#Always run NeuroRD with the following command line, to direct output into the o utput directory. #To start multiple NeuroRD simulations at once, add & at end of each line. #run the batch file using: at -f NeuroRD.bat NOW (or you can specify a different time) #place the following at the top of the file to get additional output #set -ex #First line will elminate output, #java -Dstochdiff.writers= -jar stochdiff #Alternatively, can get only h5, only text, or both #-Dstochdiff.writers=h5 #-Dstochdiff.writers=text #-Dstochdiff.writers=text,h5 #To avoid information scrolling on screen (and not getting a huge .log file): #> /dev/null #To run things in parallel (instead of batch file): #parallel --gnu java -Dstochdiff.writers=text -Dstochdiff.log=false -jar /home/neuroware/stochdif/stochdiff-3.0.0-1.jar ::: Model_cAMPassaySoma*.xml #result: ran very fast: 3 min for 9 voxel model (2.1.9 required 33 min) #ptdump to look at h5 file. #-Dneurord.writers=h5,text for text output #-Dneurord.trials=3 specify number of trials #-Dneurord.threads=1 to use a single processor for multiple trials. Omit to run in parallel # other switches have to come after the jar file specification # -v to get more information (but not too much) in log (eventually including number of particles injected for each type), -vv to get way too much information #-Dneurord.SDRun.runtime=1 will override the runtime in the Model file # --ic-time -1 --ic ss_bath/Model_SPNspineCaMKII_DagL_AChm4R-nostim.h5 Specify file from which to obtain initial conditions (for re-start), specify time to take IC. #java -jar -Dneurord.writers=h5 /home/neuroware/stochdif/neurord-3.1.2.jar -Dneurord.SDRun.runtime=1 -v Model_SPNspineCaMKII_DagL_AChm4R_Gshydr5_AC1-nostim.xml#This will be useful to avoid awkward updating of initial conditions, or to have very little initial simulation time for equilibrium #Unknown how this command will work with multi-trial h5 files #ls UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca*.xml |xargs sed -i s/"<runtime> 100000"/"<runtime> 150000"/g #stimulate 1 spine, evaluate dendritic signature vs spine, and spatial specificity #6 processors available bath-block and PDE block (2 sets of 2) : #java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-BlockOA-bathCa.xml ss_bath/ & #java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-BlockCyA-bathCa.xml ss_bath/ #1 -T java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca100m-dhpg25.xml UchiNew/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca100m-dhpg0.xml UchiNew/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca100m-dhpg1.xml UchiNew/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca100m-dhpg5.xml UchiNew/ #1.3 java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca1s-dhpg25.xml UchiNew/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca1s-dhpg5.xml UchiNew/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca1s-dhpg0.xml UchiNew/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca1s-dhpg1.xml UchiNew/ #1.6 java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca5s-dhpg0.xml UchiNew/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca5s-dhpg1.xml UchiNew/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca5s-dhpg25.xml UchiNew/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca5s-dhpg5.xml UchiNew/ #3 -W java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-blockPap.xml ss_bath/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-blockRoli.xml ss_bath/ & #Da dur java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-Da0.1.xml ss_bath/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-Da0.3.xml ss_bath/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-Da1.xml ss_bath/ java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-Da10.xml ss_bath/ & # 4 -W java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-noACh.xml ss_bath/ & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_DaDelay.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcCtrl.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcCtrl.xml #5 -R java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_Da.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_Da.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcIC.xml java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcIC.xml & #6 -R aft java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_Da_IC.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_Da_IC.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_IC.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_IC.xml #Da or PKA blocked (no Da) should worsen theta LTP and enhance 20hz LTD -F aft java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noDa.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-noDa.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockPKA2.xml & java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockPKA2.xml #7 begin Fri Jun 30 - takes two weeks - ready mid July java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp2adj-stim20hz.xml& java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp2other-stimtheta.xml& java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp2other-stim20hz.xml & #re-run into different directory: ############## 3 spine sims: java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp3sep-stimtheta.xml& java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp3sep-stim20hz.xml #re-run into different directory (start once 3 spine sims are completed): java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp2sep-stimtheta.xml ss_bath/ & ############# Start the new DaDelay THurs aft - DONE java -jar /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_DaDelay.xml &