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| ||<tablewidth=""" tableheight=""" tablestyle="" & quot; & amp; quot; & amp; amp; quot; & amp; amp; amp; quot; & amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; 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amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; 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amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; quot& amp; amp; amp; quot; ; & amp; amp; amp; amp; quot& amp; amp; amp; quot; ; & amp; amp; amp; amp; quot& amp; amp; amp; quot& amp; amp; quot; ; & amp; amp; amp; quot& amp; amp; quot; ; & amp; amp; amp; quot& amp; amp; quot& amp; quot; ; & amp; amp; quot& amp; quot; ; & amp; amp; quot& amp; quot& quot; ; & amp; quot& quot; ; & amp; quot& quot" ;&quot";&quot"">Nombre ||Clustertalca3 (GPU) || | ||<tablewidth=""" tableheight=""" tablestyle="" & quot; & amp; quot; & amp; amp; quot; & amp; amp; amp; quot; & amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; 425px& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; 104px& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; 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amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; quot; ; & amp; amp; amp; amp; amp; quot& amp; amp; amp; amp; quot& amp; amp; amp; quot; ; & amp; amp; amp; amp; quot& amp; amp; amp; quot; ; & amp; amp; amp; amp; quot& amp; amp; amp; quot& amp; amp; quot; ; & amp; amp; amp; quot& amp; amp; quot; ; & amp; amp; amp; quot& amp; amp; quot& amp; quot; ; & amp; amp; quot& amp; quot; ; & amp; amp; quot& amp; quot& quot; ; & amp; quot& quot; ; & amp; quot& quot" ;&quot";&quot"">Nombre ||Clustertalca3 (GPU) || |
| Línea 39: | Línea 39: |
| #!/bin/sh | #!/bin/sh |
| Línea 62: | Línea 62: |
| [[attachment:slurm-namd.sh|Descarga el archivo]] |
• Inicio
Tabla de Contenidos
Clustertalca:
Características:
Nombre |
Clustertalca3 (GPU) |
Marca |
Supermicro |
Modelo |
SSG-6048R-E1CR24N |
Nodos |
9 (8 esclavos y 1 cabecera) |
Procesadores disponibles |
256 |
GPU por nodo |
2 * 16 Tesla K80 y 6 * 8 Geforce GTX 1080 Ti |
Total GPU |
80 |
Procesadores por nodo disponibles |
32 |
Disco Total (headnode) |
30 TB |
Memoria distriuida Total (nodos) |
1 TB |
Red |
56 Gb/sec (4X FDR) |
Red |
Ethernet 1 Gbps |
IP |
10.1.1.103 |
Nodos Master (s) |
1 |
Nodos Esclavos |
8 |
Nodos totales |
9 |
Sistema Operativo |
CentOS Linux release 7.5 |
Acceso
Para lograr acceso primero debe enviar una solicitud al director de Escuela con copia al Administrador de Sistemas de la escuela, en donde se especifíque las razones del requerimiento. Una vez aprobada la generación de la cuenta se le entregarán las credenciales (usuario y contraseña) para la utilización y un par de recomendaciones extras.
Tenga presente que el acceso a esta supercomputadora es mediante el protocolo SSH, pudiendo utilizar tú cliente SSH favorito.
Para el caso se encuentre localizado al interior de la Escuela de Ingeniería Civil en Bioinformática, la forma de conectar sería del siguiente modo:
ssh user@ip-servidor
Pero si se está fuera de las dependencias de la escuela de Ingeniería en bioinformática, se debe solicitar también el acceso al servidor bioinfo.utalca.cl.
Una vez han sido entregado los permisos a bioinfo, se recomienda utilizar Proxycommand de SSH. Para su comprensión de uso puede visitar el link https://srvbioinf1.utalca.cl/wiki/cluster/ssh-proxycommand
La utilización SSH junto a ProxyCommand hacia los equipos cluster se verá más simpleficada. Un ejemplo sería el caso de necesitar realizar un copiado de datos mediante scp, solo se tendría que hacer:
scp fichero.local user@alias-servidor:
No olvidar que después del dos puntos (:) va en referencia al directorio personal ($HOME) del usuario.
Software
El equipo tiene un sistema de colas llamado SLURM que cumple la labor de organizar, priorizar los trabajos enviados por los usuarios.
Namd
La versión instalada es 2.13
Archivo SLURM NAMD
#!/bin/sh
#SBATCH --job-name namd
#SBATCH -o slurm-gpu-job.out
#SBATCH -p defq #SBATCH --gres=gpu:4
#SBATCH --ntasks=12 #SBATCH --time 24:00:00
#SBATCH --error=error.log
#SBATCH --output=output
# choose version of NAMD to use
# VERSION=2.13
NAMD_DIR=/cm/shared/apps/NAMD/2.13/CUDA
# execute
##################################################################
#CONFIG: change this
jobcfg=<entrada>
jobout=<salida>
#END CONFIG
##################################################################
${NAMD_DIR}/namd2 +idlepoll +p $SLURM_NTASKS ${jobcfg} +isomalloc_sync >& ${jobout}
wait