MPI
MrBayes MPI
1.
lamboot -v lamhosts
2.
nohup mpirun -np 8 pmb ActinoPhilic.nex > ActinoPhilic.log &
mpirun -np 8 pmb.050908.grove.unix cyn.96.nex > log.file &
[mpirun -np 8 -ssi rpi usysv pmb datafile.nex > datafile.log &]
3.
lamhalt -v lamhosts
[hamhosts の job を kill]
wipe -v lamhosts
PAUP portable version
paup>lset ?
lamboot -v lamhosts
ps -aux |grep inoue
[job をみる]
鍵の作成
ディレクトリがない場合は，.ssh ディレクトリを作成する．
mkdir .ssh
自分だけが読み書きできるようにパーミションを変更する
chmod 700 .ssh
秘密鍵を作成します．
ssh-keygen -t dsa
.ssh ディレクトリに入って，
cat id_dsa.pub
して，作成したキー (全文) をコピーします．
(id_dsa.pub あるいは id_rsa.pub ファイルの内容をコピーするだけかも知れない)
ホストのホームディレクトリに ssh で入って，.ssh ディレクトリにある
authorized_keys2
にキーをペーストして加えます．
こちらのサイトを参考にしました．
.ssh にある known host ファイルに hpc を認識するキーがある．これを削除することで，new version の hpc system に入ることができる．
#!/bin/bash -l
#PBS -N NAME
#PBS -j oe
#PBS -l walltime=00:04:59
#PBS -l pmem=2048M
#PBS -l pvmem=8GB
#PBS -A ucl/BioinfCompBio/mol_evol
export OMP_NUM_THREADS=1
cd ~/Prank_analysis_23Oct
prank -d=ENSG00000000003 -fixedbranches=0.1 -t=Tree_ENSG00000000003 -o=Out_ENSG00000000003 -nopost -noxml -notree
cp Out_ENSG00000000003 MYRESULTS/Out_ENSG00000000003
* About walltime
http://www.ucl.ac.uk/research-computing/information/resource_allocation
* Add the job to the Legion
qsub MYSCRIPT
* Shell script
#!/bin/sh
cd myscripts
qsub script1; sleep 0.1;
qsub script2; sleep 0.1;
....
Login to node for running
slogin -X usertest11
QSTAT*
qstat | tr -s " " | awk 'BEGIN {count1=0; count2=0; count3=0; count4=0;}{count1++} $3 == "ucbtiju" {Found = 1;} NR > 2 && Found != 1 {count2++}$3 == "ucbtiju" {count3++} $3 == "ucbtiju" && $4 == "0" {count4++} END{print "\n No. of jobs in queue in total: " count1"\n No. above your 1st job in queue: " count2"\n No. of your jobs in queue: " count3"\n No. of your jobs running: " count3-count4 "\n ";}'date
Useful commands
Check the number of files
ls -laR | grep -c '^-'
qstat
To list *every* job in the queue
qstat
To list all of ucbtiju's jobs
qstat | grep ucbtiju
To do either of these with one page at a time which is more useful:
qstat | less
qstat | grep ucbtiju | less
You can check individual jobs using e.g.
checkjob 12467864.qm01
or for a more detailed description:
checkjob -v 12467864.qm01
This will tell you how long you are queueing and why the job hasn't
started yet etc...
Kill job
If you want to kill a job in the queue:
qdel 1052353432.qm01
...you get the number 1052353432.qm01 from looking at qstat.
There are other variations, e.g. 'addding | wc -l'counts the number of
lines, so these two tell you how many jobs in the queue, and how many you
have in the queue:
qstat | wc -l
qstat | grep ucbpwaf | wc -l