From 64c1991681346b019280579961ab83a735f61ac7 Mon Sep 17 00:00:00 2001 From: Jakub Kropacek <jakub.kropacek@vsb.cz> Date: Wed, 7 Sep 2022 08:51:42 +0200 Subject: [PATCH] update submission examples --- docs.it4i/general/capacity-computing.md | 12 +++++++----- docs.it4i/general/capacity.zip | Bin 19602 -> 19683 bytes .../general/job-submission-and-execution.md | 17 ++++++++++++----- 3 files changed, 19 insertions(+), 10 deletions(-) diff --git a/docs.it4i/general/capacity-computing.md b/docs.it4i/general/capacity-computing.md index a58b3722a..d279b286f 100644 --- a/docs.it4i/general/capacity-computing.md +++ b/docs.it4i/general/capacity-computing.md @@ -48,19 +48,21 @@ Then we create a jobscript: ```bash #!/bin/bash -#PBS -A PROJECT_ID +#PBS -A OPEN-00-00 #PBS -q qprod -#PBS -l select=1:ncpus=24,walltime=02:00:00 +#PBS -l select=1,walltime=02:00:00 # change to scratch directory -SCR=/scratch/work/user/$USER/$PBS_JOBID -mkdir -p $SCR ; cd $SCR || exit +SCRDIR=/scratch/project/${PBS_ACCOUNT,,}/${USER}/${PBS_JOBID} +mkdir -p $SCRDIR +cd $SCRDIR || exit # get individual tasks from tasklist with index from PBS JOB ARRAY TASK=$(sed -n "${PBS_ARRAY_INDEX}p" $PBS_O_WORKDIR/tasklist) # copy input file and executable to scratch -cp $PBS_O_WORKDIR/$TASK input ; cp $PBS_O_WORKDIR/myprog.x . +cp $PBS_O_WORKDIR/$TASK input +cp $PBS_O_WORKDIR/myprog.x . # execute the calculation ./myprog.x < input > output diff --git a/docs.it4i/general/capacity.zip b/docs.it4i/general/capacity.zip index 9ea4db6e7e6ec6c0b86bef89fbe69933957d9016..28d838bade2719b2b5a73f6ecee2f35f17eb10cb 100644 GIT binary patch literal 19683 zcmb8$30#fY|G@F9#TF`ii&RXJt-IeVTPg_=kw$3nBO&dQs4Qg-smV5D8B5m5(oBOw zi4-y<+ALXqDnmjcjNiT8^B?DY&GG*>^UBP;UNi64x#v00dCqfv#%-jwPD_FMkLkm# zCp7#G`K5)xR4`*&z_b~@A>sWdjBg>(o;bMk4E0awLOnqfoeFJ%py3y{e~1B&))U-L zdJk=(BGf-^X=0Y|yqRJ}U*Gu+mb+c&8R{Qk4WBu0p1-+R(UL`bcC^~ZMWtdCDis6t zxiIJy7Zr(6s7M4*yVNJCTvUNW6%aiWnCQqwWw<$&!8vuU9&m(<DsgkFgmb#IsD5;F 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z8N(Y&(Cs%6JqMPI;Ta|9dSfn2#_*C7baOG6C1ZF@3A%mt(Q{zQ7~WHYt{3LAWDHL# zK{p3;Su%!Km7v?l06hnmjNxG==&r=vf6cgk+J}!TK{g9yp{b=TWck$cZx<`=GCmpv zW$Qt}LHs4lCWJCsJ|X-E86Uraa?#+wm1R>nnJk~e{ez5;u0Z+XP(c3w1WSg>Cs-KT WMfR;w4rhhzpT)8Z(jG4V)&Brn%K7#H diff --git a/docs.it4i/general/job-submission-and-execution.md b/docs.it4i/general/job-submission-and-execution.md index de9ada0a8..071b794f9 100644 --- a/docs.it4i/general/job-submission-and-execution.md +++ b/docs.it4i/general/job-submission-and-execution.md @@ -346,9 +346,12 @@ The recommended way to run production jobs is to change to the `/scratch` direct ```bash #!/bin/bash -# change to scratch directory, exit on failure -SCRDIR=/scratch/$USER/myjob +cd $PBS_O_WORKDIR + +SCRDIR=/scratch/project/open-00-00/${USER}/myjob mkdir -p $SCRDIR + +# change to scratch directory, exit on failure cd $SCRDIR || exit # copy input file to scratch @@ -389,10 +392,12 @@ Example jobscript for an MPI job with preloaded inputs and executables, options #PBS -q qprod #PBS -N MYJOB #PBS -l select=100:mpiprocs=1:ompthreads=16 -#PBS -A OPEN-0-0 +#PBS -A OPEN-00-00 + +# job is run using project resources; here ${PBS_ACCOUNT,,} translates to "open-00-00" +SCRDIR=/scratch/project/${PBS_ACCOUNT,,}/${USER}/myjob # change to scratch directory, exit on failure -SCRDIR=/scratch/$USER/myjob cd $SCRDIR || exit # load the MPI module @@ -407,7 +412,9 @@ mpirun ./mympiprog.x exit ``` -In this example, input and executable files are assumed to be preloaded manually in the `/scratch/$USER/myjob` directory. Note the `mpiprocs` and `ompthreads` qsub options controlling the behavior of the MPI execution. `mympiprog.x` is executed as one process per node, on all 100 allocated nodes. If `mympiprog.x` implements OpenMP threads, it will run 16 threads per node. +In this example, input and executable files are assumed to be preloaded manually in the `/scratch/project/open-00-00/$USER/myjob` directory. Because we used the `qprod` queue, we had to specify which project's resources we want to use, and our `PBS_ACCOUNT` variable will be set accordingly (OPEN-00-00). `${PBS_ACCOUNT,,}` uses one of the bash's built-in functions to translate it into lower case. + +Note the `mpiprocs` and `ompthreads` qsub options controlling the behavior of the MPI execution. `mympiprog.x` is executed as one process per node, on all 100 allocated nodes. If `mympiprog.x` implements OpenMP threads, it will run 16 threads per node. ### Example Jobscript for Single Node Calculation -- GitLab