denData':None,
-						'presId': None,
-						'presData': None,
-						'velId': None,
-						'velData':None,
-						'velCoordSys':None,
-						'magId': 'GOES12_K0_MAG',
-						'magData': 'B_GSM_c',
-						'magCoordSys': 'GSM'
-						}
-	scDic['GEOTAIL'] = {'ephemId':'GE_K0_MGF',
-						'ephemData':'POS',
-						'ephemCoordSys':'GSE',
-						'denId':'GE_H0_CPI',
-						'denData':'SW_P_Den',
-						'presId': None,
-						'presData': None,
-						'velId': 'GE_H0_CPI',
-						'velData':'SW_Vc',
-						'velCoordSys':'GSE',
-						'magId': 'GE_K0_MGF',
-						'magData': 'IB_vector',
-						'magCoordSys': 'GSE'
-						}
-	scDic['RBSPA'] = {'ephemId':'RBSP-A_MAGNETOMETER_1SEC-GSM_EMFISIS-L3',
-						'ephemData':'coordinates',
-						'ephemCoordSys':'GSM',
-						'denId':'RBSPA_REL04_ECT-HOPE-MOM-L3',
-						'denData':'Dens_p_30',
-						'presId': None,
-						'presData': None,
-						'velId': None,
-						'velData':None,
-						'velCoordSys':None,
-						'magId': 'RBSP-A_MAGNETOMETER_1SEC-GSM_EMFISIS-L3',
-						'magData': 'B_vec_xyz_gse__C1_CP_FGM_SPIN',
-						'magCoordSys': 'GSE'
-						}
-	scDic['CLUSTER1'] = {'ephemId':'C1_CP_FGM_SPIN',
-						'ephemData':'sc_pos_xyz_gse__C1_CP_FGM_SPIN',
-						'ephemCoordSys':'GSE',
-						'denId':'C1_PP_CIS',
-						'denData':'N_p__C1_PP_CIS',
-						'presId': None,
-						'presData': None,
-						'velId': 'C1_PP_CIS',
-						'velData':'V_p_xyz_gse__C1_PP_CIS',
-						'velCoordSys':'GSE',
-						'magId': 'C1_CP_FGM_SPIN',
-						'magData': 'B_vec_xyz_gse__C1_CP_FGM_SPIN',
-						'magCoordSys': 'GSE'
-						}
-	scDic['MMS1'] = {'ephemId':'MMS1_FGM_SRVY_L2',
-						'ephemData':'mms1_fgm_r_gsm_srvy_l2',
-						'ephemCoordSys':'GSM',
-						'denId':'MMS1_FPI_FAST_L2_DIS-MOMS',
-						'denData':'mms1_dis_numberdensity_fast',
-						'presId': 'MMS1_FPI_FAST_L2_DIS-MOMS',
-						'presData': 'mms1_dis_pres_bg_fast',
-						'velId': 'MMS1_FPI_FAST_L2_DIS-MOMS',
-						'velData':'mms1_dis_bulkv_gse_fast',
-						'velCoordSys':'GSE',
-						'magId': 'MMS1_FGM_SRVY_L2',
-						'magData': 'mms1_fgm_b_gsm_srvy_l2',
-						'magCoordSys': 'GSM'
-						}
-	scDic['MMS2'] = {'ephemId':'MMS2_FGM_SRVY_L2',
-						'ephemData':'mms2_fgm_r_gsm_srvy_l2',
-						'ephemCoordSys':'GSM',
-						'denId':'MMS2_FPI_FAST_L2_DIS-MOMS',
-						'denData':'mms2_dis_numberdensity_fast',
-						'presId': 'MMS2_FPI_FAST_L2_DIS-MOMS',
-						'presData': 'mms2_dis_pres_bg_fast',
-						'velId': 'MMS2_FPI_FAST_L2_DIS-MOMS',
-						'velData':'mms2_dis_bulkv_gse_fast',
-						'velCoordSys':'GSE',
-						'magId': 'MMS2_FGM_SRVY_L2',
-						'magData': 'mms2_fgm_b_gsm_srvy_l2',
-						'magCoordSys': 'GSM'
-						}
-	scDic['MMS3'] = {'ephemId':'MMS3_FGM_SRVY_L2',
-						'ephemData':'mms3_fgm_r_gsm_srvy_l2',
-						'ephemCoordSys':'GSM',
-						'denId':'MMS3_FPI_FAST_L2_DIS-MOMS',
-						'denData':'mms3_dis_numberdensity_fast',
-						'presId': 'MMS3_FPI_FAST_L2_DIS-MOMS',
-						'presData': 'mms3_dis_pres_bg_fast',
-						'velId': 'MMS3_FPI_FAST_L2_DIS-MOMS',
-						'velData':'mms3_dis_bulkv_gse_fast',
-						'velCoordSys':'GSE',
-						'magId': 'MMS3_FGM_SRVY_L2',
-						'magData': 'mms3_fgm_b_gsm_srvy_l2',
-						'magCoordSys': 'GSM'
-						}
-	scDic['MMS4'] = {'ephemId':'MMS4_FGM_SRVY_L2',
-						'ephemData':'mms4_fgm_r_gsm_srvy_l2',
-						'ephemCoordSys':'GSM',
-						'denId':'MMS4_FPI_FAST_L2_DIS-MOMS',
-						'denData':'mms4_dis_numberdensity_fast',
-						'presId': 'MMS4_FPI_FAST_L2_DIS-MOMS',
-						'presData': 'mms1_dis_pres_bg_fast',
-						'velId': 'MMS4_FPI_FAST_L2_DIS-MOMS',
-						'velData':'mms4_dis_bulkv_gse_fast',
-						'velCoordSys':'GSE',
-						'magId': 'MMS1_FGM_SRVY_L2',
-						'magData': 'mms4_fgm_b_gsm_srvy_l2',
-						'magCoordSys': 'GSM'
-						}
-
-	return scDic
-
 def pullVar(cdaObsId,cdaDataId,t0,t1,deltaT):
 	cdas = CdasWs()
 	status,data =  cdas.get_data(cdaObsId,cdaDataId,t0,t1,
@@ -211,6 +80,11 @@ def getSatData(scDic,t0,t1,deltaT):
 		status1 = addVar(mydata,scDic,'Velocity','velId','velData')
 		status1 = addVar(mydata,scDic,'Density','denId','denData')
 		status1 = addVar(mydata,scDic,'Pressure','presId','presData')
+		#Add any metavar since they might be needed for unit/label determination
+		search_key = 'metavar'
+		res = [key for key,val in data.items() if search_key in key]
+		for name in res:
+			mydata[name] = dm.dmarray(data[name],attrs=data[name].attrs)

 	return status,mydata

@@ -318,90 +192,98 @@ def convertGameraVec(x,y,z,ut,fromSys,fromType,toSys,toType):
 	outvec = invec.convert(toSys,toType)
 	return outvec

-def extractGAMERA(data,scDic,mjd0,fdir,cmd):
+def extractGAMERA(data,scDic,mjd0,sec0,fdir,ftag,cmd,keep):
 	Re = 6380.0
 	toRe = 1.0
-	if "km" in data['Ephemeris'].attrs['UNITS']:
-		toRe = 1.0/Re
-		if 'SM' == scDic['ephemCoordSys']:
-			smpos = Coords(data['Ephemeris']*toRe,'SM','car')
-			smpos.ticks = Ticktock(data['Epoch_bin'])
-		elif 'GSM' == scDic['ephemCoordSys'] :
-			scpos = Coords(data['Ephemeris']*toRe,'GSM','car')
-			scpos.ticks = Ticktock(data['Epoch_bin'])
-			smpos = scpos.convert('SM','car')
-		elif 'GSE'== scDic['ephemCoordSys']:
-			scpos = Coords(data['Ephemeris']*toRe,'GSE','car')
-			scpos.ticks = Ticktock(data['Epoch_bin'])
-			smpos = scpos.convert('SM','car')
-		else:
-			print('Coordinate system transformation failed')
-			return
-		elapsedSecs = (smpos.ticks.getMJD()-mjd0)*86400.0
-		scId = scDic['ephemId']
-		fOut = os.path.join(fdir,scId+"sctrack.h5")
-		with h5py.File(fOut,'w') as hf:
-			hf.create_dataset("T" ,data=elapsedSecs)
-			hf.create_dataset("X" ,data=smpos.x)
-			hf.create_dataset("Y" ,data=smpos.y)
-			hf.create_dataset("Z" ,data=smpos.z)
-		chimpxml = kaiTools.genSCXML(scid=scId,h5traj=os.path.basename(fOut))
-		xmlfile = os.path.join(fdir,scId+'.xml')
-		with open(xmlfile,"w") as f:
-			f.write(chimpxml.toprettyxml())
+	if 'UNITS' in data['Ephemeris'].attrs:
+		if "km" in data['Ephemeris'].attrs['UNITS']:
+			toRe = 1.0/Re
+	elif 'UNIT_PTR' in data['Ephemeris'].attrs:
+		if data[data['Ephemeris'].attrs['UNIT_PTR']][0]:
+			toRe = 1.0/Re
+	if 'SM' == scDic['ephemCoordSys']:
+		smpos = Coords(data['Ephemeris'][:,0:3]*toRe,'SM','car')
+		smpos.ticks = Ticktock(data['Epoch_bin'])
+	elif 'GSM' == scDic['ephemCoordSys'] :
+		scpos = Coords(data['Ephemeris'][:,0:3]*toRe,'GSM','car')
+		scpos.ticks = Ticktock(data['Epoch_bin'])
+		smpos = scpos.convert('SM','car')
+	elif 'GSE'== scDic['ephemCoordSys']:
+		scpos = Coords(data['Ephemeris'][:,0:3]*toRe,'GSE','car')
+		scpos.ticks = Ticktock(data['Epoch_bin'])
+		smpos = scpos.convert('SM','car')
+	else:
+		print('Coordinate system transformation failed')
+		return
+	elapsedSecs = (smpos.ticks.getMJD()-mjd0)*86400.0+sec0
+	scId = scDic['ephemId']
+	fOut = os.path.join(fdir,scId+"sctrack.h5")
+	with h5py.File(fOut,'w') as hf:
+		hf.create_dataset("T" ,data=elapsedSecs)
+		hf.create_dataset("X" ,data=smpos.x)
+		hf.create_dataset("Y" ,data=smpos.y)
+		hf.create_dataset("Z" ,data=smpos.z)
+	chimpxml = kaiTools.genSCXML(fdir,ftag,
+		scid=scId,h5traj=os.path.basename(fOut))
+	xmlfile = os.path.join(fdir,scId+'.xml')
+	with open(xmlfile,"w") as f:
+		f.write(chimpxml.toprettyxml())

-		sctrack = subprocess.run([cmd, xmlfile], cwd=fdir,
-								stdout=subprocess.PIPE, stderr=subprocess.PIPE,
-								text=True)
+	sctrack = subprocess.run([cmd, xmlfile], cwd=fdir,
+							stdout=subprocess.PIPE, stderr=subprocess.PIPE,
+							text=True)

-		h5name = os.path.join(fdir, scId + '.sc.h5')
-		h5file = h5py.File(h5name, 'r')
-		ut = kaiTools.MJD2UT(h5file['MJDs'][:])
+	h5name = os.path.join(fdir, scId + '.sc.h5')
+	h5file = h5py.File(h5name, 'r')
+	ut = kaiTools.MJD2UT(h5file['MJDs'][:])

-		bx = h5file['Bx']
-		by = h5file['By']
-		bz = h5file['Bz']
-		if scDic['magCoordSys'] is None:
-			toCoordSys = 'GSM'
-		else:
-			toCoordSys = scDic['magCoordSys']
-		lfmb_out = convertGameraVec(bx[:],by[:],bz[:],ut,
-			'SM','car',toCoordSys,'car')
-		data['GAMERA_MagneticField'] = dm.dmarray(lfmb_out.data,
-			attrs={'UNITS':bx.attrs['Units'],
-			'CATDESC':'Magnetic Field, cartesian'+toCoordSys,
-			'FIELDNAM':"Magnetic field",'AXISLABEL':'B'})
-		vx = h5file['Vx']
-		vy = h5file['Vy']
-		vz = h5file['Vz']
-		if scDic['velCoordSys'] is None:
-			toCoordSys = 'GSM'
-		else:
-			toCoordSys = scDic['velCoordSys']
-		lfmv_out = convertGameraVec(vx[:],vy[:],vz[:],ut,
-			'SM','car',scDic['magCoordSys'],'car')
-		data['GAMERA_Velocity'] = dm.dmarray(lfmv_out.data,
-			attrs={'UNITS':vx.attrs['Units'],
-			'CATDESC':'Velocity, cartesian'+toCoordSys,
-				   'FIELDNAM':"Velocity",'AXISLABEL':'V'})
-		den = h5file['D']
-		data['GAMERA_Density'] = dm.dmarray(den[:],
-			attrs={'UNITS':den.attrs['Units'],
-			'CATDESC':'Density','FIELDNAM':"Density",'AXISLABEL':'n'})
-		pres = h5file['P']
-		data['GAMERA_Pressure'] = dm.dmarray(pres[:],
-			attrs={'UNITS':pres.attrs['Units'],
-			'CATDESC':'Pressure','FIELDNAM':"Pressure",'AXISLABEL':'P'})
-		temp = h5file['T']
-		data['GAMERA_Temperature'] = dm.dmarray(temp[:],
-			attrs={'UNITS':pres.attrs['Units'],
-			'CATDESC':'Temperature','FIELDNAM':"Temperature",
-			'AXISLABEL':'T'})
+	bx = h5file['Bx']
+	by = h5file['By']
+	bz = h5file['Bz']
+	if scDic['magCoordSys'] is None:
+		toCoordSys = 'GSM'
+	else:
+		toCoordSys = scDic['magCoordSys']
+	lfmb_out = convertGameraVec(bx[:],by[:],bz[:],ut,
+		'SM','car',toCoordSys,'car')
+	data['GAMERA_MagneticField'] = dm.dmarray(lfmb_out.data,
+		attrs={'UNITS':bx.attrs['Units'],
+		'CATDESC':'Magnetic Field, cartesian'+toCoordSys,
+		'FIELDNAM':"Magnetic field",'AXISLABEL':'B'})
+	vx = h5file['Vx']
+	vy = h5file['Vy']
+	vz = h5file['Vz']
+	if scDic['velCoordSys'] is None:
+		toCoordSys = 'GSM'
+	else:
+		toCoordSys = scDic['velCoordSys']
+	lfmv_out = convertGameraVec(vx[:],vy[:],vz[:],ut,
+		'SM','car',scDic['magCoordSys'],'car')
+	data['GAMERA_Velocity'] = dm.dmarray(lfmv_out.data,
+		attrs={'UNITS':vx.attrs['Units'],
+		'CATDESC':'Velocity, cartesian'+toCoordSys,
+			   'FIELDNAM':"Velocity",'AXISLABEL':'V'})
+	den = h5file['D']
+	data['GAMERA_Density'] = dm.dmarray(den[:],
+		attrs={'UNITS':den.attrs['Units'],
+		'CATDESC':'Density','FIELDNAM':"Density",'AXISLABEL':'n'})
+	pres = h5file['P']
+	data['GAMERA_Pressure'] = dm.dmarray(pres[:],
+		attrs={'UNITS':pres.attrs['Units'],
+		'CATDESC':'Pressure','FIELDNAM':"Pressure",'AXISLABEL':'P'})
+	temp = h5file['T']
+	data['GAMERA_Temperature'] = dm.dmarray(temp[:],
+		attrs={'UNITS':pres.attrs['Units'],
+		'CATDESC':'Temperature','FIELDNAM':"Temperature",
+		'AXISLABEL':'T'})

+	if not keep:
 		subprocess.run(['rm',h5name])
 		subprocess.run(['rm',xmlfile])
 		subprocess.run(['rm',fOut])
-		return
+	return
+
+

 if __name__ == '__main__':
 	MainS = """Extracts information from satellite trajectory for various
@@ -419,12 +301,18 @@ if __name__ == '__main__':
 		help='Path to directory containing REMIX files (default: %(default)s)')
 	parser.add_argument('-cmd',type=str,metavar='command',default=None,
 		help='Full path to sctrack.x command')
+	parser.add_argument('-satId',type=str,metavar='Satellite Id',
+		default=None,help='Name of Satellite to compare')
+	parser.add_argument('--keep',action='store_true',
+		help='Keep intermediate files')

 	args = parser.parse_args()

 	fdir = args.path
 	ftag = args.id
 	cmd = args.cmd
+	scRequested = args.satId
+	keep = args.keep

 	if fdir == '.':
 		fdir = os.getcwd()
@@ -436,13 +324,13 @@ if __name__ == '__main__':
 		print(cmd,'either not found or not executable')
 		sys.exit()

-	scIds = getScIds()
+	scIds = kaiTools.getScIds()

 	#print(cmddir)
 	#print('Extracting GAMERA data along',scId, 'trajectory')
 	#cmd = "/Users/wiltbemj/src/kaiju/build/bin/sctrack.x"
 	#Pull the timestep information from the magnetosphere files
-	fname = os.path.join(fdir,ftag+'.mix.h5')
+	(fname,isMPI,Ri,Rj,Rk) = kaiTools.getRunInfo(fdir,ftag)
 	nsteps,sIds=kaiH5.cntSteps(fname)
 	gamMJD=kaiH5.getTs(fname,sIds,aID='MJD')
 	gamT=kaiH5.getTs(fname,sIds,aID='time')
@@ -454,9 +342,15 @@ if __name__ == '__main__':
 	t1 = gamUT[-1]
 	deltaT = np.round(gamT[loc+1]-gamT[loc])
 	mjd0 = gamMJD[loc]
+	sec0 = gamT[loc]

 	#scToDo =['CLUSTER1']
-	scToDo = scIds
+	if None == scRequested:
+		scToDo = scIds
+	else:
+		scToDo = []
+		scToDo.append(scRequested)
+
 	for scId in scToDo:
 		print('Getting spacecraft data for', scId)
 		status,data = getSatData(scIds[scId],
@@ -467,7 +361,7 @@ if __name__ == '__main__':
 			print('No data available for', scId)
 		else:
 			print('Extracting GAMERA data')
-			extractGAMERA(data,scIds[scId],mjd0,fdir,cmd)
+			extractGAMERA(data,scIds[scId],mjd0,sec0,fdir,ftag,cmd,keep)
 			cdfname = os.path.join(fdir, scId + '.comp.cdf')
 			if os.path.exists(cdfname):
 				print('Deleting %s' % cdfname)