Access to computing facility

Alessio Sarti Uncategorised

Tips and documentation for accessing the ReCas computing centre resources

FRIDA members have access, upon request, to the ReCas - Bari centre.

Getting an account

To get an account on the ReCas centre you have to complete the registration form. For doing this you need a valid ID document.

For any doubt or question, please email Alessio.Sarti at uniroma1.it. 

 

Accessing the computing resources

The ReCas site provide a guide for the HPC access with the instructions to setup the environment and run on the cluster. 

Once the admin have activated your account you can access the HPC centre by issuing the following command:

ssh -X -Y -C This email address is being protected from spambots. You need JavaScript enabled to view it.

Once you have successfully logged on the cluster, you can access the resources setting up your favourite environment according to the instructions on the manual.

Once your executable is ready, you can submit the jobs to the farm using condor. A condor manual in Italian can be found here.

 

User activities

The code has to be developed under the user area. Each user has order of 100 GB area allowed for development and interactive work. The development area is accessible under:

/lustrehome/username

The output of large jobs or productions has to be stored in a general experiment area under:

/lustre/frida

we need to coordinate, as a collaboration, the use of the area. Before starting any massive production, please contact Alessio.Sarti at uniroma1.it

Each user can submit jobs to the cluster using condor. To understand how to configure the job, please read the manual.

It is important that the CPUs requested by the user are strictly the ones used by the job. As the infrastructure has been optimised for parallel computing activities, once the user has achieved a job with a reasonable length, it is highly recommended to submit parallel jobs, instead of requiring more CPUs!

Eg: it is better to submit 1k jobs that are 1h long instead of submitting 10 jobs that are 10h long on 10 CPUs!

Single user software.

The policy of the data center is that the software for the various users/experiments is managed in a 'local' way. It is therefore foreseen that each user/experiment installs the necessary software in the user/experiment area. Some software is 'common' in use and therefore will be available below
/lustre/frida/software.

As of today there are two installed softwares: cmake 3.20 and root.

  • to use cmake 3.20:
export PATH=/lustre/frida/software/cmake/cmake-3.20.1/bin:$PATH
  • to use root:
scl enable devtoolset-9 bash
and then
export ROOTSYS=/lustre/frida/software/root_62610/root_62604install

export LD_LIBRARY_PATH=$ROOTSYS/lib/root:$ROOTSYS/lib

export PATH=$PATH:$ROOTSYS/bin

If you need to install additional software, you can contact Alessio.Sarti at roma1.infn.it directly

 

Documentation

The ReCas web page that contains the manuals and infos can be reached here.

Steering Committee

The steering committee of FRIDA is composed by the WP coordinators and the local units coordinators [FRIDA Organisation]. 

Useful links and materials

Alessio Sarti Uncategorised

WP1: FLASH effect understanding

Alessio Sarti Uncategorised

WP1 Coordinators

The coordinators for the WP1 are:  G. I. Forte and E. Scifoni

WP1 Participants

The WP1 Participants are as listed in the following table:

Name Unit FTE Name Unit FTE Name Unit FTE
CNR Grant Holder TIFPA 0.4 Cella Zanacchi F. PI 0.1 Minafra L. LNS 0.1
Attili A. TIFPA 0.2 Cordoni F. TIFPA 0.3 Monti V. TO 0.3
Bellinzona V.E. TIFPA 0.2 Costa M. PI 0.1 Russo G. LNS 0.5
Bisio A. TIFPA 0.5 Croci S. TIFPA 0.6 Scifoni E. TIFPA 0.3
Bortolussi S. MI 0.2 Ficarra M. LNS 1 Sokol O. TIFPA  0.1
Boscolo D. TIFPA 0.1 Forte G.I. LNS 0.7 Strettoi E. PI 0.1
Bravatà V. LNS 0.5 Fuss M. TIFPA 0.1 Tinganelli W. TIFPA 0.1
Calvaruso M. LNS 0.5 La Tessa C. TIFPA 0.2 Tommasini F. TIFPA 0.2
Cammarata F. LNS 0.1 Manghi M. TIFPA 0.5 Vannini E. PI 0.1

Main Goals

The WP1 activity is devoted to gaining insights in understanding the still poorly explained FLASH effect mechanism. For this goal, the WP1 is articulated in 4 main tasks:

Task 1 -  Biophysical modeling

Different approaches will be used to analyze the spatiotemporal damage evolution at high dose rates, to obtain a dose enhancement factor, dependent on all the relevant parameters connected to the FLASH effect, to realize a biologically driven TPS. The modeling will explore:

i) the heterogeneous chemical stage, by expanding the TRAX-CHEM Monte Carlo chemical track structure code;

ii) the homogeneous chemical stage, by plugging an analytical model of tissue O2 diffusion-reaction;

iii) The DNA repair kinetics in Flash/Conv conditions;

iv) advanced Normal Tissue Complication Probability modelling as a function of different irradiation and target condition.

Task 2 - In vitro Experiments

The in vitro experiments aim to highlight biological processes activated by flash mode irradiation, to perform a “tuning” of physical irradiation parameters (dose, dose/rate, dose/pulse), selecting the combinations that enable to appreciate the effect at microscopic level. Two breast cell lines, the non-tumorigenic MCF10A and the tumorigenic MDA-MB-231, will be used and experiments will be performed varying doses, dose rates and oxygen concentration, to evaluate the following biological endpoints: survival and DNA damage; cell death (apoptosis/necrosis) and senescence; cells redox status; profiling of secreted immunological markers; RNA-seq on irradiated cells; microtubule integrity and collagen structure modification studies. The feasibility of using the organ-on-a-chip technology will be investigated, to provide insights into normal human organ functions. This activity will be carried out by CT (in-kind) in collaboration with the University of Surrey.

Task 3 - Ex vivo Experiments

Starting from retinal cell cultures ARPE19 cells (a model of retina-pigment epithelium) the effect of FLASH/CONV approaches identifying effective and damaging doses will be studied. Then, whole mouse retinas will be exposed to FLASH/CONV irradiation. Endpoints evaluated will be: local microglia activation, apoptosis and oxidative stress.

Task 4 - Upgrade of UNITO Linac and TIFPA p-Lab

TO unit will modify a conventional clinical ELEKTA LINAC (4-18 MeV) of TO and Physics Department (UNITO), fully dedicated to research. The modification will allow delivering electron beams achieving FLASH RT rates, controlling electron pulses, beam output stability, pulse constancy and beam flatness. The dosimetric calibration will be performed in collaboration with the CT unit. The upgraded LINAC will be used to test beam monitors/dosimeters. The TIFPA team will upgrade, in collaboration with IBA, the proton beam experimental facility to deliver ultra-high dose rates.

WP1 Deliverables

The WP1 Deliverables are summarized in the following table:

Deliv. Short Name Description When (M) Deliv. Short Name Description When (M)
D1.1 RadChem Modelling Report of radchem extension to the heterogeneous stage. 1-16 D2.4 Radbio consolidation and insights Repetition of some radiobiological experimental sets requiring statistical robustness or potential irradiation for selected end points using other beams with different characteristics. 24-36
D1.2 DDRK Modelling Report on DDRK Modelling studies. 1-24 D2.5 Radbio on 3D under FLASH and CONV Report on the effects of CONV vs. FLASH irradiation on the 3D collagen scaffold. Data collected mainly with 2nd harmonic/two photon microscopy. 1-24
D1.3 DMF Modelling Report on DMF Modelling studies. 16-36 D2.6 Radbio on cytoskeleton under FLASH and CONV Report on the effects of CONV vs. FLASH irradiation on the cytoskeleton (i.e microtubules) fiber integrity. Data collected mainly with advanced microscopy techniques. 1-32
D2.1 Radbio under Conventional Irradiation Report on Cell survival/DNA repair and redox status under conventional irradiation. Collecting of conventionally irradiated medium and pellets for future immunological profiling and RNAseq. 1-12 D3.1 Retina Cells Report on tumor cells and retina-pigment cells studies. 16
D2.2 Radbio under Flash Irradiation Report on Cell survival/DNA repair and redox status under Flash irradiation. Collecting of conventionally irradiated medium and pellets for future immunological profiling and RNAseq. 13-20 D3.2 Retina explanted  Report on explanted mouse retina. 24
D2.3 Radbio profiling Immunological profiling and RNAseq. 13-24 D4.1 TO-Linac dosimetric calibration The dosimetric calibration of the INFN Torino LINAC, after its modification, will be performed in collaboration with Catania section. 24
        D4.2 TIFPA-pFLASH dosimetric calibration The dosimetric calibration of the TIFPA FLASH beam, after its modification, will be performed in collaboration with PI and CT. 24

Materials, documents and links of interest for WP1 activities

WP2: FLASH beam delivery

Alessio Sarti Uncategorised

WP2 Coordinators

The coordinators for the WP2 are:  G. A. P. Cirrone and A. Mostacci

WP2 Participants

The WP2 Participants are as listed in the following table:

Name Unit FTE Name Unit FTE Name Unit FTE
Bacci A. MI 0.2 Giuliano L. RM1 0.4 Migliorati M. RM1 0.1
Borghesi M LNS 0.05 Gizzi L. PI 0.2 Milluzzo G. LNS 0.2
Cirrone G. A. P. LNS 0.3 Guarrera M. LNS 0.2 Mostacci A. RM1 0.3
Cuttone G. LNS 0.1 Labate L. PI 0.2 Palumbo L. RM1 0.3
Del Sarto D. PI 0.2 Mararsciulli A. PI 0.5 Russo P. MI 0.1
Drebot I. MI 0.2 Margarone D. MI 0.1 Sarnu A. MI 0.1
Faillace L. RM1 0.1 Massa R. MI 0.1 Serafini L. MI 0.2
Ficcadenti L. RM1 0.1 Mauro G.S. LNS 0.1 Sorbello G. LNS 0.1
Giove D. MI 0.2 Mettiver G. MI 0.1 Torrisi G. LNS 0.1

Main Goals

The WP2 aims to design, develop and test new approaches for the generation of charged particle or high energies photon beams with FLASH characteristics. WP2 will be organised in 5 Tasks covering the most novel worldwide accelerator R&D to allow reliable flash beams. WP2 explores conventional approaches for high gradient and high charge acceleration as well as plasma based compact sources for protons and electrons.

Task 1 -  Compact accelerating structure for C-band VHEE LINAC

6GHz accelerating structures may provide 100 MeV electron beams in a few meters. Beam dynamics simulation and RF design of the main LINAC will be pursued. A full-scale prototype will be realized and bench tested.

Task 2 - RF Pulse compressor SLED for C-band VHEE LINAC

Task 2 focuses on the design of a klystron pulse compressor for a high-field and compact LINAC. A full scale prototype will be realised and bench tested.

Task 3 - Proton beams from laser-plasma interactions

New and specifically designed coil-shaped targets coupled with permanent magnetic quadrupoles will be used to improve the emittance and the energy of the laser-accelerated proton beams. This scheme will be studied and optimised to obtain a never reached regime of tens of Gy in tens of nanoseconds over a 1 cm in diameter homogeneous beam spot size.

Task 4 - Electron beams from laser-plasma interactions

The VHEE electron beam already available at the CNR-INO ILIL laboratory will be optimised to:

i) further increase the dose/dose-rate, also using a dedicated transport beamline (CNR in-kind contribution to the project);

ii) enhance the control on the energy spectrum.

The experimental set up will enable in depth dosimetry of a VHEE pencil-beam configuration with high dose rate.

Task 5 - High current medium energy electron beams for medical applications

Feasibility studies will be performed for the generation of up to 10 MeV photon beams and impressive flux of 1016 photons/s. This will be possible thanks to the activities related to the future BriXsino accelerator (MI) that will be able to produce electron bunches with a charge up to 50 pC at a repetition rate up to 100 MHz.

WP2 Deliverables

The WP2 Deliverables are summarized in the following table:

Deliv. Short Name Description When (M) Deliv. Short Name Description When (M)
D2.1.1 VHEE linac beam dynamics Design and Layout of a compact VHEE Linac, beam dynamics simulations and optimization of the main system parameters. 6 M2.3.1.2 Target procurem Acquisition of the new developed targets from the RAL laboratory. 11-15
D2.1.2 RF accelerating structure and design Design of the high gradient accelerating prototype. 18 M2.3.1.3 Experimental tests and analysis  Experimental tests in laser facilities and beam characterisation in this new laser-matter interaction scheme. 16-36
D2.2.1 RF compr. design Design of the SLED RF pulse compressor. 18 D2.4.1 High dose VHEE from LWFA Report on the delivery of the Laser driven VHEE pencil beam with about 1Gy/shot dose. 36
D2.1.3 RF accel. structure manufacturing Manufacturing high gradient accelerating prototype. 24 M2.4.1 LWFA modelling  Particle in Cell modelling for controlled spectral properties. 12
D2.2.2 RF compressor manufacturing Manufacturing of the pulse compressor prototype. 24 M2.4.2 Dose simulation Modelling of dosimetric set up with MC simulations. 24
D2.1.4 RF accelerating structure test Low power RF tests of accelerating prototype. 36 M2.4.3 LWFA beam Dosimetric measurements with optimized VHEE beam. 34
 D.2.2.3 RF compr. test  Low power RF tests of the SLED prototype.  36 M2.5.1.1 Study and analysis Study of the setup for high charge electron bunches and radiobiological applications. Study of the mechanism involved in X ray generation by intense high energy electron beams 1-18
 D2.3.1 Flash protons from laser-plasma Deliver collimated and ultra-intense (up to 1 kGy/shot) proton beams generated in laser-plasma interaction and using new acceleration and tansport scheme. 36  M2.5.1.2 Accelerator design Design of a suitable geometrical, mechanical and thermal configuration of the tungsten anode for ultra high-rate bremsstrahlung production.  19-30
 M2.3.1.1 Monte Carlo Simulations Monte Carlo and analytical simulations (in collaboration with QUB and ELI) of the new laser-matter interaction and transport scheme using the coil targets coupled with the quadrupoles. Final design of the coil-target for the use with the QUB and ELI laser-generated beams.  1-10  M2.5.1.3 Experimental tests Preliminary tests using available electron beams on a small scaled prototype. 31-36

Materials, documents and links of interest for WP2 activities

 

WP3: FLASH beam monitoring & dosimetry

Alessio Sarti Uncategorised

WP3 Coordinators

The coordinators for the WP3 are:  M. G. Bisogni and A. Vignati

WP3 Participants

The WP3 Participants are as listed in the following table:

Name Unit FTE Name Unit FTE Name Unit FTE
Abujami M. TO 1 D'oca M. C. CT 0.6 Picollo F. TO 0.2
Amato E. CT 0.3 Di Martino F. PI 0.1 Romano F. CT 0.5
Apra' P. TO 0.3 Franciosini G. RM1 0.1 Sportelli G. PI 0.1
Barlotta A. CT 0.6 Italiano A. CT 0.2 Tomarchio E. CT 0.6
Belcari N. PI 0.1 Marafini M. RM1 0.1 Toppi M. RM1 0.1
Bisogni M. G. PI 0.4 Marrale M. CT 0.5 Traini G. RM1 0.1
Borghese R. F. CT 0.5 Marti' Villareal O.A TO 1 Trigilio A. RM1 0.1
Catalano R. LNS 0.1 Morrocchi M. PI 0.2 Vignati A TO 1
Cirio R. TO 0.5 Petringa G. LNS 0.1      

Main Goals

The main goal of the WP3 is the development of methods and tools to characterise FLASH beams and to precisely measure radiation dose to assure reliable beam delivery to the patient. The first two WP3 tasks focus on the development and characterization of detector systems for Beam Monitoring and Dosimetry. These are functional to the last task: the delivery of guidelines for reference dosimetry and beams characterisation.

Task 1 -  Development and test of new Beam Monitoring systems

The online control of FLASH beams delivery will be addressed with the innovative approach of air fluorescence by Roma1 and with the promising, never used in clinical settings so far, Integrating Current Transformers developed by LNS. The performances of thin silicon and diamond detectors, properly optimized by TO to stand the FLASH requirements, and “Free-standing membranes” SiC detectors (developed by STLab) available in-kind and characterized by CT, will be compared.

Task 2 - Development and test of new dosimetric systems

Different approaches will be pursued to perform the FLASH dosimetry of electron and proton/ion beams. CT will develop a dose rate independent portable calorimeter for electron and proton beams absolute dosimetry. Scintillator based detectors will be studied at PI for both absolute and relative dosimetry of electron beams SiC detectors available in-kind from the CSN5 PRAGUE project will be tested as relative dosimeters with protons/ions by LNS .

Task 3 - Intercomparisons, calibrations and guidelines

The beams developed within the project will be characterised with available in-kind BM systems (dual gap chamber, SEM, FC) and with dose rate independent reference dosimeters (FC, alanine, RCF). Campaigns of intercomparisons and calibrations of the developed BMs and dosimeters will be carried out at the beam facilities available within the project and at collaborating institutions. Finally, guidelines and recommendations for monitoring and dosimetry of FLASH beams will be prepared.

 

WP3 Deliverables

The WP3 Deliverables are summarized in the following table:

Deliv. Short Name Description When (M) Deliv. Short Name Description When (M)
D3.1.1 Air fluorescence Design, realization and test of air monitoring based detector for electrons. 16 D3.2.3 SiC Dosimeters SiC detectors optimization and test for relative dosimetry with proton/electron beams. 16
D3.1.2 ICB Design, realization and test of an ICT specifically tailored for intense and short proton/ion beams. 16 M3.2 Dosimeters R&D end Production and test of the first dosimeter prototypes. 16
D3.1.3 Silicon and Diamond Tests of silicon/diamond prototypes with proton and electron beams. 16 D3.3.1 Beam characterization Dosimetric characterization of the beams with available BM systems (dual gap chamber, SEM, FC) and reference dosimeters (Faraday cup, alanine, RCF, IC). 24
D3.1.4 SiC "Free standing Membrane" SiC detectors tests with electrons/protons for beam monitoring. 16 D3.3.2 Intercomparisons Intercomparisons and calibrations of the developed BMs and dosimeters. 32
M3.1 BM R&D end Production and test of the first BM prototypes. 16 D3.3.3 Guidelines Guidelines and recommendations for the monitoring and dosimetry of FLASH beams (what have we learnt so far). 36
D3.2.1  Calorimeter Portable calorimeter prototype development and characterization with electrons/protons. 16 M3.3 Prototype commissioning BM and Dosimetric systems prototypes commissioning. 36
 D3.2.2 Scintillators   Development and test of scintillator-based dosimeters with RO electronics. 16        

Materials, documents and links of interest for WP3 activities