[Gate-users] GATE in CLUSTER
Parisa Khateri
parisa.khateri at cern.ch
Fri May 24 15:33:09 CEST 2019
Hi Deae-eddine,
To run your simulations in parallel using SLURM, you need to run Gate for all of the generated macro files. If you look into Macro files, you will find out that the time is actually splitted. To run them, you can create a configuration file, e.g. "multi_gate.config" which includes these lines for 100 split jobs:
0 Gate macro100.mac
1-99 Gate macro%t.mac
Then run the jobs in parallel using:
srun -e gate_stderr.log -o gate_stdout.log --nodes=30 --ntasks-per-node=30 --multi-prog multi_gate.config &
At the end you will get many rootfiles as you results which you can analyse or combine to get the finale result.
Bests,
Parisa
________________________________
From: Gate-users [gate-users-bounces at lists.opengatecollaboration.org] on behalf of Deae Eddine [eddinedeae at gmail.com]
Sent: 09 May 2019 15:13
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] GATE in CLUSTER
Hi Meryem ;
I'm a phd student like you, in medical physics and I have a question for you.
I'm using a HPC platform with SLURM like you. And I’m using the gjs Gate job splitter on a cluster too (parallel mode), but when I run my script I find just one Job and a lot of macros. My main macro is splitte to 10 macros (example) but just 1 job !!!
So my question is : How I can use a lot of jobs in the same time ?
Best regards
Deae-eddine
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Subject: Gate-users Digest, Vol 156, Issue 5
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Message: 1
Date: Thu, 9 May 2019 12:45:23 +0000
From: Deae Eddine <eddinedeae at gmail.com>
To: "gate-users at lists.opengatecollaboration.org"
<gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Gate-users Digest, Vol 156, Issue 1
Message-ID: <5cd420e3.1c69fb81.48fde.61d5 at mx.google.com>
Content-Type: text/plain; charset="utf-8"
Hi Meryem ;
I'm a phd student like you, in medical physics and I have a question for you.
I'm using a HPC platform with SLURM like you. And I’m using the gjs Gate job splitter on a cluster too (parallel mode), but when I run my script I find just one Job and a lot of macros. My main macro is splitte to 10 macros (example) but just 1 job !!!
So my question is : How I can use a lot of jobs in the same time ?
Best regards
Deae-eddine
Sent from Mail for Windows 10
From: gate-users-request at lists.opengatecollaboration.org
Sent: Friday, May 3, 2019 10:37 AM
To: gate-users at lists.opengatecollaboration.org
Subject: Gate-users Digest, Vol 156, Issue 1
Send Gate-users mailing list submissions to
gate-users at lists.opengatecollaboration.org
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
or, via email, send a message with subject or body 'help' to
gate-users-request at lists.opengatecollaboration.org
You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Gate-users digest..."
Today's Topics:
1. GATE in CLUSTER (Abderrahim Abderrahim)
2. Re: GATE in CLUSTER (Consuelo Guardiola)
3. (no subject) (Federico Budelli)
----------------------------------------------------------------------
Message: 1
Date: Thu, 2 May 2019 17:13:14 +0000
From: Abderrahim Abderrahim <abderrahimphy at gmail.com>
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] GATE in CLUSTER
Message-ID:
<CAEVfJTsH8z5JPasgEZ1mGXORYEm1HdUEryKJ9rKP719s0eim7Q at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
*Hello every body ;*
*First' I'm PhD student in medical physics.*
*I have an problem , How to running GATE in cluster with SLURM ? please can
you help me everyone !!*
*My E-Mail: abderrahimphy at gmail.com <abderrahimphy at gmail.com>*
*Best regards*
*Thank you !!*
*Abderrahim *
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Message: 2
Date: Thu, 2 May 2019 20:28:25 +0200 (CEST)
From: Consuelo Guardiola <guardiola at imnc.in2p3.fr>
To: Abderrahim Abderrahim <abderrahimphy at gmail.com>
Cc: gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] GATE in CLUSTER
Message-ID:
<252787471.15732954.1556821705394.JavaMail.zimbra at imnc.in2p3.fr>
Content-Type: text/plain; charset="utf-8"
Hi Abderrahim,
Below there are some tips regarding a similar question. I hope it works for you.
Best,
Consuelo.
De: "Consuelo Guardiola" <guardiola at imnc.in2p3.fr>
À: "meryem fiak" <fiakmeryem.13 at gmail.com>
Envoyé: Dimanche 24 Mars 2019 12:23:33
Objet: Re: [Gate-users] GATE ON CLUSTER
Hi Meryem,
You are welcome.
The last part is the execution of Gate of ALL the jobs that are inside .Gate/folder. It is: when you, first, export GC_DOT_GATE_DIR = /home/m.fiak/mywork and right after make ¨gjs -c openmosix -n 100 main.mac" (assuming that you are splitting100 jobs, for example, of a main job called "main.mac"), it will create a folder of split jobs inside .Gate/main/ path automatically, i.e. main1.mac, main2.mac, main3.mac...to main100.mac. Therefore, the script
#!/bin/bash
Gate .Gate/main/main$ (($SLURM_PROCID+1)).mac
runs Gate of ALL the main1.mac, main2.mac....to main100.mac of the 100 split jobs above.
Try it and let me know if it works,
Best
Consuelo
De: "meryem fiak" <fiakmeryem.13 at gmail.com>
À: "Consuelo Guardiola" <guardiola at imnc.in2p3.fr>
Envoyé: Samedi 23 Mars 2019 17:42:12
Objet: Re: [Gate-users] GATE ON CLUSTER
Hi Consuelo,
Thank you so much for your reply and reactivity. I understood that I have to export GC_DOT_GATE_DIR. to my working directory as indicated in the GATE users guide, but I didn't completely understand the last part :
------------------------------------------------------------------
#!/bin/bash
Gate .Gate/main/main$ (($SLURM_PROCID+1)).mac
-------------------------------------------------------------------
Here is my working directory: /home/m.fiak/mywork.
Here is my script Job.sl that I use for running GATE in sequential mode.
===================================================================
#!/bin/bash
#SBATCH -J GATE-Jobs
#SBATCH -o %x-%j.out
#SBATCH -e %x-%j.err
#SBATCH --partition=mediumq
ml xerces-c/gcc/64
ml qt/gcc/64
ml geant4/gcc/64/4.10.04.p02
ml root/gcc/64/6.14.02
ml gate/gcc/64/8.1.p01
mkdir -p $PWD/$SLURM_JOB_ID
cp $PWD/*.mac $PWD/*.db $PWD/$SLURM_JOB_ID
cd $PWD/$SLURM_JOB_ID
Gate main.mac
=====================================================
Best Regards.
Le ven. 22 mars 2019 à 11:34, Consuelo Guardiola < [ mailto:guardiola at imnc.in2p3.fr | guardiola at imnc.in2p3.fr ] > a écrit :
Hi Meriem,
I'm using a HPC platform with SLURM, which is not a problem for GATE submission jobs since it is just an utility for batch processing. A job (i.e. one of the files in which you split your main macro file) is the execution unit for SLURM. To ensure the proper scheduling of jobs, you have to fit together nodes and cores that can be used at the same time in a group (number of total jobs).
That said, you may split your macro as usual with the gjs splitter tool (***Note: before it, you must export GC_DOT_GATE_DIR= "where_you_want_to_store_the_data"). Then, you can launch your jobs using "sbatch" command as follows:
> sbatch "job_script"
where your "job_script" can be something like this (e.g. 480 jobs):
-----------------------------------------------------------------
#!/bin/bash
#SBATCH --ntasks 480
#SBATCH --qos=prace
#SBATCH --time=24:00:00
#SBATCH --job-name=O
#SBATCH --output=c_%j.out
#SBATCH --error=c_%j.err
srun ./Beam.sh
-----------------------------------------------------------------
in turn, "Beam.sh" file is:
------------------------------------------------------------------
#!/bin/bash
Gate .Gate/main/main$(($SLURM_PROCID+1)).mac
-------------------------------------------------------------------
which executes Gate for all your jobs that are into .Gate/ folder (pointed at ***)
I hope it works!
Best,
Consuelo
De: "Grevillot Loic" < [ mailto:loic.grevillot at medaustron.at | loic.grevillot at medaustron.at ] >
À: "meryem fiak" < [ mailto:fiakmeryem.13 at gmail.com | fiakmeryem.13 at gmail.com ] >
Cc: "gate-users" < [ mailto:gate-users at lists.opengatecollaboration.org | gate-users at lists.opengatecollaboration.org ] >
Envoyé: Vendredi 22 Mars 2019 10:56:41
Objet: Re: [Gate-users] GATE ON CLUSTER
Dear Meriem,
please always use the GATE mailing-list. For cluster business, I am sure you will find much more experienced users than I am…
Best,
Loïc
From: meryem fiak [mailto: [ mailto:fiakmeryem.13 at gmail.com | fiakmeryem.13 at gmail.com ] ]
Sent: Freitag, 22. März 2019 00:02
To: Grevillot Loic < [ mailto:loic.grevillot at medaustron.at | loic.grevillot at medaustron.at ] >
Subject: GATE ON CLUSTER
Hello,
I'm a phd student in medical physics and I have a question regarding "Running GATE on a cluster".
I'm working on MC simulation of linacs in radiotherapy via GATE/GEANT4 platforme and i'm hoping to use the gjs Gate jobsplitter on a cluster (parallel mode), but the cluster uses Slurm which does not belong to the 4 clusterplatform listed by GATE ( HT Condor, openPBS, openmosix and Xgrid).
I would like to know how can I split my Gate macros into several jobs using slurm (job scheduler).
I already posted the problem in Gate-users list forum but I haven't received any response.
Thank you so much for your help.
Kind regards.
--
Ms . FIAK Meriem
-------------------------------------------------------------------
Job Title: Phd Student
--------------------------------------------------------------------
De: "Abderrahim Abderrahim" <abderrahimphy at gmail.com>
À: gate-users at lists.opengatecollaboration.org
Envoyé: Jeudi 2 Mai 2019 19:13:14
Objet: [Gate-users] GATE in CLUSTER
Hello every body ;
First' I'm PhD student in medical physics.
I have an problem , How to running GATE in cluster with SLURM ? please can you help me everyone !!
My E-Mail: [ mailto:abderrahimphy at gmail.com | abderrahimphy at gmail.com ]
Best regards
Thank you !!
Abderrahim
_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
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Message: 3
Date: Fri, 3 May 2019 11:36:35 +0200
From: Federico Budelli <fe.budex at gmail.com>
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] (no subject)
Message-ID:
<CANee7ExYassL4z+WcYTeZw_XVrQnebBDoenJUuROkgTSYiFdFQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi GATE users!
I'm bothering you, just to have an help in my simulation.
Like you can see in the commands below, i have to build 7 contiguous 3D
hexagone, each of them with a cilinder in the middle and one in each
vertices. The idea is to model the geometry of 7 contiguous liver lobules.
After that i would like to put radioactive sources in lobules and so to
have a complete dose map of the entire geometry.
I know that the code below is not good and that in this way of course i
have an overlap problem with the volumes. How can i manage with this
problem, keeping this kind of geometry and the output desired?
Thanks to all!
#==========
#SET WORLD
#==========
/gate/world/geometry/setXLength 10 mm
/gate/world/geometry/setYLength 10 mm
/gate/world/geometry/setZLength 10 mm
#====================
#SET GEOMETRY LOBULE1
#====================
/gate/world/daughters/name lobule
/gate/world/daughters/insert hexagone
/gate/lobule/geometry/setRadius 0.6 mm
/gate/lobule/geometry/setHeight 1.5 mm
/gate/lobule/setMaterial Liver
/gate/lobule/vis/setColor white
#====================
#SET GEOMETRY LOBULE2
#====================
/gate/lobule/daughters/name lobule2
/gate/lobule/daughters/insert hexagone
/gate/lobule2/geometry/setRadius 0.6 mm
/gate/lobule2/geometry/setHeight 1.5 mm
/gate/lobule2/placement/setTranslation 0. 1.2 0. mm
/gate/lobule2/setMaterial Liver
/gate/lobule2/vis/setColor white
#====================
#SET GEOMETRY LOBULE3
#====================
/gate/lobule/daughters/name lobule3
/gate/lobule/daughters/insert hexagone
/gate/lobule3/geometry/setRadius 0.6 mm
/gate/lobule3/geometry/setHeight 1.5 mm
/gate/lobule3/placement/setTranslation 0. -1.2 0. mm
/gate/lobule3/setMaterial Liver
/gate/lobule3/vis/setColor white
#====================
#SET GEOMETRY LOBULE4
#====================
/gate/lobule/daughters/name lobule4
/gate/lobule/daughters/insert hexagone
/gate/lobule4/geometry/setRadius 0.6 mm
/gate/lobule4/geometry/setHeight 1.5 mm
/gate/lobule4/placement/setTranslation -1.035 0.6 0. mm
/gate/lobule4/setMaterial Liver
/gate/lobule4/vis/setColor white
#====================
#SET GEOMETRY LOBULE5
#====================
/gate/lobule/daughters/name lobule5
/gate/lobule/daughters/insert hexagone
/gate/lobule5/geometry/setRadius 0.6 mm
/gate/lobule5/geometry/setHeight 1.5 mm
/gate/lobule5/placement/setTranslation 1.035 0.6 0. mm
/gate/lobule5/setMaterial Liver
/gate/lobule5/vis/setColor white
#====================
#SET GEOMETRY LOBULE6
#====================
/gate/lobule/daughters/name lobule6
/gate/lobule/daughters/insert hexagone
/gate/lobule6/geometry/setRadius 0.6 mm
/gate/lobule6/geometry/setHeight 1.5 mm
/gate/lobule6/placement/setTranslation -1.035 -0.6 0. mm
/gate/lobule6/setMaterial Liver
/gate/lobule6/vis/setColor white
#====================
#SET GEOMETRY LOBULE7
#====================
/gate/lobule/daughters/name lobule7
/gate/lobule/daughters/insert hexagone
/gate/lobule7/geometry/setRadius 0.6 mm
/gate/lobule7/geometry/setHeight 1.5 mm
/gate/lobule7/placement/setTranslation 1.035 -0.6 0. mm
/gate/lobule7/setMaterial Liver
/gate/lobule7/vis/setColor white
#=================
#SET CENTRAL VEIN1
#=================
/gate/lobule/daughters/name cvein
/gate/lobule/daughters/insert cylinder
/gate/cvein/geometry/setRmin 0.028 mm
/gate/cvein/geometry/setRmax 0.033 mm
/gate/cvein/geometry/setHeight 1.3 mm
/gate/cvein/placement/setTranslation 0. 0. 0.1 mm
/gate/cvein/setMaterial Muscle
/gate/cvein/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name cveinint
/gate/lobule/daughters/insert cylinder
/gate/cveinint/geometry/setRmin 0 mm
/gate/cveinint/geometry/setRmax 0.028 mm
/gate/cveinint/geometry/setHeight 1.3 mm
/gate/cveinint/placement/setTranslation 0. 0. 0.1 mm
/gate/cveinint/setMaterial Blood
/gate/cveinint/vis/setColor red
/gate/geometry/rebuild
#=================
#SET CENTRAL VEIN2
#=================
/gate/lobule/daughters/name cvein2
/gate/lobule/daughters/insert cylinder
/gate/cvein2/geometry/setRmin 0.028 mm
/gate/cvein2/geometry/setRmax 0.033 mm
/gate/cvein2/geometry/setHeight 1.3 mm
/gate/cvein2/placement/setTranslation 0. 1.2 0.1 mm
/gate/cvein2/setMaterial Muscle
/gate/cvein2/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name cveinint2
/gate/lobule/daughters/insert cylinder
/gate/cveinint2/geometry/setRmin 0 mm
/gate/cveinint2/geometry/setRmax 0.028 mm
/gate/cveinint2/geometry/setHeight 1.3 mm
/gate/cveinint2/placement/setTranslation 0. 1.2 0.1 mm
/gate/cveinint2/setMaterial Blood
/gate/cveinint2/vis/setColor red
/gate/geometry/rebuild
#=================
#SET CENTRAL VEIN3
#=================
/gate/lobule/daughters/name cvein3
/gate/lobule/daughters/insert cylinder
/gate/cvein3/geometry/setRmin 0.028 mm
/gate/cvein3/geometry/setRmax 0.033 mm
/gate/cvein3/geometry/setHeight 1.3 mm
/gate/cvein3/placement/setTranslation 0. -1.2 0.1 mm
/gate/cvein3/setMaterial Muscle
/gate/cvein3/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name cveinint3
/gate/lobule/daughters/insert cylinder
/gate/cveinint3/geometry/setRmin 0 mm
/gate/cveinint3/geometry/setRmax 0.028 mm
/gate/cveinint3/geometry/setHeight 1.3 mm
/gate/cveinint3/placement/setTranslation 0. -1.2 0.1 mm
/gate/cveinint3/setMaterial Blood
/gate/cveinint3/vis/setColor red
/gate/geometry/rebuild
#=================
#SET CENTRAL VEIN4
#=================
/gate/lobule/daughters/name cvein4
/gate/lobule/daughters/insert cylinder
/gate/cvein4/geometry/setRmin 0.028 mm
/gate/cvein4/geometry/setRmax 0.033 mm
/gate/cvein4/geometry/setHeight 1.3 mm
/gate/cvein4/placement/setTranslation -1.035 0.6 0.1 mm
/gate/cvein4/setMaterial Muscle
/gate/cvein4/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name cveinint4
/gate/lobule/daughters/insert cylinder
/gate/cveinint4/geometry/setRmin 0 mm
/gate/cveinint4/geometry/setRmax 0.028 mm
/gate/cveinint4/geometry/setHeight 1.3 mm
/gate/cveinint4/placement/setTranslation -1.035 0.6 0.1 mm
/gate/cveinint4/setMaterial Blood
/gate/cveinint4/vis/setColor red
/gate/geometry/rebuild
#=================
#SET CENTRAL VEIN5
#=================
/gate/lobule/daughters/name cvein5
/gate/lobule/daughters/insert cylinder
/gate/cvein5/geometry/setRmin 0.028 mm
/gate/cvein5/geometry/setRmax 0.033 mm
/gate/cvein5/geometry/setHeight 1.3 mm
/gate/cvein5/placement/setTranslation 1.035 0.6 0.1 mm
/gate/cvein5/setMaterial Muscle
/gate/cvein5/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name cveinint5
/gate/lobule/daughters/insert cylinder
/gate/cveinint5/geometry/setRmin 0 mm
/gate/cveinint5/geometry/setRmax 0.028 mm
/gate/cveinint5/geometry/setHeight 1.3 mm
/gate/cveinint5/placement/setTranslation 1.035 0.6 0.1 mm
/gate/cveinint5/setMaterial Blood
/gate/cveinint5/vis/setColor red
/gate/geometry/rebuild
#=================
#SET CENTRAL VEIN6
#=================
/gate/lobule/daughters/name cvein6
/gate/lobule/daughters/insert cylinder
/gate/cvein6/geometry/setRmin 0.028 mm
/gate/cvein6/geometry/setRmax 0.033 mm
/gate/cvein6/geometry/setHeight 1.3 mm
/gate/cvein6/placement/setTranslation -1.035 -0.6 0.1 mm
/gate/cvein6/setMaterial Muscle
/gate/cvein6/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name cveinint6
/gate/lobule/daughters/insert cylinder
/gate/cveinint6/geometry/setRmin 0 mm
/gate/cveinint6/geometry/setRmax 0.028 mm
/gate/cveinint6/geometry/setHeight 1.3 mm
/gate/cveinint6/placement/setTranslation -1.035 -0.6 0.1 mm
/gate/cveinint6/setMaterial Blood
/gate/cveinint6/vis/setColor red
/gate/geometry/rebuild
#=================
#SET CENTRAL VEIN7
#=================
/gate/lobule/daughters/name cvein7
/gate/lobule/daughters/insert cylinder
/gate/cvein7/geometry/setRmin 0.028 mm
/gate/cvein7/geometry/setRmax 0.033 mm
/gate/cvein7/geometry/setHeight 1.3 mm
/gate/cvein7/placement/setTranslation 1.035 -0.6 0.1 mm
/gate/cvein7/setMaterial Muscle
/gate/cvein7/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name cveinint7
/gate/lobule/daughters/insert cylinder
/gate/cveinint7/geometry/setRmin 0 mm
/gate/cveinint7/geometry/setRmax 0.028 mm
/gate/cveinint7/geometry/setHeight 1.3 mm
/gate/cveinint7/placement/setTranslation 1.035 -0.6 0.1 mm
/gate/cveinint7/setMaterial Blood
/gate/cveinint7/vis/setColor red
/gate/geometry/rebuild
#===========================================================
#SET HEPATIC ARTERY FOR EACH VERTICE OF THE HEXAGONE/LOBULE1
#===========================================================
#1
/gate/lobule/daughters/name artery1
/gate/lobule/daughters/insert cylinder
/gate/artery1/geometry/setRmin 0.015 mm
/gate/artery1/geometry/setRmax 0.024 mm
/gate/artery1/geometry/setHeight 1.3 mm
/gate/artery1/placement/setTranslation -0.345 0.6 0.1 mm
/gate/artery1/setMaterial Muscle
/gate/artery1/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery1int
/gate/lobule/daughters/insert cylinder
/gate/artery1int/geometry/setRmin 0. mm
/gate/artery1int/geometry/setRmax 0.015 mm
/gate/artery1int/geometry/setHeight 1.3 mm
/gate/artery1int/placement/setTranslation -0.345 0.6 0.1 mm
/gate/artery1int/setMaterial Blood
/gate/artery1int/vis/setColor red
/gate/geometry/rebuild
#2
/gate/lobule/daughters/name artery2
/gate/lobule/daughters/insert cylinder
/gate/artery2/geometry/setRmin 0.015 mm
/gate/artery2/geometry/setRmax 0.024 mm
/gate/artery2/geometry/setHeight 1.3 mm
/gate/artery2/placement/setTranslation 0.345 0.6 0.1 mm
/gate/artery2/setMaterial Muscle
/gate/artery2/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery2int
/gate/lobule/daughters/insert cylinder
/gate/artery2int/geometry/setRmin 0. mm
/gate/artery2int/geometry/setRmax 0.015 mm
/gate/artery2int/geometry/setHeight 1.3 mm
/gate/artery2int/placement/setTranslation 0.345 0.6 0.1 mm
/gate/artery2int/setMaterial Blood
/gate/artery2int/vis/setColor red
/gate/geometry/rebuild
#3
/gate/lobule/daughters/name artery3
/gate/lobule/daughters/insert cylinder
/gate/artery3/geometry/setRmin 0.015 mm
/gate/artery3/geometry/setRmax 0.024 mm
/gate/artery3/geometry/setHeight 1.3 mm
/gate/artery3/placement/setTranslation 0.69 0. 0.1 mm
/gate/artery3/setMaterial Muscle
/gate/artery3/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery3int
/gate/lobule/daughters/insert cylinder
/gate/artery3int/geometry/setRmin 0. mm
/gate/artery3int/geometry/setRmax 0.015 mm
/gate/artery3int/geometry/setHeight 1.3 mm
/gate/artery3int/placement/setTranslation 0.69 0. 0.1 mm
/gate/artery3int/setMaterial Blood
/gate/artery3int/vis/setColor red
/gate/geometry/rebuild
#4
/gate/lobule/daughters/name artery4
/gate/lobule/daughters/insert cylinder
/gate/artery4/geometry/setRmin 0.015 mm
/gate/artery4/geometry/setRmax 0.024 mm
/gate/artery4/geometry/setHeight 1.3 mm
/gate/artery4/placement/setTranslation 0.345 -0.6 0.1 mm
/gate/artery4/setMaterial Muscle
/gate/artery4/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery4int
/gate/lobule/daughters/insert cylinder
/gate/artery4int/geometry/setRmin 0. mm
/gate/artery4int/geometry/setRmax 0.015 mm
/gate/artery4int/geometry/setHeight 1.3 mm
/gate/artery4int/placement/setTranslation 0.345 -0.6 0.1 mm
/gate/artery4int/setMaterial Blood
/gate/artery4int/vis/setColor red
/gate/geometry/rebuild
#5
/gate/lobule/daughters/name artery5
/gate/lobule/daughters/insert cylinder
/gate/artery5/geometry/setRmin 0.015 mm
/gate/artery5/geometry/setRmax 0.024 mm
/gate/artery5/geometry/setHeight 1.3 mm
/gate/artery5/placement/setTranslation -0.345 -0.6 0.1 mm
/gate/artery5/setMaterial Muscle
/gate/artery5/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery5int
/gate/lobule/daughters/insert cylinder
/gate/artery5int/geometry/setRmin 0. mm
/gate/artery5int/geometry/setRmax 0.015 mm
/gate/artery5int/geometry/setHeight 1.3 mm
/gate/artery5int/placement/setTranslation -0.345 -0.6 0.1 mm
/gate/artery5int/setMaterial Blood
/gate/artery5int/vis/setColor red
/gate/geometry/rebuild
#6
/gate/lobule/daughters/name artery6
/gate/lobule/daughters/insert cylinder
/gate/artery6/geometry/setRmin 0.015 mm
/gate/artery6/geometry/setRmax 0.024 mm
/gate/artery6/geometry/setHeight 1.3 mm
/gate/artery6/placement/setTranslation -0.69 0. 0.1 mm
/gate/artery6/setMaterial Muscle
/gate/artery6/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery6int
/gate/lobule/daughters/insert cylinder
/gate/artery6int/geometry/setRmin 0. mm
/gate/artery6int/geometry/setRmax 0.015 mm
/gate/artery6int/geometry/setHeight 1.3 mm
/gate/artery6int/placement/setTranslation -0.69 0. 0.1 mm
/gate/artery6int/setMaterial Blood
/gate/artery6int/vis/setColor red
/gate/geometry/rebuild
#===========================================================
#SET HEPATIC ARTERY FOR EACH VERTICE OF THE HEXAGONE/LOBULE2
#===========================================================
#1
/gate/lobule/daughters/name artery2.1
/gate/lobule/daughters/insert cylinder
/gate/artery2.1/geometry/setRmin 0.015 mm
/gate/artery2.1/geometry/setRmax 0.024 mm
/gate/artery2.1/geometry/setHeight 1.3 mm
/gate/artery2.1/placement/setTranslation -0.345 1.8 0.1 mm
/gate/artery2.1/setMaterial Muscle
/gate/artery2.1/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery2.1int
/gate/lobule/daughters/insert cylinder
/gate/artery2.1int/geometry/setRmin 0. mm
/gate/artery2.1int/geometry/setRmax 0.015 mm
/gate/artery2.1int/geometry/setHeight 1.3 mm
/gate/artery2.1int/placement/setTranslation -0.345 1.8 0.1 mm
/gate/artery2.1int/setMaterial Blood
/gate/artery2.1int/vis/setColor red
/gate/geometry/rebuild
#2
/gate/lobule/daughters/name artery2.2
/gate/lobule/daughters/insert cylinder
/gate/artery2.2/geometry/setRmin 0.015 mm
/gate/artery2.2/geometry/setRmax 0.024 mm
/gate/artery2.2/geometry/setHeight 1.3 mm
/gate/artery2.2/placement/setTranslation 0.345 1.8 0.1 mm
/gate/artery2.2/setMaterial Muscle
/gate/artery2.2/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery2.2int
/gate/lobule/daughters/insert cylinder
/gate/artery2.2int/geometry/setRmin 0. mm
/gate/artery2.2int/geometry/setRmax 0.015 mm
/gate/artery2.2int/geometry/setHeight 1.3 mm
/gate/artery2.2int/placement/setTranslation 0.345 1.8 0.1 mm
/gate/artery2.2int/setMaterial Blood
/gate/artery2.2int/vis/setColor red
/gate/geometry/rebuild
#3
/gate/lobule/daughters/name artery2.3
/gate/lobule/daughters/insert cylinder
/gate/artery2.3/geometry/setRmin 0.015 mm
/gate/artery2.3/geometry/setRmax 0.024 mm
/gate/artery2.3/geometry/setHeight 1.3 mm
/gate/artery2.3/placement/setTranslation 0.69 1.2 0.1 mm
/gate/artery2.3/setMaterial Muscle
/gate/artery2.3/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery2.3int
/gate/lobule/daughters/insert cylinder
/gate/artery2.3int/geometry/setRmin 0. mm
/gate/artery2.3int/geometry/setRmax 0.015 mm
/gate/artery2.3int/geometry/setHeight 1.3 mm
/gate/artery2.3int/placement/setTranslation 0.69 1.2 0.1 mm
/gate/artery2.3int/setMaterial Blood
/gate/artery2.3int/vis/setColor red
/gate/geometry/rebuild
#6
/gate/lobule/daughters/name artery2.6
/gate/lobule/daughters/insert cylinder
/gate/artery2.6/geometry/setRmin 0.015 mm
/gate/artery2.6/geometry/setRmax 0.024 mm
/gate/artery2.6/geometry/setHeight 1.3 mm
/gate/artery2.6/placement/setTranslation -0.69 1.2 0.1 mm
/gate/artery2.6/setMaterial Muscle
/gate/artery2.6/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery2.6int
/gate/lobule/daughters/insert cylinder
/gate/artery2.6int/geometry/setRmin 0. mm
/gate/artery2.6int/geometry/setRmax 0.015 mm
/gate/artery2.6int/geometry/setHeight 1.3 mm
/gate/artery2.6int/placement/setTranslation -0.69 1.2 0.1 mm
/gate/artery2.6int/setMaterial Blood
/gate/artery2.6int/vis/setColor red
/gate/geometry/rebuild
#===========================================================
#SET HEPATIC ARTERY FOR EACH VERTICE OF THE HEXAGONE/LOBULE3
#===========================================================
#3
/gate/lobule/daughters/name artery3.3
/gate/lobule/daughters/insert cylinder
/gate/artery3.3/geometry/setRmin 0.015 mm
/gate/artery3.3/geometry/setRmax 0.024 mm
/gate/artery3.3/geometry/setHeight 1.3 mm
/gate/artery3.3/placement/setTranslation 0.69 -1.2 0.1 mm
/gate/artery3.3/setMaterial Muscle
/gate/artery3.3/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery3.3int
/gate/lobule/daughters/insert cylinder
/gate/artery3.3int/geometry/setRmin 0. mm
/gate/artery3.3int/geometry/setRmax 0.015 mm
/gate/artery3.3int/geometry/setHeight 1.3 mm
/gate/artery3.3int/placement/setTranslation 0.69 -1.2 0.1 mm
/gate/artery3.3int/setMaterial Blood
/gate/artery3.3int/vis/setColor red
/gate/geometry/rebuild
#4
/gate/lobule/daughters/name artery3.4
/gate/lobule/daughters/insert cylinder
/gate/artery3.4/geometry/setRmin 0.015 mm
/gate/artery3.4/geometry/setRmax 0.024 mm
/gate/artery3.4/geometry/setHeight 1.3 mm
/gate/artery3.4/placement/setTranslation 0.345 -1.8 0.1 mm
/gate/artery3.4/setMaterial Muscle
/gate/artery3.4/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery3.4int
/gate/lobule/daughters/insert cylinder
/gate/artery3.4int/geometry/setRmin 0. mm
/gate/artery3.4int/geometry/setRmax 0.015 mm
/gate/artery3.4int/geometry/setHeight 1.3 mm
/gate/artery3.4int/placement/setTranslation 0.345 -1.8 0.1 mm
/gate/artery3.4int/setMaterial Blood
/gate/artery3.4int/vis/setColor red
/gate/geometry/rebuild
#5
/gate/lobule/daughters/name artery3.5
/gate/lobule/daughters/insert cylinder
/gate/artery3.5/geometry/setRmin 0.015 mm
/gate/artery3.5/geometry/setRmax 0.024 mm
/gate/artery3.5/geometry/setHeight 1.3 mm
/gate/artery3.5/placement/setTranslation -0.345 -1.8 0.1 mm
/gate/artery3.5/setMaterial Muscle
/gate/artery3.5/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery3.5int
/gate/lobule/daughters/insert cylinder
/gate/artery3.5int/geometry/setRmin 0. mm
/gate/artery3.5int/geometry/setRmax 0.015 mm
/gate/artery3.5int/geometry/setHeight 1.3 mm
/gate/artery3.5int/placement/setTranslation -0.345 -1.8 0.1 mm
/gate/artery3.5int/setMaterial Blood
/gate/artery3.5int/vis/setColor red
/gate/geometry/rebuild
#6
/gate/lobule/daughters/name artery3.6
/gate/lobule/daughters/insert cylinder
/gate/artery3.6/geometry/setRmin 0.015 mm
/gate/artery3.6/geometry/setRmax 0.024 mm
/gate/artery3.6/geometry/setHeight 1.3 mm
/gate/artery3.6/placement/setTranslation -0.69 -1.2 0.1 mm
/gate/artery3.6/setMaterial Muscle
/gate/artery3.6/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery3.6int
/gate/lobule/daughters/insert cylinder
/gate/artery3.6int/geometry/setRmin 0. mm
/gate/artery3.6int/geometry/setRmax 0.015 mm
/gate/artery3.6int/geometry/setHeight 1.3 mm
/gate/artery3.6int/placement/setTranslation -0.69 -1.2 0.1 mm
/gate/artery3.6int/setMaterial Blood
/gate/artery3.6int/vis/setColor red
/gate/geometry/rebuild
#===========================================================
#SET HEPATIC ARTERY FOR EACH VERTICE OF THE HEXAGONE/LOBULE4
#===========================================================
#1
/gate/lobule/daughters/name artery4.1
/gate/lobule/daughters/insert cylinder
/gate/artery4.1/geometry/setRmin 0.015 mm
/gate/artery4.1/geometry/setRmax 0.024 mm
/gate/artery4.1/geometry/setHeight 1.3 mm
/gate/artery4.1/placement/setTranslation -1.38 1.2 0.1 mm
/gate/artery4.1/setMaterial Muscle
/gate/artery4.1/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery4.1int
/gate/lobule/daughters/insert cylinder
/gate/artery4.1int/geometry/setRmin 0. mm
/gate/artery4.1int/geometry/setRmax 0.015 mm
/gate/artery4.1int/geometry/setHeight 1.3 mm
/gate/artery4.1int/placement/setTranslation -1.38 1.2 0.1 mm
/gate/artery4.1int/setMaterial Blood
/gate/artery4.1int/vis/setColor red
/gate/geometry/rebuild
#5
/gate/lobule/daughters/name artery4.5
/gate/lobule/daughters/insert cylinder
/gate/artery4.5/geometry/setRmin 0.015 mm
/gate/artery4.5/geometry/setRmax 0.024 mm
/gate/artery4.5/geometry/setHeight 1.3 mm
/gate/artery4.5/placement/setTranslation -1.38 0. 0.1 mm
/gate/artery4.5/setMaterial Muscle
/gate/artery4.5/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery4.5int
/gate/lobule/daughters/insert cylinder
/gate/artery4.5int/geometry/setRmin 0. mm
/gate/artery4.5int/geometry/setRmax 0.015 mm
/gate/artery4.5int/geometry/setHeight 1.3 mm
/gate/artery4.5int/placement/setTranslation -1.38 0. 0.1 mm
/gate/artery4.5int/setMaterial Blood
/gate/artery4.5int/vis/setColor red
/gate/geometry/rebuild
#6
/gate/lobule/daughters/name artery4.6
/gate/lobule/daughters/insert cylinder
/gate/artery4.6/geometry/setRmin 0.015 mm
/gate/artery4.6/geometry/setRmax 0.024 mm
/gate/artery4.6/geometry/setHeight 1.3 mm
/gate/artery4.6/placement/setTranslation -1.725 0.6 0.1 mm
/gate/artery4.6/setMaterial Muscle
/gate/artery4.6/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery4.6int
/gate/lobule/daughters/insert cylinder
/gate/artery4.6int/geometry/setRmin 0. mm
/gate/artery4.6int/geometry/setRmax 0.015 mm
/gate/artery4.6int/geometry/setHeight 1.3 mm
/gate/artery4.6int/placement/setTranslation -1.725 0.6 0.1 mm
/gate/artery4.6int/setMaterial Blood
/gate/artery4.6int/vis/setColor red
/gate/geometry/rebuild
#===========================================================
#SET HEPATIC ARTERY FOR EACH VERTICE OF THE HEXAGONE/LOBULE5
#===========================================================
#2
/gate/lobule/daughters/name artery5.2
/gate/lobule/daughters/insert cylinder
/gate/artery5.2/geometry/setRmin 0.015 mm
/gate/artery5.2/geometry/setRmax 0.024 mm
/gate/artery5.2/geometry/setHeight 1.3 mm
/gate/artery5.2/placement/setTranslation 1.38 1.2 0.1 mm
/gate/artery5.2/setMaterial Muscle
/gate/artery5.2/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery5.2int
/gate/lobule/daughters/insert cylinder
/gate/artery5.2int/geometry/setRmin 0. mm
/gate/artery5.2int/geometry/setRmax 0.015 mm
/gate/artery5.2int/geometry/setHeight 1.3 mm
/gate/artery5.2int/placement/setTranslation 1.38 1.2 0.1 mm
/gate/artery5.2int/setMaterial Blood
/gate/artery5.2int/vis/setColor red
/gate/geometry/rebuild
#3
/gate/lobule/daughters/name artery5.3
/gate/lobule/daughters/insert cylinder
/gate/artery5.3/geometry/setRmin 0.015 mm
/gate/artery5.3/geometry/setRmax 0.024 mm
/gate/artery5.3/geometry/setHeight 1.3 mm
/gate/artery5.3/placement/setTranslation 1.725 0.6 0.1 mm
/gate/artery5.3/setMaterial Muscle
/gate/artery5.3/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery5.3int
/gate/lobule/daughters/insert cylinder
/gate/artery5.3int/geometry/setRmin 0. mm
/gate/artery5.3int/geometry/setRmax 0.015 mm
/gate/artery5.3int/geometry/setHeight 1.3 mm
/gate/artery5.3int/placement/setTranslation 1.725 0.6 0.1 mm
/gate/artery5.3int/setMaterial Blood
/gate/artery5.3int/vis/setColor red
/gate/geometry/rebuild
#4
/gate/lobule/daughters/name artery5.4
/gate/lobule/daughters/insert cylinder
/gate/artery5.4/geometry/setRmin 0.015 mm
/gate/artery5.4/geometry/setRmax 0.024 mm
/gate/artery5.4/geometry/setHeight 1.3 mm
/gate/artery5.4/placement/setTranslation 1.38 0. 0.1 mm
/gate/artery5.4/setMaterial Muscle
/gate/artery5.4/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery5.4int
/gate/lobule/daughters/insert cylinder
/gate/artery5.4int/geometry/setRmin 0. mm
/gate/artery5.4int/geometry/setRmax 0.015 mm
/gate/artery5.4int/geometry/setHeight 1.3 mm
/gate/artery5.4int/placement/setTranslation 1.38 0. 0.1 mm
/gate/artery5.4int/setMaterial Blood
/gate/artery5.4int/vis/setColor red
/gate/geometry/rebuild
#===========================================================
#SET HEPATIC ARTERY FOR EACH VERTICE OF THE HEXAGONE/LOBULE6
#===========================================================
#5
/gate/lobule/daughters/name artery6.5
/gate/lobule/daughters/insert cylinder
/gate/artery6.5/geometry/setRmin 0.015 mm
/gate/artery6.5/geometry/setRmax 0.024 mm
/gate/artery6.5/geometry/setHeight 1.3 mm
/gate/artery6.5/placement/setTranslation -1.38 -1.2 0.1 mm
/gate/artery6.5/setMaterial Muscle
/gate/artery6.5/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery6.5int
/gate/lobule/daughters/insert cylinder
/gate/artery6.5int/geometry/setRmin 0. mm
/gate/artery6.5int/geometry/setRmax 0.015 mm
/gate/artery6.5int/geometry/setHeight 1.3 mm
/gate/artery6.5int/placement/setTranslation -1.38 -1.2 0.1 mm
/gate/artery6.5int/setMaterial Blood
/gate/artery6.5int/vis/setColor red
/gate/geometry/rebuild
#6
/gate/lobule/daughters/name artery6.6
/gate/lobule/daughters/insert cylinder
/gate/artery6.6/geometry/setRmin 0.015 mm
/gate/artery6.6/geometry/setRmax 0.024 mm
/gate/artery6.6/geometry/setHeight 1.3 mm
/gate/artery6.6/placement/setTranslation -1.725 -0.6 0.1 mm
/gate/artery6.6/setMaterial Muscle
/gate/artery6.6/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery6.6int
/gate/lobule/daughters/insert cylinder
/gate/artery6.6int/geometry/setRmin 0. mm
/gate/artery6.6int/geometry/setRmax 0.015 mm
/gate/artery6.6int/geometry/setHeight 1.3 mm
/gate/artery6.6int/placement/setTranslation -1.725 -0.6 0.1 mm
/gate/artery6.6int/setMaterial Blood
/gate/artery6.6int/vis/setColor red
/gate/geometry/rebuild
#===========================================================
#SET HEPATIC ARTERY FOR EACH VERTICE OF THE HEXAGONE/LOBULE7
#===========================================================
#3
/gate/lobule/daughters/name artery7.3
/gate/lobule/daughters/insert cylinder
/gate/artery7.3/geometry/setRmin 0.015 mm
/gate/artery7.3/geometry/setRmax 0.024 mm
/gate/artery7.3/geometry/setHeight 1.3 mm
/gate/artery7.3/placement/setTranslation 1.725 -0.6 0.1 mm
/gate/artery7.3/setMaterial Muscle
/gate/artery7.3/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery7.3int
/gate/lobule/daughters/insert cylinder
/gate/artery7.3int/geometry/setRmin 0. mm
/gate/artery7.3int/geometry/setRmax 0.015 mm
/gate/artery7.3int/geometry/setHeight 1.3 mm
/gate/artery7.3int/placement/setTranslation 1.725 -0.6 0.1 mm
/gate/artery7.3int/setMaterial Blood
/gate/artery7.3int/vis/setColor red
/gate/geometry/rebuild
#4
/gate/lobule/daughters/name artery7.4
/gate/lobule/daughters/insert cylinder
/gate/artery7.4/geometry/setRmin 0.015 mm
/gate/artery7.4/geometry/setRmax 0.024 mm
/gate/artery7.4/geometry/setHeight 1.3 mm
/gate/artery7.4/placement/setTranslation 1.38 -1.2 0.1 mm
/gate/artery7.4/setMaterial Muscle
/gate/artery7.4/vis/setColor blue
/gate/geometry/rebuild
/gate/lobule/daughters/name artery7.4int
/gate/lobule/daughters/insert cylinder
/gate/artery7.4int/geometry/setRmin 0. mm
/gate/artery7.4int/geometry/setRmax 0.015 mm
/gate/artery7.4int/geometry/setHeight 1.3 mm
/gate/artery7.4int/placement/setTranslation 1.38 -1.2 0.1 mm
/gate/artery7.4int/setMaterial Blood
/gate/artery7.4int/vis/setColor red
/gate/geometry/rebuild
--
*Federico Budelli*
<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
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