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--- howto:amber [2015/06/19 10:21]
ischeepers
+++ howto:amber [2024/10/09 12:42] (current)
alopis
@@ Line 1: / Line 1: @@
-===== Amber job on GPU nodes =====
+===== Amber jobs on non-GPU nodes =====
-<code>
+When running jobs for either AMBER14, AMBER18 or AMBER20 use the easy setup and submission scripts provided on the login node.
-#!/bin/sh
-#PBS -N eric.job
-#PBS -l select=1:ncpus=12:mpiprocs=12
-#PBS -l walltime=1:00:00
-#PBS -q kepla_k20
-#PBS -m be
-#PBS -o /export/home/username/amber/amber12/eric.out
-#PBS -e /export/home/username/amber/amber12/eric.err
-#PBS -M email@mail.com
-cd $PBS_O_WORKDIR
+**Note**, please first include this **module load** - even better if your add this line to your .bashrc, then the Easy Scripts should be visible and available:
-pwd
+  module load chpc/easy_scripts
-echo "My job starts here"
-date
-source /etc/profile.d/modules.sh
-module add intel-XE/c8000 cuda/5.0-c8000 mvapich2/c8000 amber/k20
-module add amber/k20
-exe=pmemd.cuda.MPI
-nproc=`cat $PBS_NODEFILE|wc -l`
-time mpirun -np $nproc -machinefile $exe -O -i mdin -o mdout -p prmtop -c inpcrd
-echo "My job ends here"
-date
-</code>
+Just execute **qamber_14** or **qamber_18** or **qamber_20**.
+Examples of what the scripts look like are provided below.
-===== Amber job on non-GPU nodes =====
+           EXAMPLE1
+  Enter project name/shortname
+  CHEM0100
+  Enter input file (with .in extension)
+  test.in
+  Enter parameter and topology file
+  prmtop
+  Enter coordinate file
+  inpcrd
+  What do you wish to run SANDER, PMEMD or MDGX
+  SANDER
+  Enter number of nodes on which to run job
+
+  Enter total walltime (hour:minute)
+:00
+  Enter email address
+  testing@gmail.com
+  Generated pbs file for test
+  Do you wish to submit job to cluster (y/n)
+  y
-<code>
+        EXAMPLE2 (TAKE NOTE OF THE EMPTY SPACES)
-#!/bin/sh
+  Enter project name/shortname
-#PBS -N eric.job
+  CHEM0100
-#PBS -l select=1:ncpus=12:mpiprocs=12
+  Enter input file (with .in extension)
-#PBS -l walltime=1:00:00
+  test.in
-#PBS -q workq
+  Enter parameter and topology file
-#PBS -m abe
-#PBS -o /export/home/username/amber/amber12/eric.out
+  Enter coordinate file
-#PBS -e /export/home/username/amber/amber12/eric.err
-#PBS -M email@mail.com
+  What do you wish to run SANDER, PMEMD or MDGX
+  Enter number of nodes on which to run job
+  Enter total walltime (hour:minute)
+  Enter email address
+  testing@gmail.com
+  Generated pbs file for test
+  Do you wish to submit job to cluster (y/n)
+  y
+====== AMBER18 and AMBER20 on GPU ======
-cd $PBS_O_WORKDIR
+** //Please note that you need to first be added to the gpu_1 queue before you can submit jobs to the GPU cluster// **
-pwd
+Execute **qamber_18_gpu** on login node and follow the prompts.
+Examples of script execution are provided below.
-source /etc/profile.d/modules.sh
+                    EXAMPLE1
-module add intel-XE/13.0 openmpi/openmpi-1.6.5-intel amber/12
+  Enter research programme name
+  CHEM01
+  Enter input file (with .in extension)
+  test.in
+  Enter parameter and topology file
+  prmtop
+  Enter coordinate file
+  inpcrd
+  Enter total walltime (hour:minute)
+:00
+  Enter email address
+  testing@gmail.com
+  Generated pbs file for test
+  Do you wish to submit job to cluster (y/n)
+  y
-echo "My job starts here"
-date
-exe=sander.MPI
+    EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES]
+  Enter research programme name
-nproc=`cat $PBS_NODEFILE|wc -l`
+  CHEM01
-time mpirun -np $nproc -machinefile $exe -O -i mdin -o mdout -p prmtop -c inpcrd
+  Enter input file (with .in extension)
-echo "My job ends here"
+  test.in
-date
+  Enter parameter and topology file
-</code>
+  Enter coordinate file
+  Enter total walltime (hour:minute)
+  Enter email address
+  testing@gmail.com
+  Generated pbs file for test
+  Do you wish to submit job to cluster (y/n)
+  y

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