Smith

"Smith" is a computer cluster based on the Intel and Intel-compatible CPUs.

Login nodes

To use the "Smith" system, log in to the following nodes:

  • [smith] 133.1.116.161
  • [rafiki] 133.1.116.162
  • [tiamat] 133.1.116.211

To use the "sb100" system, use the following node:

  • [sb100] 133.1.116.165

How to login the login node

To login "smith" type

ssh -l [userID] 133.1.116.161

or

ssh [userID]@133.1.116.161

In a case you allow the X11 forwarding, use

ssh -Y -l [userID] 133.1.116.161

or

ssh -Y [userID]@133.1.116.161

Currently, you get the following message upon login

-bash: /usr/local/g09/D01/g09/bsd/g09.profile: Permission denied

but it does not affect your work mostly.

NOTE: When you log in for the first time, change your initial password by typing

passwd

How to submit your jobs

To execute your program, use the queueing system, usually using a job script (see below). For instance, to execute a script "job.sh" using the node (24 cores) in the group 10, type

qsub -q xh1.q -pe x24 24 job.sh

Note group and number of cores can be specified in the job script. To see the job status, type

qstat

To see the job status of the specific user, type

qstat -u [user ID]

To cancel a job, use

qdel [job ID]

where the job ID can be obtained by using qstat (the number appearing in the first column).

Examples of job script

In the following, examples for each groups (queues) are listed. In this case, you just type

qsub job.sh

and do not have to specify the queue group and number of processors explicitly.

  • Groups 4
    #$ -S /bin/bash
    #$ -cwd
    #$ -q xe1.q
    #$ -pe x8 8
    #$ -N JOB_NAME
    source /opt/setting/2016.4/intel-compiler.sh
    source /opt/setting/2016.4/intel-mpi.sh
    # Above settings should be consistent with those used in the compilation
    mpirun ./a.out < input.dat > output.dat
  • Groups 5
    #$ -S /bin/bash
    #$ -cwd
    #$ -q xe2.q
    #$ -pe x12 12
    #$ -N JOB_NAME
    source /opt/setting/2016.4/intel-compiler.sh
    source /opt/setting/2016.4/intel-mpi.sh
    # Above settings should be consistent with those used in the compilation
    mpirun ./a.out < input.dat > output.dat
  • Group 7 (sb100)
    • Hybrid parallelization (ex. use 12 cores with 6 threads parallelization)
      #$ -S /bin/bash
      #$ -cwd
      #$ -q all.q
      #$ -pe x6 12
      #$ -N JOB_NAME
      source /opt/setting/2016.4/intel-compiler.sh
      source /opt/setting/2016.4/intel-mpi.sh
      # Above settings should be consistent with those used in the compilation
      OMP_NUM_THREADS 6
      mpirun -perhost 1 -np $NHOSTS ./a.out < input.dat > output.dat
    • Flat parallelization (12 cores)
      #$ -S /bin/bash
      #$ -cwd
      #$ -q xe2.q
      #$ -pe x12 x12
      #$ -N JOB_NAME
      source /opt/setting/2016.4/intel-compiler.sh
      source /opt/setting/2016.4/intel-mpi.sh
      # Above settings should be consistent with those used in the compilation
      mpirun -np $NSLOTS ./a.out < input.dat > output.dat
  • Group 8
    #$ -S /bin/bash
    #$ -cwd
    #$ -q xs2.q
    #$ -pe x16 16
    #$ -N JOB_NAME
    source /opt/setting/2016.4/intel-compiler.sh
    source /opt/setting/2016.4/intel-mpi.sh
    # Above settings should be consistent with those used in the compilation
    MPI_COMMAND=mpirun
    I_MPI_PIN=1
    setenv I_MPI_ADJUST_ALLGATHERV 2
    OMP_NUM_THREADS=1
    cat $PE_HOSTFILE | awk '{ print $1":"$2/ENVIRON["OMP_NUM_THREADS"] }' > 
    hostfile.$JOB_ID
    $MPI_COMMAND ./a.out < input.dat > output.dat
  • Group 9
    #$ -S /bin/bash
    #$ -cwd
    #$ -q xi1.q
    #$ -pe x16 16
    #$ -N JOB_NAME
    source /opt/setting/2016.4/intel-compiler.sh
    source /opt/setting/2016.4/intel-mpi.sh
    # Above settings should be consistent with those used in the compilation
    MPI_COMMAND=mpirun
    I_MPI_PIN=1
    setenv I_MPI_ADJUST_ALLGATHERV 2
    OMP_NUM_THREADS=1
    cat $PE_HOSTFILE | awk '{ print $1":"$2/ENVIRON["OMP_NUM_THREADS"] }' > 
    hostfile.$JOB_ID
    $MPI_COMMAND ./a.out < input.dat > output.dat
  • Groups 10
    #$ -S /bin/bash
    #$ -cwd
    #$ -q xh1.q
    #$ -pe x24 48
    #$ -N JOB_NAME
    #$ -j y
    source /opt/setting/2016.4/intel-compiler.sh
    source /opt/setting/2016.4/intel-mpi.sh
    # Above settings should be consistent with those used in the compilation
    MPI_COMMAND=mpirun
    I_MPI_PIN=1
    I_MPI_FABRICS=shm:ofa
    OMP_NUM_THREADS=1
    cat $PE_HOSTFILE | awk '{ print $1":"$2/ENVIRON["OMP_NUM_THREADS"] }' > 
    hostfile.$JOB_ID
    $MPI_COMMAND ./a.out < input.dat > output.dat
  • Groups 11
    #$ -S /bin/bash
    #$ -cwd
    #$ -q xh2.q
    #$ -pe x24 48
    #$ -N JOB_NAME
    #$ -j y
    source /opt/setting/2016.4/intel-compiler.sh
    source /opt/setting/2016.4/intel-mpi.sh
    # Above settings should be consistent with those used in the compilation
    MPI_COMMAND=mpirun
    I_MPI_PIN=1
    I_MPI_FABRICS=shm:ofa
    OMP_NUM_THREADS=1
    cat $PE_HOSTFILE | awk '{ print $1":"$2/ENVIRON["OMP_NUM_THREADS"] }' > 
    hostfile.$JOB_ID
    $MPI_COMMAND ./a.out < input.dat > output.dat
  • Group 13
    #$ -S /bin/bash
    #$ -cwd
    #$ -q xb1.q
    #$ -pe x32 32
    #$ -N JOB_NAME
    #$ -j y
    source /opt/setting/2016.4/intel-compiler.sh
    source /opt/setting/2016.4/intel-mpi.sh
    # Above settings should be consistent with those used in the compilation
    MPI_COMMAND=mpirun
    I_MPI_PIN=1
    I_MPI_FABRICS=shm:ofa
    OMP_NUM_THREADS=1
    cat $PE_HOSTFILE | awk '{ print $1":"$2/ENVIRON["OMP_NUM_THREADS"] }' > 
    hostfile.$JOB_ID
    $MPI_COMMAND ./a.out < input.dat > output.dat
  • Group 14
    #$ -S /bin/bash
    #$ -cwd
    #$ -q x17.q
    #$ -pe x32 32
    #$ -N JOB_NAME
    #$ -j y
    source /opt/setting/2016.4/intel-compiler.sh
    source /opt/setting/2016.4/intel-mpi.sh
    # Above settings should be consistent with those used in the compilation
    MPI_COMMAND=mpirun
    I_MPI_PIN=1
    I_MPI_FABRICS=shm:dapl
    OMP_NUM_THREADS=1
    cat $PE_HOSTFILE | awk '{ print $1":"$2/ENVIRON["OMP_NUM_THREADS"] }' > 
    hostfile.$JOB_ID
    $MPI_COMMAND ./a.out < input.dat > output.dat

Computer nodes and queues

GroupProc.#CORE/#CPUSubmission nodequeue paral. environ.Inter-node
4xeon  8/2smith/rafiki/tiamatxe1.qx8
5xeon  12/2smith/rafiki/tiamatxe2.qx12
7core i7 sandy-bridge6/1sb100all.qx6
8xeon sandy-bridge16/2smith/rafiki/tiamatxs2.qx16
xeon ivy-bridge16/2smith/rafiki/tiamatxi1.qx16
10xeon Haswell24/2smith/rafiki/tiamatxh1.qx24infini-band
11xeon Haswell24/2smith/rafiki/tiamatxh2.qx24infini-band
13xeon Broadwell32/2smith/rafiki/tiamatxb1.qx32infini-band
14xeon Skylake32/2smith/rafiki/tiamatx17.qx32infini-band

NOTE:

  • To submit a job to group 8 nodes, login to sb100 and execute qsub
  • To submit a job to other group nodes, login to smith and execute qsub

Group 4, 5 "xe" system

The "xe" system is composed of the nodes with the Xeon CPU, which have 2 CPUs (8 or 12 cores) per node. The parallel environment is x8 and x12.

Group 7 "sb100" system

The "sb100" system is based on the Core i7 CPUs with the Sandy-bridge architecture. Each node has 1 CPU (6cores) with 16 GB memory. Fast calculations are possible thanks to the AVX function. The parallel environment is x6.

Group 8 "xs" system

The "xs" system is based on the Xeon CPUs with the Sandy-bridge architecture. Each node has 1 CPU (6cores) with 32 GB memory. Fast calculations are possible thanks to the AVX function. The parallel environment is x16.

Group 9 "xi" system

The "xi" system is based on the Xeon CPUs with the Ivy-bridge architecture. Each node has 2 CPUs (16cores) with 128 GB memory. Fast calculations are possible thanks to the AVX function. It is recommend to use this system for Gaussian calculations. The parallel environment is x16.

Group 10, 11, 12 "xh" system

The "xh" system is composed of the nodes with 2 Xeon CPUs (24 cores in total) and 64 GB memory. The parallel environment is x24.

Group 13 "xb" system

The "xb" system is composed of the nodes with 2 Xeon Broadwell CPUs (32 cores in total) and 64 GB memory. The parallel environment is x32.

Group 14 "x17" system

The "x17" system is composed of the nodes with 2 Xeon Skylake CPUs (32 cores in total) and 64 GB memory. The parallel environment is x32.

Network structure

  • "|" indicates a network connection, "[]" name, for the computer node

    + Engineering intranet, ODINS network
    |
    |           Backbone network( no access outside of engineering network)
    |               |
    +- [smith] -----+                          133.1.116.161 Login & application server & backup server & file server 
    +- [rafiki] ----+                          133.1.116.162 Login & application server & backup server 
    +- [tiamat] ----+                          133.1.116.211 Login & Application server
    |               |
    |               +-- [xe00], [xe01]         Calc. node, group 4 (each node has 8 cores (2CPUs)) paral. env.=x8 queue=xe1.q
    |               +-- [xe02]-[xe06]          Calc. node, group 5 (each node has 8 cores (2CPUs)) paral. env.=x8 queue=xe1.q
    |               |
    |               +-- [xs01]-[xs18]          Calc. node, group 8 (each node has 16 cores (2CPUs)) paral. env.=x16 queue=xs2.q
    |               |
    |               +-- [xi01]-[xi12]          Calc. node, group 9 (each node has 16 cores (2CPUs)) paral. env.=x16 queue=xi1.q
    |               |
    |               +-- [xh01]-[xh17]
    |               +-- [xh19]-[xh34]          Calc. node, group 10 (each node has 16 cores (2CPUs)) paral. env.=x16 queue=xe1.q                        
    |               +-- [xh18],[xh35]-[xh43]   Calc. node, group 11 (each node has 24 cores (2CPUs)) paral. env.=x24 queue=xh2.q
    |               +-- [xb01]-[xb14]          Calc. node, group 13 (each node has 32 cores (2CPUs)) paral. env.=x32 queue=xb1.q
    |               +-- [x1701]-[x1706]        Calc. node, group 14 (each node has 32 cores (2CPUs)) paral. env.=x32 queue=x17.q
    |               |
    |               |
    +- [sb100] -----+                          133.1.116.165 Login node for other groups
                    |
                    +-- [sb101]-[sb120]        Calc. node, group 7 (each node has 6 cores (1 CPU))
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Last-modified: 2019-11-07 (木) 12:15:08 (15d)