Računanje s Gaussianom na gridu CRO-NGI

Darko Babić

Institut “Ruđer Bošković”, Zagreb

Gaussian je na Isabelli i CRO-NGI-u najviše zastupljena pojedinačna aplikacija

Gaussian je samo jedan od programskih sustava za molekulsko modeliranje.

Kad bi se dodalo učešće sličnih programa (Gamess, Orca, Amber, Gromacs,

Abinit i Siesta), ukupan udjel bio bi veći od 70%.

Isabella

prosjek: 51%

CRO-NGI

prosjek: 33%

Isabella & CRO-NGI

prosjek: 46%

Licencu za Gaussian plaća MZOŠ, a programski paket nabavlja Srce kroz projekt

“Referalni centar za Gaussian”.

Licenca se nabavlja samo za ustanove Sveučilišta u Zagrebu. Korisnici npr. s

Instituta “Ruđer Bošković” nemaju pravo korištenja.

Cijena akademske licence za Gaussian 09: 5750 USD (za ustanove koje dodjeljuju

doktorat). Cijena za ustanove kao što je IRB: 40250 USD.

Gaussian je samo jedan od programa za molekulsko modeliranje. Njemu su slični:

B E S P L A T N I Z A A K A D E M S K E U S T A N O V E

Gordon research group at Iowa State University

F. Neese, with contributions from U. Becker, D. Ganiouchine,

S. Koßmann, T. Petrenko, C. Riplinger and F. Wennmohs

Chair of Theoretical Chemistry, University of Bonn

K O M E R C I J A L N I P R O G R A M I Z A K V A N T N U K E M I J U

http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid_state_physics_software

Projekt: Dizajn, sinteza i svojstva organometalnih kompleksnih spojevavoditelj: dr. Ljerka Tušek Božić, Institut “Ruđer Bošković”, Zagreb

sinteza i eksperimentalna karakterizacija ciklopaladiranih azobenzena: Manda Ćurić

cis-trans fotoizomerizacija azobenzena

Važne funkcionalnosti:

▪ proširena delokalizacija konjugiranog elektronskog sustava

▪ velika strukturna varijabilnost

Reakcija priprave:

1H NMR spektar diciklopaladiranog aminoazobenzena s bipiridinom

eksperimentalni spektar

izračunati spektar

izlazak otapala iz kompleksa u čvrstom stanju!?!

infracrveni spektar diciklopaladiranog azobenzena s dmf-om

eksperimentalni spektar

originalnog kompleksa

eksperimentalni spektar

kompleksa bez dmf-a

izračunati spektar

originalnog kompleksa

izračunati spektar

hipotetskog kompleksa

UV-vis spektri diciklopaladiranih azobenzena s bipiridinom

eksperimenteksperiment

eksperimenteksperiment

račun

račun

račun

račun

Reakcijski mehanizam ciklopaladiranja azobenzena

+

R

TS1

I

TS2

P1

P2

TS3

%mem=12288mb

%chk=C2-AAB-4TPP-exc.chk

#P B3LYP/GEN Int=(Grid=Ultrafine) Pseudo=Read SCF=(NoIncFock,NoVarAcc)

TD=(Singlet,NStates=32) SCRF=(PCM,Solvent=Chloroform)

Title Card

0 1

C,0,-6.351464207,2.0211747584,-1.0271924272

C,0,2.8499737825,0.2186870618,-2.7765359876

C,0,7.0572555212,-4.1089445771,1.0474940935

C,0,5.7082555169,-3.8770938063,0.7784007587

C,0,-7.713549091,1.8823352678,-0.7544287583

C,0,2.2450145477,0.2281238841,-4.0385166603

C,0,5.9470139403,2.2743190384,-1.4650769191

...

...

Izvođenje računa na gridu CRO-NGI

1. Ulazni podaci (input-datoteka), npr. C2-AAB-4TPP-exc.com:

2. Na Isabelli: skripta s izvršnim naredbama, npr. run-C2-AAB-4TPP-exc

dog09 C2-AAB-4TPP-exc

[dbabic@tannat]$ qsub –pe mpisingle 8 run-C2-AAB-4TPP-exc podnošenje posla batch-sustavu (SGE)

[dbabic@cs1]$ condor_submit job-C2-AAB-4TPP-exc

2. (nastavak) Na CRO-NGI: opis posla, npr. job-C2-AAB-4TPP-exc

Executable = /usr/local/bin/dog09

Arguments = C2-AAB-4TPP-exc

TransferExecutable = False

should_transfer_files = yes

WhenToTransferOutput = ON_EXIT

transfer_input_files = C2-AAB-4TPP-exc.com

transfer_output_files = C2-AAB-4TPP-exc.log,C2-AAB-4TPP-exc.chk

Log = job-C2-AAB-4TPP-exc.log

Output = job-C2-AAB-4TPP-exc.out

Error = job-C2-AAB-4TPP-exc.err

universe = grid

environment = "PE_MODE=single"

globusrsl = (jobType=single)(count=8)

grid_resource = gt2 ce.gradri.cro-ngi.hr/jobmanager-sge

queue

podnošenje posla grid upravitelju (Condor)

[dbabic@cs1]$ condor_status

Name OpSys Arch State Activity LoadAv Mem ActvtyTime

ce.etfos.cro-ngi.h LINUX x86_64 Claimed Busy 1.000 16384 [Unknown]

ce.fesb.cro-ngi.hr LINUX x86_64 Unclaimed Idle 0.219 16384 [Unknown]

ce.gradri.cro-ngi. LINUX x86_64 Unclaimed Idle 0.125 16384 [Unknown]

ce.irb.cro-ngi.hr LINUX x86_64 Unclaimed Idle 0.172 16384 [Unknown]

ce.srce.cro-ngi.hr LINUX x86_64 Claimed Busy 1.000 65536 [Unknown]

Što radi /usr/local/bin/dog09 ?

%mem=12288mb

%chk=C2-AAB-4TPP-exc.chk

#P B3LYP/GEN .......

Title Card

0 1

C,0,-6.351464207,2.0211747584,-1.0271924272

...

...

--Link1—

%mem=12288mb

%chk=C2-AAB-4TPP-exc.chk

....

%nprocshared=8

%mem=12288mb

%chk=/home/dbabic/gram_scratch_cQBanIFaUw/C2-AAB-4TPP-exc.chk

#P B3LYP/GEN .......

Title Card

0 1

C,0,-6.351464207,2.0211747584,-1.0271924272

...

...

--Link1—

%nprocshared=8

%mem=12288mb

%chk=/home/dbabic/gram_scratch_cQBanIFaUw/C2-AAB-4TPP-exc.chk

....

%lindaworkers=node014.gradri.cro-ngi.hr:4,node015.gradri.cro-ngi.hr:4

%mem=12288mb

%chk=/home/dbabic/gram_scratch_cQBanIFaUw/C2-AAB-4TPP-exc.chk

#P B3LYP/GEN .......

Title Card

0 1

C,0,-6.351464207,2.0211747584,-1.0271924272

...

...

--Link1—

%lindaworkers=node014.gradri.cro-ngi.hr:4,node015.gradri.cro-ngi.hr:4

%mem=12288mb

%chk=/home/dbabic/gram_scratch_cQBanIFaUw/C2-AAB-4TPP-exc.chk

....

OMP paralelizacija

paralelizacija Lindom

node014 ce.gradri.cro-ngi.hr

/scratch/35720.1.all.q

„eksportiran‟ kroz NFS:

/home/dbabic/gram_scratch_cQBanIFaUw

radni

direktorij?

3. Da li posao čeka ili se izvršava ili je gotov?

[dbabic@cs1]$ less job-C2-AAB-4TPP-exc.log

000 (151104.000.000) 11/30 14:01:46 Job submitted from host:

...

017 (151104.000.000) 11/30 14:01:59 Job submitted to Globus

RM-Contact: ce.gradri.cro-ngi.hr/jobmanager-sge

JM-Contact: https://ce.gradri.cro-ngi.hr:20888/22972/1291122118/

Can-Restart-JM: 1

...

027 (151104.000.000) 11/30 14:01:59 Job submitted to grid resource

GridResource: gt2 ce.gradri.cro-ngi.hr/jobmanager-sge

GridJobId: gt2 ce.gradri.cro-ngi.hr/jobmanager-sge https://ce.gradri.cro-ngi.hr:20888/22972/1291122118/

...

001 (151104.000.000) 11/30 14:02:30 Job executing on host: gt2 ce.gradri.cro-ngi.hr/jobmanager-sge

...

005 (151104.000.000) 11/30 14:14:20 Job terminated.

(1) Normal termination (return value 0)

Usr 0 00:00:00, Sys 0 00:00:00 - Run Remote Usage

Usr 0 00:00:00, Sys 0 00:00:00 - Run Local Usage

Usr 0 00:00:00, Sys 0 00:00:00 - Total Remote Usage

Usr 0 00:00:00, Sys 0 00:00:00 - Total Local Usage

0 - Run Bytes Sent By Job

0 - Run Bytes Received By Job

0 - Total Bytes Sent By Job

0 - Total Bytes Received By Job

[dbabic@cs1]$ globus-job-run ce.gradri.cro-ngi.hr \

/bin/env SGE_ROOT=/opt/sge /opt/sge/bin/lx24-amd64/qstat -f

[dbabic@cs1]$ globus-job-run ce.fesb.cro-ngi.hr /opt/pbs/bin/qstat -a

Direktniji uvid:

4. Međurezultati?

[dbabic@cs1]$ uberftp ce.gradri.cro-ngi.hr “get gram_scr*/C2-AAB-4TPP-exc.log”

/home/dbabic/.../.../.../

ulazni & izlazni podaci posla

/home/dbabic/JOBS/...

opis posla, podaci o tijeku,

„standard & error output‟

ce.gradri.cro-ngi.hr

/home/dbabic/.globus/job/ce.gradri.cro-ngi.hr/22972.1291122118/sge_job_script.7548

SCRATCH_DIRECTORY=/home/dbabic//gram_scratch_g3RTeYL5zM

/home/dbabic/gram_scratch_cQBanIFaUw/C2-AAB-4TPP-exc.log

ce.srce.cro-ngi.hr

/home/dbabic/gram_scratch_...

ce.etfos.cro-ngi.hr

/home/dbabic/gram_scratch_...

ce.fesb.cro-ngi.hr

/home/dbabic/gram_scratch_...

ce.irb.cro-ngi.hr

/home/dbabic/gram_scratch_...

u job-C2-AAB-4TPP-exc.log:

GridJobId: gt2 ................ https://ce.gradri.cro-ngi.hr:20888/22972/1291122118/

Važno je voditi računa o različitom značenju %mem s OMP i Lindom!

%mem=12288mb

%chk=C2-AAB-4TPP-exc.chk

#P B3LYP/GEN .......

Title Card

0 1

C,0,-6.351464207,2.0211747584,-1.0271924272

...

...

--Link1—

%mem=12288mb

%chk=C2-AAB-4TPP-exc.chk

....

Executable = /usr/local/bin/dog09

Arguments = C2-AAB-4TPP-exc

TransferExecutable = False

should_transfer_files = yes

WhenToTransferOutput = ON_EXIT

transfer_input_files = C2-AAB-4TPP-exc.com

transfer_output_files = C2-AAB-4TPP-exc.log,C2-AAB-4TPP-exc.chk

Log = job-C2-AAB-4TPP-exc.log

Output = job-C2-AAB-4TPP-exc.out

Error = job-C2-AAB-4TPP-exc.err

universe = grid

environment = "PE_MODE=single"

globusrsl = (jobType=single)(count=8)

grid_resource = gt2 ce.gradri.cro-ngi.hr/jobmanager-sge

queue

%mem=12288mb

%chk=C2-AAB-4TPP-exc.chk

#P B3LYP/GEN .......

Title Card

0 1

C,0,-6.351464207,2.0211747584,-1.0271924272

...

...

--Link1—

%mem=12288mb

%chk=C2-AAB-4TPP-exc.chk

....

Executable = /usr/local/bin/dog09

Arguments = C2-AAB-4TPP-exc

TransferExecutable = False

should_transfer_files = yes

WhenToTransferOutput = ON_EXIT

transfer_input_files = C2-AAB-4TPP-exc.com

transfer_output_files = C2-AAB-4TPP-exc.log,C2-AAB-4TPP-exc.chk

Log = job-C2-AAB-4TPP-exc.log

Output = job-C2-AAB-4TPP-exc.out

Error = job-C2-AAB-4TPP-exc.err

universe = grid

# environment = "PE_MODE=single"

globusrsl = (jobType=single)(count=8)

grid_resource = gt2 ce.gradri.cro-ngi.hr/jobmanager-sge

queue

OK!

nije OK!

Tipični zahtjevi poslova s Gaussianom:

PARALELIZACIJA: 4 – 8 jezgri (do 16, maksimalno 32?)

RAM: 0.5 (malo), 1 (srednje), 1.5 (vrlo zahtjevni poslovi) Gb / jezgri

DISK: 1 – 10 Gb (MP2 može tražiti više)

WALLTIME: 1 – 10 dana (do mjesec-dva)

Prijenos .chk datoteke u oba smjera ...

Executable = /usr/local/bin/dog09

Arguments = C2-AAB-4TPP-exc

TransferExecutable = False

should_transfer_files = yes

WhenToTransferOutput = ON_EXIT

transfer_input_files = C2-AAB-4TPP-exc.com,CHK/C2-AAB-4TPP-exc.chk

transfer_output_files = C2-AAB-4TPP-exc.log,C2-AAB-4TPP-exc.chk

Log = job-C2-AAB-4TPP-exc.log

Output = job-C2-AAB-4TPP-exc.out

Error = job-C2-AAB-4TPP-exc.err

universe = grid

environment = "PE_MODE=single"

globusrsl = (jobType=single)(count=8)

grid_resource = gt2 ce.gradri.cro-ngi.hr/jobmanager-sge

queue