Merge branch 'master' of https://github.com/JanThorbecke/OpenSource

Author: Jbrackenhoff

marchenko/demo/oneD/p5all.scr

@@ -16,16 +16,15 @@ while (( ishot < nshots ))
 do
 
 	(( xsrc = -2250000 + ${ishot}*${dxshot} ))
-	(( tr1 = 901 - ${ishot} ))
-	(( tr2 = ${tr1} + 900 ))
+	(( tr1 = $nshots - ${ishot} ))
+	(( tr2 = ${tr1} + $nshots - 1 ))
 	echo xsrc=$xsrc tr1=$tr1 tr2=$tr2
 
 	(( ishot = $ishot + 1))
 
 	suwind < shot5_rp.su key=tracl min=$tr1 max=$tr2 | \
 	sushw key=sx,gx,fldr,trwf \
-	a=$xsrc,-2250000,$ishot,901 b=0,5000,0,0 j=0,901,0,0 | \
+	a=$xsrc,-2250000,$ishot,$nshots b=0,$dxshot,0,0 j=0,$nshots,0,0 | \
 	suchw key1=offset key2=gx key3=sx c=-1 d=1000 >> shotsdx5_rp.su
 
 done
-

marchenko3D/demo/WS15/MarchenkoWorkshop.pdf

@@ -0,0 +1,66 @@
+
+*1* Source the setup.sh script that you can find on 
+
+source /home/users/jan/WS15setup.sh
+
+The setup.sh script completes the following tasks:
+
+-a-Set PATH to find Seismic Unix and Marchenko code 
+export CWPROOT=/home/users/jan/SeisUnix/
+export PATH=.:$CWPROOT/bin:/lus/scratch/$USER/OpenSource/bin:$PATH:
+
+-b- Create working directory 
+/lus/scratch/$USER
+
+-c- set up compilation environment with the Intel compiler
+
+-d- Get the Marchenko software (and other utilities modeling code))
+git clone https://github.com/JanThorbecke/OpenSource.git
+
+if the git clone takes too much time you can copy the source code:
+
+cp -rp /lus/snx11029/jan/OpenSource /lus/scratch/$USER/
+ 
+
+*2* after the set-up the code can be compiled 
+
+cd OpenSource
+cp Make_include_swan Make_include
+make clean
+make 
+
+After succesfull complication the code can be used for running the exercises and demo's
+
+
+*3* Running jobs 
+
+To run example jobs must be submitted to the Workload Manager PBSpro.
+An example script can be found on:
+
+/lus/scratch/$USER/OpenSource/WS15/job.pbs
+
+in job.pbs leave the number of nodes set to 1; the code is not MPI parallel and cannot use more than 1 node. The number of OMP_NUM_THREADS can be changed and is currently set to 40.
+Add the ...scr command (that can be found in the demo directories) as the last line in the aprun command line and submit the job to the queue with 'qsub job.pbs'
+you can check the status of your job in the queue with 'qstat'
+
+
+*4* Display of results:
+
+suximage < result.su perc=99 &
+
+if X11 display is too slow:
+
+supsimage < result.su perc=99 > results.eps
+convert results.eps ~/results.png
+
+copy png file to your laptop you are working on
+
+scp [email protected]:~/*png . 
+
+
+*5* Usefull job monitor commands specific for Cray
+
+apstat : status of applications running
+xtnodestat : placement of application on system
+xtprocadmin -A : details of installed nodes
+

marchenko3D/demo/WS15/README.1

@@ -0,0 +1,40 @@
+
+Marchenko demo/twoD: reproduce the figures from the paper, but with a 2D model.
+
+cd /lus/scratch/$USER/OpenSource/marchenko/demo/twoD
+
+# Copy pre-computed shots
+cp -rp /lus/scratch/jan/OpenSource/marchenko/demo/twoD/shots .
+cp /lus/scratch/$USER/OpenSource/marchenko/demo/WS15/job.pbs .
+
+Interactively run a progam to create the numerical model used to compute the reference reults.
+
+./model.scr
+
+When that is completed continue by adapting job.pbs to 
+
+Compute the intial focusing operator placed at a depth of 1100 m by running 
+
+initialFocus.scr
+
+To compare the Green's function computed by marchenko generate the reference output
+
+adapt job.pbs to run referenceShot.scr
+
+run the marchenko program interactively (no need to submit job to queue);
+ 
+./marchenko.scr
+
+Compare the Green's function computed by marchenko with the reference (adapt job.pbs to run referenceShot.scr)
+
+The script eps.scr generates .eps and .png files that can be copied back to your local laptop for display.
+
+You can experiment with 
+-amplitude of R: scale with a constant ampltiude 
+-investigate the wavelet that is used to model R
+-number of iterations, 
+-intial focusing position, 
+-investigate at intermediate results (see ../oneD/marchenkoIter.scr as an example).
+
+
+

marchenko3D/demo/WS15/README.2

@@ -0,0 +1,13 @@
+Plane waves
+
+Marchenko method works as well with plane-waves, in stead of modeling a foccus point response for the initial operaror and plane wave is modeled. 
+
+Submit the initialPlane.scr to the queue to compute the intial operator. The marchenkoPlane.scr script computes the Macrehnko solution for the plane-wave response. 
+
+The script epsPlane.scr generates .eps and .png files that can be copied back to your local laptop for display.
+
+DISCUSSION:
+In epsPlane.scr there is a convolution between f1minPlane and p0lpus; 
+	- why is this 'needed'?
+	- does the result have the correct amplitude?
+	- would this also work with focal points?

marchenko3D/demo/WS15/README.3

@@ -0,0 +1,11 @@
+
+To generate a shot record with Primaries reflections only submit the demo/twoD/primaries.scr to the queue. 
+
+The script epsPrimaries.scr generates .eps and .png files that can be copied back to your local laptop for display.
+
+The directory demo/invisible contains the Reflection data to analyse:
+
+shotsdx4_rp.su
+
+Try to find out, by ONLY using the program marchenko_primaries, how many reflectors there are.
+

marchenko3D/demo/WS15/README.4

@@ -0,0 +1,19 @@
+To generate the raytimes and the estimated amplitudes for the virtual source and receivers, run in demo/twoD
+
+rayvsp.scr
+
+After the raytimes have been determined you can create the source function of the homogeneous Green's function by running:
+
+marchenko_ray.pbs
+
+A reference Green's function can be modeled by running
+
+homg_reference.scr
+
+To view the retrieved and reference Green's function, run:
+
+homgview.scr
+
+Or to convert the data to eps and png, run:
+
+homgpng.scr

marchenko3D/demo/WS15/README.5

@@ -0,0 +1,25 @@
+#!/bin/bash 
+#PBS -N Marchenko
+#PBS -j oe
+#PBS -l place=scatter,select=1
+#PBS -S /bin/bash
+#PBS -V
+#PBS -q bw44-sm
+# PBS -q sk40-sm
+#PBS -l walltime=00:10:00
+
+set -x
+cd $PBS_O_WORKDIR
+ulimit -s unlimited
+
+export KMP_AFFINITY=disabled
+export OMP_NUM_THREADS=40
+
+starttime=`date +%s%N`
+
+aprun -n1 -d $OMP_NUM_THREADS 
+
+endtime=`date +%s%N`
+runtime=$(echo "scale=9; 1.0*10^(-9)*(${endtime}-${starttime})" | bc -l)
+echo "Runtime = $runtime seconds" 
+

marchenko3D/demo/WS15/job.pbs

@@ -0,0 +1,14 @@
+
+export CWPROOT=/home/users/jan/SeisUnix/
+export PATH=.:$CWPROOT/bin:/lus/scratch/$USER/OpenSource/bin:$PATH:
+alias lt='ls -lart'
+
+module swap PrgEnv-cray PrgEnv-intel
+module list
+
+mkdir -p /lus/scratch/$USER
+
+cd /lus/scratch/$USER
+rsync -av /lus/scratch/jan/OpenSource .
+#git clone https://github.com/JanThorbecke/OpenSource.git
+