Displaying 4 results from an estimated 4 matches for "pbs_o_workdir".
2012 Mar 18
1
install R package on Unix cluster
Hi R users,
Working from a PC, I am trying to install the spatstat package on a Unix cluster. I created the following PBS file to send a job array:
#!/bin/bash -ue
#PBS -m ae
#PBS -M my email
#PBS -J 1-45
#PBS -A my username
#PBS -N job name
#PBS -l resources
#PBS -l walltime
cd $PBS_O_WORKDIR
module load R/2.14.1
R CMD INSTALL -l /path/to/library spatstat
R CMD BATCH /path/to/folder/Script_$PBS_ARRAY_INDEX.R
Obviosuly I failed to understand pag 19 of the R admin manual because I keep getting the following error message:
Warning: invalid package ‘spatstat’
Error: ERROR: no packages...
2010 Oct 11
1
running R script on linux server
...running my R code on a Linux cluster. What I did was
write a .pbs file to instruct the cluster on what to do and how:
#!/bin/sh
#PBS -m ae
#PBS -M uqlcatta@uq.edu.au
#PBS -A uq-CSER
#PBS -N job1_lollo
#PBS -l select=1:ncpus=1:NodeType=fast:mem=8GB
#PBS -l walltime=999:00:00
cd $PBS_O_WORKDIR
source /usr/share/modules/init/bash
module load R/2.11.1
/home/uqlcatta/script/diag.sh
The .pbs file calls a .sh file, which is located on my home directory on
the cluster, and which contains the R script (enclosed in " ") to run
#!/bin/bash
echo " mat <- m...
2007 Jul 30
1
random number generator in batch jobs
...quot;
"
#!/bin/bash
export var
for var in $(seq 1 5)
do
qsub -v var do_test
done
exit 0
"
Through "do_mul", 5 "do_test" script files are submitted to the cluster.
The script file "do_test":
"
#!/bin/bash -l
#PBS -l ncpus=1
#PBS -l walltime=0:05:00
cd $PBS_O_WORKDIR
mkdir test$var
cd test$var
module load R/2.5.0
R --vanilla< test
exit 0
"
The content in R file "test" is :
"rm(list=ls(all=TRUE))
sample(10)
"
I expect to have different samples each time. However, for these 5
replications, the first 3 jobs giving me the same samples...
2013 Jul 20
7
Failure to Launch (was override -q option)
Attached is the very verbose ssh output. Just to be perverse, this time two
nodes lost connectivity. The only thing I see is lines saying that the two
connections are lost, although being honest I have no idea what everything
else means. For reference, 8 ssh cinnections were being made at the same
time for a 8x8mpi task.
N.B., since the OS I am using does not have rsh, I am currently using the