Marenostrum: Difference between revisions
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[http://10.0.7.240/wiki/images/files/Marenostrum/BSC.pdf User's Guide Manual ] | [http://10.0.7.240/wiki/images/files/Marenostrum/BSC.pdf User's Guide Manual ] | ||
How to connect to your bsc account: | |||
ssh -X {username}@mn4.bsc.es (or mn3.bsc.es or mn2.bsc.es or mn1.bsc.es) | |||
Usualy the username is "iciqNNNNN" where N are different numbers for each user. | |||
How to kill the jobs | |||
mncancel <jobid> | |||
To check the status of your jobs: | |||
mnq | |||
To check a job: | |||
checkjob <job_id> | |||
obtains detailed information about a specific job, including the assigned nodes and the possible | |||
reasons preventing the job from running. | |||
To know the estimated time to start execution: | |||
mnstart <job_id> | |||
To block a job: | |||
mnhold -j <job_id> | |||
To release a job, the same command must be run with -r option. | |||
To see the usage of space | |||
quota -v | |||
== ADF == | == ADF == | ||
How to | * For''' Carles Bo''' group: | ||
How to check the status of your jobs | |||
llme | |||
How to check the status of the entire group's jobs | |||
llgr | |||
On the first connection (and only then), remember to set up your environment | On the first connection (and only then), remember to set up your environment | ||
| Line 23: | Line 61: | ||
It seems better to use multiple of 4 for the number of processors | It seems better to use multiple of 4 for the number of processors | ||
36h is the upper limit for now with the low priority we have | 36h is the upper limit for now with the low priority we have | ||
How to transfer an input-file from your local computer | |||
scp <input-file> {username}@mn1.bsc.es:'/home/iciq38/{username}/DEST_MN_directory' | |||
WATCH OUT!! | WATCH OUT!! | ||
| Line 35: | Line 77: | ||
If you need to keep the TAPE21 file, copy it back at the end of the job, namely after <eor>. | If you need to keep the TAPE21 file, copy it back at the end of the job, namely after <eor>. | ||
(for example: cp TAPE21 $HOME/example.t21) | (for example: cp TAPE21 $HOME/example.t21) | ||
== NWChem == | == NWChem == | ||
To submit | To submit [[NWCHEM]] calculations in Marenostrum you will need to submit a .cmd file. You can automatically create the cmd file and submit the job by using the script: [[Send_mn.sh]]. | ||
You will need to copy it in your own bin and call it by typing ''' | You will need to copy it in your own bin and call it by typing '''send_mn.sh namefile n XX:XX:XX''', where '''n''' is the number of nodes you would like to use and '''XX:XX:XX''' the time you will allow for the job to run. | ||
Be aware that apart from the options that appear in send.sh, more options can be described in the cmd, such as the type of job... | Be aware that apart from the options that appear in send.sh, more options can be described in the cmd, such as the type of job... | ||
NWChem is quite slow, so it is recommended to use at least 64 nodes. | |||
== DLPOLY == | == DLPOLY == | ||
Latest revision as of 10:37, 30 September 2011
go back to Main Page, Computational Resources, Clusters, External Resources
Early in 2004 the Ministry of Education and Science (Spanish Government), Generalitat de Catalunya (local Catalan Government) and Technical University of Catalonia (UPC) took the initiative of creating a National Supercomputing Center in Barcelona. BSC-CNS (Barcelona Supercomputing Center – Centro Nacional de Supercomputación) is the National Supercomputing Facility in Spain and was officially constituted in April 2005. BSC-CNS manages MareNostrum, one of the most powerful supercomputer in Europe ([1]), located at the Torre Girona chapel. The mission of BSC-CNS is to investigate, develop and manage information technology in order to facilitate scientific progress. With this aim, special dedication has been taken to areas such as Computational Sciences, Life Sciences and Earth Sciences.
How to connect to your bsc account:
ssh -X {username}@mn4.bsc.es (or mn3.bsc.es or mn2.bsc.es or mn1.bsc.es)
Usualy the username is "iciqNNNNN" where N are different numbers for each user.
How to kill the jobs
mncancel <jobid>
To check the status of your jobs:
mnq
To check a job:
checkjob <job_id> obtains detailed information about a specific job, including the assigned nodes and the possible reasons preventing the job from running.
To know the estimated time to start execution:
mnstart <job_id>
To block a job:
mnhold -j <job_id> To release a job, the same command must be run with -r option.
To see the usage of space
quota -v
ADF[edit]
- For Carles Bo group:
How to check the status of your jobs
llme
How to check the status of the entire group's jobs
llgr
On the first connection (and only then), remember to set up your environment
cat /gpfs/projects/iciq38/BASHRC >> .bashrc
How to submit jobs
qs -n <Numbers_Proc> <Input_Name> <time_in_hours> (for example: qs -n 16 test.in 36h) It seems better to use multiple of 4 for the number of processors 36h is the upper limit for now with the low priority we have
How to transfer an input-file from your local computer
scp <input-file> {username}@mn1.bsc.es:'/home/iciq38/{username}/DEST_MN_directory'
WATCH OUT!!
At variance with kimik, one should use the "real" adf input:
#! /bin/sh
$ADFBIN/adf << eor
Here you put your input like you would do on Kimik
eor
If you need to keep the TAPE21 file, copy it back at the end of the job, namely after <eor>.
(for example: cp TAPE21 $HOME/example.t21)
NWChem[edit]
To submit NWCHEM calculations in Marenostrum you will need to submit a .cmd file. You can automatically create the cmd file and submit the job by using the script: Send_mn.sh.
You will need to copy it in your own bin and call it by typing send_mn.sh namefile n XX:XX:XX, where n is the number of nodes you would like to use and XX:XX:XX the time you will allow for the job to run.
Be aware that apart from the options that appear in send.sh, more options can be described in the cmd, such as the type of job...
NWChem is quite slow, so it is recommended to use at least 64 nodes.
DLPOLY[edit]
GAMESS[edit]
Last update: Marsh 18 2009
1 - Available versions:
24 MAR 2007 (R6): /gpfs/apps/GAMESS/2008-03-19/gamess.00.x 12 JAN 2009 (R1): /gpfs/apps/GAMESS/2009-03-09/gamess.00.x
2 - Submiting script example:
Paste the following script in a .cmd file and use the classical command to submit it.
mnsubmit gamess_file.cmd
------------------------------------------------------------------
#! /bin/bash
#
# @ initialdir = .
# @ output = gamess_file.out
# @ error = gamess_file.err
# @ total_tasks = <NbProc>
#@ wall_clock_limit = hh:mm:ss
EXE=/gpfs/apps/GAMESS/2009-03-09/bin/rungms
INPUT=gamess_file
sl_get_machine_list > node_list$SLURM_JOBID
rm node_list-myri$SLURM_JOBID
cat node_list$SLURM_JOBID | while read node; do
echo $node-myrinet1 >> node_list-myri$SLURM_JOBID
done
${EXE} ${INPUT} 00 $SLURM_NPROCS node_list-myri$SLURM_JOBID
rm node_list$SLURM_JOBID
rm node_list-myri$SLURM_JOBID
------------------------------------------------------------------
rungms will run the gamess.00.x executable
If no scratch directory are specified, you could recover your .dat file in the following directory
/gpfs/scratch/usergroup/username/tmp/
3 - Manual:
Gamess' manual could be found at the following website http://www.msg.ameslab.gov/GAMESS/documentation.html
Carefull: it is possible that some keywords change between the two proposed versions
VASP[edit]
Molden[edit]
You can use Molden 4.8 by including /gpfs/apps/MOLDEN/4.8/ in your path (PATH="${PATH}":/home/iciq26/iciq26280/bin/:/gpfs/apps/MOLDEN/4.8/)
Contact[edit]
BSC Support
e-mail : support@bsc.es Fax : 934137721
User Support
David Vicente e-mail : david.vicente@bsc.es
Phone : 934054226