Difference between revisions of "CD task8 protocol"
From Bioinformatikpedia
(→Preparation) |
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export PATH=$PATH:$HOME/AGroS/ |
export PATH=$PATH:$HOME/AGroS/ |
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| − | *Job script |
+ | *Job script: job.sh |
| + | #!/bin/bash |
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| − | --- |
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| + | #SBATCH -o /home/hpc/pr58ni/di34fog/jobs/wt/wt_md.out |
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| + | #SBATCH -D /home/hpc/pr58ni/di34fog/jobs/wt |
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| + | #SBATCH -J wt_MD |
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| + | #SBATCH --partition=mpp1_inter |
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| + | #SBATCH --get-user-env |
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| + | #SBATCH --ntasks=32 |
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| + | #SBATCH --mail-type=end |
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| + | #SBATCH --mail-user=susann.vorberg@cmapus.lmu.de |
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| + | #SBATCH --export=NONE |
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| + | #SBATCH --time=02:00:00 |
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| + | source /etc/profile.d/modules.sh |
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| + | module load gromacs |
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| + | export PATH="$HOME/AGroS:$PATH" |
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| + | export PATH="$HOME/apps/bin/:$PATH" |
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| + | export PATH="$HOME/software/scwrl/:$PATH" |
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| + | AGroS 2O4H_chainA.pdb -dir /home/hpc/pr58ni/di34fog/jobs/wt -threads 32 |
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| + | |||
| − | *Start jobs on: |
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| + | *Log in to: |
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| − | ssh -X lxia4-1 |
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| + | ssh -X di34fog@lxia4-1 |
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| + | batch job.sh |
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Revision as of 14:40, 27 June 2012
Preparation
- Load LRZ tools:
module load lrztools
- Load git
module load git
- clone git repository:
git clone git://github.com/offmarc/AGroS.git
- SetPath
export PATH=$PATH:$HOME/AGroS/
- Job script: job.sh
#!/bin/bash #SBATCH -o /home/hpc/pr58ni/di34fog/jobs/wt/wt_md.out #SBATCH -D /home/hpc/pr58ni/di34fog/jobs/wt #SBATCH -J wt_MD #SBATCH --partition=mpp1_inter #SBATCH --get-user-env #SBATCH --ntasks=32 #SBATCH --mail-type=end #SBATCH --mail-user=susann.vorberg@cmapus.lmu.de #SBATCH --export=NONE #SBATCH --time=02:00:00 source /etc/profile.d/modules.sh module load gromacs export PATH="$HOME/AGroS:$PATH" export PATH="$HOME/apps/bin/:$PATH" export PATH="$HOME/software/scwrl/:$PATH" AGroS 2O4H_chainA.pdb -dir /home/hpc/pr58ni/di34fog/jobs/wt -threads 32
- Log in to:
ssh -X di34fog@lxia4-1 batch job.sh
