QUEUES for FELIU MASERAS group

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QUEUES :

Currently there are four queues where calculations can be sent:

• c4m8.q (18 NODES)

       MACHINE TYPE
               1 x Xeon X3360 2,83Ghz 2x6Mb cache (4 cores)
               4x2GB RAM DDR2 800Mhz (8GB mem)
       PE
               c4m8_mpi
               c4m8_smp

• cq4m4.q (26 NODES)

       MACHINE TYPE
               1 x  Core2 Quad Q6600 2,4GHz  8M cache (4 cores)
               4x1GB DDR2 667MHz (4GB mem)
       PE
               cq4m4_mpi
               cq4m4_smp

• c8m24.q (27 NODES)

       MACHINE TYPE
               2 x Xeon E5530 2.4GHz 8M cache (8 cores)
               6x4GB RAM DDR3 1333MHz ECC Registered (24GB mem)
       PE
               c8m24_mpi
               c8m24_smp

• c12m24.q (18 NODES)

       MACHINE TYPE
               2 X Intel(R) Xeon(R) CPU E5645 2.40GHz 12M cache (12 cores)
               6x4GB RAM DDR3 1333MHz ECC Registered (24GB mem)
       PE
               c12m24_mpi
               c12m24_smp

• c20m48.1 (4 NODES)

       MACHINE TYPE
               ???? (20 cores)
               ??? (48 GB mem)
       PE
               c20m48_mpi
               c20m48_smp

• c24m128.1 (23 NODES)

       MACHINE TYPE
               ???? (24 cores)
               ??? (128 GB mem)
       PE
               c24m128_mpi
               c24m128_smp

• c28m128.1 (4 NODES)

       MACHINE TYPE
               ???? (28 cores)
               ??? (128 GB mem)
       PE
               c28m128_mpi
               c28m128_smp

GPU's NODES :

• c12m128gpu8.1

There are some gpu nodes that can be used. Terachem, orca and other type of calculations can be achieved with them.

• Queue system management

kimik2 manages automatically calculations sent from your computer:

1- The maximum number of calculations that each user can run at a time is 25, if you send more than that they will wait in the queue until one of your spaces is free.

2- In order to keep the sharing equality of the cluster we decided that the users cannot send more than a number of calculations "nbig" in the big machines (C8m24 + c12m24 + c20m48 + c24m128 + c28m128) at the same time. You can still send more than those to the big queues but they will be queueing even if there are empty machines. The number nbig can change depending on the time: depending on the number of users and how active they the number can change up and down. So if you notice that queues are too full or too empty for a period larger than two weeks as Feliu's permision to encrease/decrease nbig.

c28m128 --- 28x4 credits --- total 112 c24m128 --- 24x5 credits --- total 120 c20m128 --- 20x6 credits --- total 120 c12m24 --- 12x10 credits --- total 120 c8m24 --- 8x0 credits --- total 0 c4m8 --- 4x0 credits --- total 0 cq4m4 --- 4x0 credits --- total 0

If you have calculations holded, you can run the script hold2run to move them from hold to run automatically. This script has been developed by Maria Besora and if you have problems with it, you can contact me (Ignacio Funes) or Maria to help you.

This is the "installation" process step-by-step:

-Download the scripts: you can download them directly from our repository ( http://aliga.iciq.es/fsn/#0 ) in /USERS_AREA/Maseras Group/Scripts-for-Maseras-Group-Queues/ there is a -tar.gz directory with three scripts. Copy them to your bin directory in kimik2. You can also create the files directly in your bin directory, copying them from the next three links (remember to change the permissions; chmod 700 namefile.ext). hold2run, holdtorun, holdtorun.awk

-Write in the command line: nohup hold2run &

-Check if the process is running using the comand: ps -ef | fgrep username If you have more than one process called sleep 600, kill them with the command kill -9 idnumber

3- The small queues (cq4m4 and c4m8) can be used freely up to complete the 25 slot allowance.

SENDING CALCULATIONS:

• Gaussian jobs

qs TYPE_OF_CALCULATION inputfile.in

where TYPE_OF_CALCULATION can be:

g09.c24m128 (24 cores smp pe)
g09.c20m48 (20 cores smp pe)
g09.c12m24 (12 cores smp pe)
g09.c8m24 (8 cores smp pe)
g09.cq4m4 (4 cores smp pe)       
g09.c4m8 (4 cores smp pe) 
g03.cq4m4 (4 cores smp pe)
g03.c4m8 (4 cores smp pe)

NOTE: remember to add the correct parameters in your inputfile.in according to the TYPE_OF_CALCULATION. %nproc=... and %mem=...

• Orca jobs

qs orcaVERSION.QUEUE NMACHINES INPUTNAME

where:

VERSION could be 27 (for version 2.7) or 28 (for version 2.8)
QUEUE could be cq4m4 or c4m8 or c8m24 or c12m24
NMACHINES is the number of the machines to use (this parameter have directly relation with ! PALX of the input file, see the ORCA page)
INPUTNAME is the name of your input

Orca 4 is also available, but not directly with "qs orcaVERSION.QUEUE NMACHINES INPUTNAME" you have to edit a submiting script submit

• Other jobs

Other type of jobs might need a customized script, like MECP searches and others. To submit them use:

qsub scriptfile