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NOTE: Amber18 is optimally run on the exx96 queue, or on the helmholtz/gibbs machines.

Submitting Jobs

Short jobs (taking less than 10 minutes to run) can be run on the cottontail head node. This includes many of our python scripts. No header is needed.

 
   sh jobname.sh

To submit a job that will take longer than this to the scheduler, a header is required (see below). Energy minimization and cpptraj will need the CPU header. Heating, equilibration, piggybacking, and dynamics will need the GPU header. To submit to the queuing system, enter into the terminal:

   bsub < jobname.sh

It is acceptable to submit several jobs as a batch, but it is good practice to wait 1-2 minutes between submissions. For sequentially named jobs, this can be done with a loop:

 
   for i in {1..5}
   do
   bsub < job_$i.sh
   sleep 60
   done

exx96 CPU Header

#!/bin/bash
#BSUB -e err
#BSUB -o out
#BSUB -q exx96
#BSUB -J "jobname_CPU"
#BSUB -n 1

# env
export PATH=/home/apps/CENTOS7/amber/amber18/bin:$PATH
export LD_LIBRARY_PATH=/home/apps/CENTOS7/amber/amber18/lib:/home/apps/CENTOS7/amber/amber18/lib64:$LD_LIBRARY_PATH
export PATH=/share/apps/openmpi/1.4.4+intel-12/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/openmpi/1.4.4+intel-12/lib:$LD_LIBRARY_PATH

# cd to working directory
cd /mindstore/home33ext/kscopino/mR146/5JUP/COD1_A2/EMIN

# call Amber18
sander.MPI -O -i inputs.in -p prmtop_wat.prmtop -c coordinates_in.rst -r coordinates_out.rst -ref restraint_reference.rst -o energy_info.out

exx96 GPU Header

#!/bin/bash
#BSUB -e err
#BSUB -o out
#BSUB -q exx96
#BSUB -J jobname_GPU
#BSUB -n 1
#BSUB -R "rusage[gpu4=1:mem=6288],span[hosts=1]"

# cuda
export CUDA_HOME=/usr/local/n37-cuda-9.2
export PATH=/usr/local/n37-cuda-9.2/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/n37-cuda-9.2/lib64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH="/usr/local/n37-cuda-9.2/lib:${LD_LIBRARY_PATH}"

# openmpi
export PATH=/share/apps/CENTOS6/openmpi/1.8.4/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/openmpi/1.8.4/lib:$LD_LIBRARY_PATH

# amber18
source /share/apps/CENTOS7/amber/amber18/amber.sh

# cd to working directory
cd /mindstore/home33ext/kscopino/mR146/5JUP/COD1_A2/EMIN

# call Amber18
sander.MPI -O -i inputs.in -p prmtop_wat.prmtop -c coordinates_in.rst -r coordinates_out.rst -ref restraint_reference.rst -o energy_info.out
n37.openmpi.wrapper pmemd.cuda -O -i inputs.in  -p prmtop_wat.prmtop -c coordinates_in.rst -r coordinates_out.rst -ref restraint_reference.rst -o energy_info.out -x trajectory.mdcrd

Useful Troubleshooting Commands

# tells you the status of your jobs and which node they are running on
bjobs

# tells you all of the jobs on a given queue or for a given user
bjobs -u all | grep queuename_or_username

# tells you the status of all queues, useful for finding open queues
bqueues

# gives GPU identity (in the form of 00000000:3B:00.0) for each job on node 85, want 1 job per GPU
ssh n85 gpu-process

# gives information on % usage of each GPU (0 to 3) on node 85
ssh n85 gpu-info

# gives information on % usage of CPU for node 85
lsload n85

Suspending and Un-suspending Jobs

# note that JOBPID can be found with the bjobs command

# to pause a job
bstop JOBPID

# to continue a paused job
bresume JOBPID

Additional Resources
Download Amber18 Manual
Wesleyan's Amber wiki
Queue exx96 wiki