We do not have a formal manual for SGE system in OIST. If you want to look of some options via google (such as array job), type,

sge task array "SGE_TASK_ID" "-t"

"SGE_TASK_ID" is an effective keyword to search about SGE system. We need to add quotation marks to use underbar and hypen as keyword.

From your terminal, type,

ssh YOUR_ID@tombo.oist.jp

When you want to login to TOMBO from outside of OIST, type,

ssh YOUR_ID@loginc01.oist.jp

Please set up the id_rsa.pub key according to "TIDA > IT Services > SSH"

We can also run the program from the computation node (not login node):

[jun-inoue:~]$ qlogin
local configuration tombo-login2.oist.jp not defined - using global configuration
Your job 419190 ("QLOGIN") has been submitted
waiting for interactive job to be scheduled ...
Your interactive job 419190 has been successfully scheduled.
Establishing builtin session to host tombo10705.oist.jp ...
[jun-inoue:~]$ hostname
tombo10705.oist.jp

Especially, we need to assign the memory usage when we use Java:

[jun-inoue:~]$ qlogin -l h_vmem=3gb
local configuration tombo-login2.oist.jp not defined - using global configuration
Your job 419192 ("QLOGIN") has been submitted
waiting for interactive job to be scheduled ...
Your interactive job 419192 has been successfully scheduled.
Establishing builtin session to host tombo10514.oist.jp ...
[jun-inoue:~]$ java -Xmx2g -version
java version "1.6.0_37"
Java(TM) SE Runtime Environment (build 1.6.0_37-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01, mixed mode)

Although more than 3gb is ideal, biggerr memory usage sometimes has a bad effect on other users [July 2013].

Make a job file, sge.sh. Run the job with "qsub sge.sh".
The node will be chosen automatically.

# This is a simple SGE batch script
#
# request Bash shell as shell for job
#$ -S /bin/bash
#$ -N nodename #[This is just the name shown by "qstat"]
#
#$ -q short
#$ -M email@oist.jp
#$ -m abe
#$ -j yes
#$ -cwd # The outfile will be saved in the current directory.
#
date
sleep 2
sleep 2
date

#$ -S /bin/bash
#$ -N DynamicTrim
#
#$ -q long
#$ -M EMAIL@oist.jp
#$ -m abe
#$ -j yes
#$ -cwd
#$ -l h_vmem=1g # Maximum memory to be expected
#$ -l virtual_free=256m # Avairable mamory before start job.
#
perl ~/bin/DynamicTrim.pl ../../Ostbic1-Eye_S2_L001_R1_001.fastq -h 20

#$ -S /bin/bash
#$ -N Trinity
#
#$ -q genomics
#$ -M EMAIL@oist.jp
#$ -m abe
#$ -j yes
#$ -cwd
#$ -pe openmpi 4
#$ -l h_vmem=100g # Maximum memory to be expected
#$ -l virtual_free=10g # Avairable mamory before start job.
#
perl /home/j/jun-inoue/bin/trinityrnaseq_r2013-02-25/Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --no_cleanup --monitoring

Newbler is a multithreaded program (not MPI). So we need to set,

#$ -pe smp 2
...
runAssembly ... -cpu ${NSLOTS} ....

#$ -S /bin/bash
#$ -q genomics
#$ -N NB3in1
#$ -M jun.inoue@oist.jp
#$ -m e
#$ -cwd
#$ -pe smp 2
#$ -l h_vmem=40G

runAssembly -cdna -cpu 2 -het -siod -qo -m OstBic1a.fastq OstBic2a.fastq

#$ -S /bin/bash
#$ -q longP
#$ -N NewbTEST
#$ -M xx.xxx@oist.jp
#$ -m e
#$ -cwd
#$ -pe smp 12
#$ -l h_vmem=40G

#########
#### initiate assembly project
newAssembly -cdna testAssembl
#### sequence input
addRun -p -lib shortPE testAssembl \*.fq
#### assembly
runProject -cpu 12 -het -siod -qo -m testAssembl
### -siod for using efficient memory
## -large for large genome over 100Mb
## -het for diploid genome

If you run RAxML with -T 8 option, set "#$ -pe smp 8". Or run using raxmlHPC (single), set "#$ -pe smp 1".
"-pe smp 4" is better for RAxML pthreads analysis.
raxmlSgeTest.tar.gz is my perl script to make sge batch for RAxML analysis.

#$ -S /bin/bash
#$ -N JOBID
#
#$ -q shortp # Use long if the seq file is large.
#$ -M xxxx@oist.jp
#$ -m abe
#$ -j yes
#$ -cwd
# #$ -o ./"outputFile directory name"
# #$ -e ./"errorFile directory name"
#$ -pe smp 4
#$ -l h_vmem=256m # Maximum memory to be expected. Use 1g if the seq file is large.
#$ -l virtual_free=256m # Avairable mamory before start job.
#
raxmlHPC-PTHREADS-SSE3 -f a -x 12345 -p 12345 -# 20 -m GTRGAMMA -s SEQUENCEFILE -q PARTITIONFILE -o OUTGROUP -n OUTFILE -T 4

The pthreads option in RAxML uses 4 slots (CPU) in a single node and assign 256 mega memory for each node.

Set "#$ -t 1-100" and "#$ -tc 10". Change values (100, 10, etc) depending on the number of your jobs .
For array job, see GridWiki or Parallel jobs in Tombo (password is required).
raxmlArrayPerl.tar.gz is my perl script to make a job file.

#$ -S /bin/bash
#$ -t 1-100
#$ -tc 10 # Less than 50 is good for the machine.
#$ -N JOBID
#$ -q shortp # Use long if the seq file is large.
#$ -M xxxx@oist.jp
#$ -m abe
#$ -j yes
#$ -cwd
# #$ -o ./"outputFile directory name"
# #$ -e ./"errorFile directory name"
#$ -pe smp 4
#$ -l h_vmem=256m #$ -l virtual_free=256m #
#[add lines as below or write loop script]
./raxmlHPC-PTHREADS-SSE3 -f a -x 12345 -p 12345 -# 10 -m GTRGAMMA -s 010_sequenceFileDir/ENSP00000400626.txt -q 0 10_partitionFileDir/ENSP00000400626.txt -o Chicken_ENSGALP00000015683_NONE -n ENSP00000400626.txt -T 2
./raxmlHPC-PTHREADS-SSE3 -f a -x 12345 -p 12345 -# 10 -m GTRGAMMA -s 010_sequenceFileDir/ENSP00000231668.txt -q 0 10_partitionFileDir/ENSP00000231668.txt -o Drosophila_FBpp0078315_CG2023 -n ENSP00000231668.txt -T 2
./raxmlHPC-PTHREADS-SSE3 -f a -x 12345 -p 12345 -# 10 -m GTRGAMMA -s 010_sequenceFileDir/ENSP00000308315.txt -q 0 10_partitionFileDir/ENSP00000308315.txt -o SeaSquirt_ENSCINP00000030254_NONE -n ENSP00000308315.txt -T 2

Before qsub script, please check your program is written as multi-thread or MPI.
Tombo Users Guide is here
(Documentation > Tutorials > Running parallel jobs on the Tombo cluster).

MPI
The option is:

#$ -pe openmpi 4

mpirun -np 8 mrbayes myfile.nxs

Multi-thread
The option is:

#$ -pe smp 4

queue availability for smp
If you want to know a queue (e.g., short) accepts smp run, try "qconf -sq short" and see the line of pe_list.

[jun-inoue:~]$ qconf -sq short
qname short
....
pe_list openmpi openmp matlab smp

qsub test.sh

Run the job.

qsub -cwd test.sh

The outfiles will be saved in the directory including job script.

The job status will be shown.

qdel 1152367

Quit your job using ID.

qdel -u USERID

Quit your job using USERID.

hostname

Make sure your login node.

qstat -j [jobid]

Make sure [jobid] job status.

qstat -u [username]

Make sure [username] job status.

#$ -q longP

Declaring one week job. shortP declares one day job.

ls | wc -l

Counting the number of files.

ls -l | grep ^d | wc -l

Counting the number of directories.

du -h -s

Checking the disk usage of each user. It takes so long time.

$ df -h

Showing the total usage (not each user) as follows:

Filesystem Size Usage Rest Use% MountPlace
/dev/mapper/vg_system-slash
16G 6.9G 7.7G 48% /
...
ddnsfa10ke-4:/genefs 599T 461T 138T 78% /genefs
tombo-mds1@tcp:tombo-mds2@tcp:/work
393T 222T 167T 58% /work
...