I am trying to run let's say 10 different codes each saved in it's respective directory named as 1,2,3,..,10.
#PBS -l nodes=10:cores=1
This means I had 1 thread each on 10 different CPU's. Now I had to submit a job so that each directory get's 1 thread of 1 CPU only, and similarly other directories 2,3..,10.
Codes are for molecular dynamics and runs for several hours, and they are independent as well. I tried by Gnu Parallel but I failed to employ each 10 CPU's. May be Gnu Parallel is made to distribute jobs in between 1 CPU cores. I know MPI can, but I don't know exactly how. May anyone please suggest.
I do not have access to a PBS cluster, but Example 2 from
https://www.nas.nasa.gov/hecc/support/kb/using-gnu-parallel-to-package-multiple-jobs-in-a-single-pbs-job_303.html might be what you are looking for:
#PBS -lselect=6:ncpus=4:model=san
#PBS -lwalltime=4:00:00
cd $PBS_O_WORKDIR
seq 64 | parallel -j 4 -u --sshloginfile $PBS_NODEFILE \
"cd $PWD; ./myscript.csh {}"
Adapted to your situation (untested):
#PBS -l place=scatter
#PBS -l nodes=10:cores=1
cd $PBS_O_WORKDIR
seq 10 | parallel -j 1 --sshloginfile $PBS_NODEFILE --wd $PBS_O_WORKDIR ./myscript {}
You need place=scatter because otherwise the same host may be listed twice in $PBS_NODEFILE, and GNU Parallel ignores duplicates.
Related
Here's the job script I use,
#!/bin/bash
#PBS -q batch
#PBS -N simulation
#PBS -j n
#PBS -o /dev/null
#PBS -l nodes=1:ppn=1,pmem=3400mb
#PBS -l ncpus=1,mem=3400mb
cd ${PBS_O_WORKDIR} && \
./executable
I get this error:
Operating system error: Cannot allocate memory
Allocation would exceed memory limit
I've tried increasing the ppn and ncpus and mem such that it matches requirement of my program (~6GB). Doesn't help either.
This doesn't happen when I run the command in terminal. It works just fine.
Try run the program with all memory in the system allocated to the job.
Then at the very end execute qstat -f $PBS_JOBID| grep resources to see what Torque thinks about used resources.
resources_used.cput = 00:00:00
resources_used.energy_used = 0
resources_used.mem = 94724kb
resources_used.vmem = 1564024kb
resources_used.walltime = 00:03:25
In regard to create a PBS script file to run long-term jobs on a server with 256 GB of RAM and two CPUs, each with 12 cores and 24 threads, yielding 48 computing unit. I tried to do it, but I think there is something wrong.
I created a PBS script named run_trinity and submitted it to server using qsub command (qsub run_trinity.sh) within the same directory that contain my desired program (trinity) and data, and it returned something like 47.chpc. But when I tried to check the status of job using qstat command, it says: unknown job id 47.chpc. I'm a biology student and really new in this field, could you please help me to figure out what happened? here is my PBS script:
#!/bin/bash
#PBS -N run_trinity
#PBS -l nodes=1:ppn=6
#PBS -l walltime=100:00:00
#PBS -l mem=200gb
#PBS -j oe
#Set stack size to unlimited
ulimit -s unlimited
cd /home/mary/software/trinityrnaseq_r20140717
perl /home/mary/software/trinityrnaseq_r20140717/Trinity.pl --seqType fq --JM 200G --normalize_reads --left reads8_1.fq.gz --right reads8_2.fq.gz --SS_lib_type FR --CPU 6 --full_cleanup --output /home/mary/software/trinityrnaseq_r20140717
Looking forward to hearing your perfect solutions.
So I'm running these following pbs files at the same time:
qsub /mnt/folder/prueba1_1
qsub /mnt/folder/prueba01
An here are the files
prueba1_1
#!/bin/bash
#PBS -N pruebaF
#PBS -V
#PBS -l nodes=1:ppn=1
#PBS -q batch
#PBS -j eo
cd /mnt/folder
mpiexec -f machinefile ./cpi2>>salida1_1.o
prueba01
#!/bin/bash
#PBS -N pruebaF
#PBS -V
#PBS -l nodes=1:ppn=1
#PBS -q batch
#PBS -j eo
cd /mnt/folder
mpiexec -f machinefile ./cpi2>>salida01.o
The file machinefile contains 2 nodes slave02 and slave03 each one with 1 processor
Although I specify that each pbs file should use just 1 node and 1 processor per job (with #PBS -l nodes=1:ppn=1) the output files seems to show that each job is using both nodes at the same time. I'm wondering why since these pbsfiles should use just one node and 1 processor, for me It should be that prueba1_1 should use slave02 with 1 processor and prueba01 should use slave02 as well but with the other processor.
the output files are here
salida1_1.o
Process 0 of 2 is on slave02
Process 1 of 2 is on slave03
pi is approximately 3.1415926535900915, Error is 0.0000000000002984
wall clock time = 14.937282
salida01.o
Process 0 of 2 is on slave02
Process 1 of 2 is on slave03
pi is approximately 3.1415926535900915, Error is 0.0000000000002984
wall clock time = 14.741892
I would change machinefile to $PBS_NODEFILE. When Torque/PBS assigns nodes to your job it creates a file containing a list of those nodes and it sets the path to that file in the variable PBS_NODEFILE. I'm guessing machinefile was created for testing and since it is not created or updated by Torque that is why your jobs are always running the same way.
I`m running a code on a computer cluster with 24 nodes, 12 processors each one and something about 64Gb memory each node. The commands I'm using to launch it are the following
#!/bin/sh
#PBS -N cclit
#PBS -l walltime=288:00:00
#PBS -l nodes=1:ppn=1
#PBS -j oe
#PBS -m n
#PBS -l mem=60000mb
Unfortunately I realized that my code need at least a virtual memory which is 120000mb. What I tried to do has been to modify the above commands as
#!/bin/sh
#PBS -N cclit
#PBS -l walltime=288:00:00
#PBS -l nodes=2:ppn=2
#PBS -j oe
#PBS -m n
#PBS -l mem=120000mb
But it doesn't seem to work... It stops again at the same point telling me that virtual memory is not sufficient.
My code is not parallelized, meaning that only 1 processor is needed. What happens when the memory of a node is totally used?? I guess Im doing something wrong with '#PBS -l mem=120000mb', or probably I need some other command... I tried to look for a solution on the web but I didn t find anything..
Can you help me?
Thanks Mirko.
Anyone have any idea which Resource manager is good for PVM? Or should I not have used PVM and instead relied on MPI (or any version of it, such as MPICH-2 [are there any other ones that are better?]). Main reason for using PVM was because the person before me who started this project assumed the use of PVM. However, now that this project is mine (he hasn't done any significant work that relies on PVM) this can be easily changed, preferably to something that is easy to install because installing and setting up PVM was a big hassle.
I'm leaning towards SunGridEngine seeing as how I have dedicated hardware, and after reading up on another post of which ones are better for dedicated hardware, SGE seems to be the winner. However I'm unsure of its performance using PVM. Wondering if anyone have had any experience with PVM and SGE?
If people use SGE, what do you use to communicate from computer to computer (or virtual machine to virtual machine)
Oh and I will be running Perl applications/lines if this matters.
Any suggestions or ideas?
Thanks in advance to all comments,
Tyug
I run PVM on Linux systems using Torque, SGE and LSF without any problems. Are you asking "Is it possible to use SGE, Torque, etc. to run PVM applications?"?
If so, check out my example Linux c-shell job scripts below. Note the scripts are nearly identical, except for the header of each script, which conforms to the appropriate format for each resource manager.
SGE job script:
#!/bin/csh
#$ -N LTR-001
#$ -o LTR-001.output
#$ -e LTR-001.error
#$ -pe comp 24
#$ -l h_rt=04:00:00
#$ -A cmit2
#$ -cwd
#$ -V
# Setup envirnoment
setenv LD_LIBRARY_PATH /lfs0/projects/cmit2/opt-intel/overture-noX/lib:${LD_LIBRARY_PATH}
setenv PVM_ARCH LINUX
setenv PVM_ROOT /lfs0/projects/cmit2/opt-intel/pvm3
setenv PVM_BIN ${PVM_ROOT}/bin
setenv PVM_RSH /usr/bin/ssh
setenv MY_HOSTS pvm_hostfile
rm -f ~/.pvmprofile
env | grep PVM_ > ~/.pvmprofile
# Create file containing _unique_ host names. Note that there are two possible sources of available hosts
sort -k 1,1 -u ${MACHINE_FILE} >! ${MY_HOSTS}
# Start PVM & add nodes
printf "%s\n%s\n" conf quit|${PVM_ROOT}/lib/pvm ${MY_HOSTS}
wait
sleep 2
#
# Run apps requiring PVM.
#
wait
# Exit PVM daemon
echo "reset" | $PVM_ROOT/lib/pvm
echo "halt" | $PVM_ROOT/lib/pvm
Torque job script:
#!/bin/csh
#PBS -N LTR-001
#PBS -o LTR-001.output
#PBS -e LTR-001.error
#PBS -l nodes=3:ppn=8
#PBS -l walltime=04:00:00
#PBS -q compute
#PBS -d .
# Setup envirnoment
setenv LD_LIBRARY_PATH /users/ps14/opt-intel/overture/lib:${LD_LIBRARY_PATH}
setenv PVM_ARCH LINUX64
setenv PVM_ROOT /users/ps14/opt-intel/pvm3
setenv PVM_BIN ${PVM_ROOT}/bin
setenv PVM_RSH ${PVM_ROOT}/ssh
setenv MY_HOSTS pvm_hostfile
rm -f ~/.pvmprofile
env | grep PVM_ > ~/.pvmprofile
# Create file containing _unique_ host names. Note that there are two possible sources of available hosts
sort -k 1,1 -u ${PBS_NODEFILE} >! ${MY_HOSTS}
# Start PVM & add nodes
printf "%s\n%s\n" conf quit|${PVM_ROOT}/lib/pvm ${MY_HOSTS}
wait
sleep 2
#
# Run apps requiring PVM.
#
wait
# Exit PVM daemon
echo "reset" | $PVM_ROOT/lib/pvm
echo "halt" | $PVM_ROOT/lib/pvm