The Center for Heliospheric Science

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====== How to use compute nodes ======
==== Compilers ====
^Compilers^Version^Licenses^
|ifort, icc, icpc|Intel oneApi 2021|2 floating|
|mpiifort, mpiicc, mpiicpc|:::|:::|
|ifort2020, icc2020, icpc2020|Intel Parellel Studio 2020|:::|
|mpiifort2020, mpiicc2020, mpiicpc2020|:::|:::|
|ifort2017, icc2017, icpc2017|Intel Parellel Studio 2017|5 floating|
|mpiifort2017, mpiicc2017, mpiicpc2017|:::|2 floating|

==== Compile Options ====

(a) optimal for Fortran
|<code>$ ifort –ipo –ip –O3 –xCASCADELAKE prog.f90</code>|Serial|
|<code>$ mpiifort –ipo –ip –O3 –xCASCADELAKE prog.f90</code>|MPI parallel|

(b) optimal for C
|<code>$ icc –ipo –ip –O3 –xCASCADELAKE prog.c</code>|Serial|
|<code>$ mpiicc –ipo –ip –O3 –xCASCADELAKE prog.c</code>|MPI parallel|

<nowiki>(c)</nowiki> optimal for C++
|<code>$ icpc –ipo –ip –O3 –xCASCADELAKE prog.cpp</code>|Serial|
|<code>$ mpiicpc –ipo –ip –O3 –xCASCADELAKE prog.cpp</code>|MPI parallel|


(d) other options
|-qopenmp|Use OpenMP|
|-parallel|Use automatic parallelization|
|-check|For debug|
|-traceback|For debug|

==== Job Queues ====
^Item \ Queue^IDLbatch^SHARED^NODEX1^NODEX4^
|Node usage|2 IDL nodes|2 Shared nodes|12 Occupied nodes|12 Occupied nodes|
|Number of nodes|1|1|1|2 - 4|
|Number of cores per node|1 - 2|1 - 26|52|52|
|Default elapsed time|24h|24h|24h|24h|
|Maximum elapsed time|120h |120h |168h |120h |
|Default memory size per node|4GB|4GB|350GB|350GB|
|Maximum memory size per node|87GB|175GB|350GB|350GB|
|Number of submissions per user|1|8|4|2|
|Number of executions per user |1|4|2|1|
|Number of executions per system|52|unlimited|unlimited|2|

NODEX1 and NODEX4 queues are for ISEE computational joint research program only. 
==== Job queuing system ====

(a) Submit a job
<code>$ qsub <options> <job script file name></code>

(b) Check status of jobs

|<code>$ qstat</code>|List all your jobs|
|<code>$ qstat -J</code>|Show all nodes used by your jobs|
|<code>$ qstat -S</code>|Show status of all nodes|
|<code>$ qstat -Q</code>|Show the number of jobs in queues|
|<code>$ qstat -f <request ID></code>|Show detailed information of a job|

<nowiki>(c)</nowiki> Delete a job
<code>$ qdel <request ID></code>
==== Sample Job Scripts ====

(a) IDLbatch queue
|<code>
#!/bin/bash
#PBS -q IDLbatch
#PBS –b 1
#PBS -l elapstim_req=96:00:00
#PBS -l cpunum_lhost=1
#PBS -l memsz_lhost=8GB
#PBS -M user@isee.nagoya-u.ac.jp
#PBS -m be

ulimit -s unlimited
cd $PBS_O_WORKDIR
idl < prog.pro
</code>|<code>
# shell : do not change
# name of queue : do not change
# number of nodes : do not change
# elapsed time : default 24:00:00, max 120:00:00
# number of cores : 1 - 2
# memory size : default 4GB, max 87GB
# send email to user@isee.nagoya-u.ac.jp
# send email at (b) "beginning" and (e) "end"

# Do not change
# Do not change
#
</code>|

(b) SHARED queue
|<code>
#!/bin/bash
#PBS -q SHARED
#PBS –b 1
#PBS -l elapstim_req=96:00:00
#PBS -l cpunum_lhost=26
#PBS -l memsz_lhost=120GB
#PBS -v OMP_STACKSIZE=512m
#PBS -v OMP_NUM_THREADS=13
#PBS -M user@isee.nagoya-u.ac.jp
#PBS -m be

ulimit -s unlimited
cd $PBS_O_WORKDIR
mpirun -n 2 ./a.out < input.txt 
</code>|<code>
# shell : do not change
# name of queue : do not change
# number of nodes : do not change
# elapsed time : default 24:00:00, max 120:00:00
# number of cores : 1 - 26
# memory size : default 4GB, max 175GB
# for OpenMP : stack size
# for OpenMP : number of threads
# send email to user@isee.nagoya-u.ac.jp
# send email at (b) "beginning" and (e) "end"

# Do not change
# Do not change
# use 2 processes (x 13 threads = 26 cores)
</code>|

<nowiki>(c)</nowiki> NODEX1 queue
|<code>
#!/bin/bash
#PBS -q NODEX1
#PBS –b 1
#PBS -l elapstim_req=96:00:00
#PBS -v OMP_STACKSIZE=512m
#PBS -v OMP_NUM_THREADS=13
#PBS -M user@isee.nagoya-u.ac.jp
#PBS -m be

ulimit -s unlimited
cd $PBS_O_WORKDIR
mpirun -n 4 ./a.out < input.txt 
</code>|<code>
# shell : do not change
# name of queue : do not change
# number of nodes : do not change
# elapsed time : default 24:00:00, max 168:00:00
# for OpenMP : stack size
# for OpenMP : number of threads
# send email to user@isee.nagoya-u.ac.jp
# send email at (b) "beginning" and (e) "end"

# Do not change
# Do not change
# use 4 processes (x 13 threads = 52 cores)
</code>|

(d) NODEX4 queue
|<code>
#!/bin/bash
#PBS -q NODEX4
#PBS –b 4
#PBS -T intmpi
#PBS -l elapstim_req=96:00:00
#PBS -v OMP_STACKSIZE=512m
#PBS -v OMP_NUM_THREADS=26
#PBS -M user@isee.nagoya-u.ac.jp
#PBS -m be

ulimit -s unlimited
cd $PBS_O_WORKDIR
mpirun -n 8 -npp 2 ./a.out < input.txt 
</code>|<code>
# shell : do not change
# name of queue : do not change
# number of nodes : 2 - 4
# Do not change
# elapsed time : default 24:00:00, max 120:00:00
# for OpenMP : stack size
# for OpenMP : number of threads
# send email to user@isee.nagoya-u.ac.jp
# send email at (b) "beginning" and (e) "end"

# Do not change
# Do not change
# use 8 processes and 2 processes per node (x 26 threads = 52 cores)
</code>|

==== In Publications ====
When submitting a publication based on results from the CIDAS system, 
users are asked to include the following line in the acknowledgements:

The computation was performed on the CIDAS computer system at the Institute for Space-Earth Environmental Research, Nagoya University. 

----
  * [[public:en:manual:cidas:start|CIDAS system manual (english)]]
  * [[public:ja:manual:cidas:start|CIDAS system manual (japanese)]]