==Submit MD++ to a cluster==

Besides running MD++ on your own computers, we can also submit MD++ jobs to clusters. Here take cluster mc2 as an example. Make a sub-directory '''Codes''' in the home directory, and extract the downloaded MD++ files there.

$ mkdir Codes
$ cd Codes
$ tar -zxvf md++-2015-01-14.tar.gz

Then we compile the potential energy we need, for example, 'ljbond', for Python files

$ cd MD++
$ make ljbond build=R SYS=mc2 PY=yes

Now we want to submit a job 'scripts/ex_polymer/polymer_expansion.py' with the potential energy 'ljbond_mc2' to the mc2 cluster. We need to prepare the following pbs script.

#!/bin/bash
#PBS -N polymer_equil
#PBS -j oe
#PBS -l nodes=1:ppn=24, walltime=96:00:00
#PBS -V
### ---------------------------------------
### BEGINNING OF EXECUTION
### ---------------------------------------
echo The master node of this job is `hostname`
echo The working directory is `echo $PBS_O_WORKDIR`
echo This job runs on the following nodes:
echo `cat $PBS_NODEFILE`
ncpu=`cat $PBS_NODEFILE | wc -w`
echo "Number of processors = $ncpu "
### end of information preamble
cd $PBS_O_WORKDIR
echo $PWD
sleep 2
bin/ljbond_mc2 scripts/ex_polymer/polymer_expansion.py

PBS is a job resource manager, and it gives queuing and execution services in a batch cluster environment. In a pbs script, '''#PBS -N polymer_equil''' specifies the name of the job. '''#PBS -j oe''' tells PBS to put both normal output and error output into the same output file. ''' #PBS -l nodes=1:ppn=24, walltime=96:00:00''' requests 1 node, 24 processes for 96 hours running time.

'''cd $PBS_O_WORKDIR''' asks to open the work directory. '''bin/ljbond_mc2 scripts/ex_polymer/polymer_expansion.py''' is the command to run the job.

When we use one process of a node, the whole node is occupied. Therefore, if we have more than one job, we can put them in the same pbs script. Moreover, We can add arguments to the MD++ scripts by adding the following lines at the beginning of the main code of the MD++ script

import sys

if len(sys.argv) == 1 :
status = 0
elif len(sys.argv) > 1 :
status = int(sys.argv[1])
print(status)

if len(sys.argv) <= 2 :
arg2 = 50
elif len(sys.argv) > 2 :
arg2 = int(sys.argv[2])
print(arg2)

if len(sys.argv) <= 3 :
arg3 = 80
elif len(sys.argv) > 3 :
arg3 = int(sys.argv[3])
print(arg3)

Then in one pbs script, we can ask to run several jobs

sleep 2
bin/ljbond_mc2 scripts/ex_polymer/polymer_expansion.py 0 40 50 &
sleep 2
bin/ljbond_mc2 scripts/ex_polymer/polymer_expansion.py 0 50 50 &
sleep 2
bin/ljbond_mc2 scripts/ex_polymer/polymer_expansion.py 0 60 50 &
wait

At the end of each command, '''&''' asks to continue to run the other commands. '''Wait''' asks to keep occupying the nodes and processes.

Saving the pbs file as 'scripts/ex_polymer/md++.pbs', we can submit the job by
qsub scripts/ex_polymer/md++.pbs
Since we run the job non-interactively, we need to comment out the interactive commands in the MD++ script, for example, openwindow(). Otherwise, the job will stop will errors.

We can check the status of the job by
qstat
If the state is '''Q''', the job is queued and waiting to start. If the state is '''R''', the job is running. We can delete the job by
qdel Job_ID
where Job_ID is the job's unique identifier and will be given when you submit the job.

More information about PBS can be found https://rcc.its.psu.edu/user_guides/system_utilities/pbs/.

==Stretch a polymer melt with MD++==

==Miscellany==
1. A.log files contain codes about font colors. If you open them as plane txt files, they cannot be well showed. Can open them using the command
$more A.log

2. Stress outputs, TSTRESS_xx and TSTRESSinMPa_xx et al, define the compressive ones as positive.

3. To run MD++ scripts written by Python or TCL languages, we need to compile different executable files for the same potential.
$ make ljbond build=R SYS=mc2
The default is for TCL language. For Python
$ make ljbond build=R SYS=mc2 PY=yes
After compile files for Python, you need to '''make clean''' before you compile files for TCL, and vice versa.

==Suggestions==

1. Add searching function in the manual website.
2. Add a comment to clear the variable input.

Submit MD++ Jobs to a Cluster

2015-03-18T01:10:51Z

Lihuajin: /* Submit MD++ to a cluster */

==Submit MD++ to a cluster==

Besides running MD++ on your own computers, we can also submit MD++ jobs to clusters. Here take cluster mc2 as an example. Make a sub-directory '''Codes''' in the home directory, and extract the downloaded MD++ files there.

$ mkdir Codes
$ cd Codes
$ tar -zxvf md++-2015-01-14.tar.gz

Then we compile the potential energy we need, for example, 'ljbond', for Python files

$ cd MD++
$ make ljbond build=R SYS=mc2 PY=yes

Now we want to submit a job 'scripts/ex_polymer/polymer_expansion.py' with the potential energy 'ljbond_mc2' to the mc2 cluster. We need to prepare the following pbs script.

#!/bin/bash
#PBS -N polymer_equil
#PBS -j oe
#PBS -l nodes=1:ppn=24, walltime=96:00:00
#PBS -V
### ---------------------------------------
### BEGINNING OF EXECUTION
### ---------------------------------------
echo The master node of this job is `hostname`
echo The working directory is `echo $PBS_O_WORKDIR`
echo This job runs on the following nodes:
echo `cat $PBS_NODEFILE`
ncpu=`cat $PBS_NODEFILE | wc -w`
echo "Number of processors = $ncpu "
### end of information preamble
cd $PBS_O_WORKDIR
echo $PWD
sleep 2
bin/ljbond_mc2 scripts/ex_polymer/polymer_expansion.py

PBS is a job resource manager, and it gives queuing and execution services in a batch cluster environment. In a pbs script, '''#PBS -N polymer_equil''' specifies the name of the job. '''#PBS -j oe''' tells PBS to put both normal output and error output into the same output file. ''' #PBS -l nodes=1:ppn=24, walltime=96:00:00''' requests 1 node, 24 processes for 96 hours running time.

'''cd $PBS_O_WORKDIR''' asks to open the work directory. '''bin/ljbond_mc2 scripts/ex_polymer/polymer_expansion.py''' is the command to run the job.

When we use one process of a node, the whole node is occupied. Therefore, if we have more than one job, we can put them in the same pbs script. Moreover, We can add arguments to the MD++ scripts by adding the following lines at the beginning of the main code of the MD++ script

import sys

if len(sys.argv) == 1 :
status = 0
elif len(sys.argv) > 1 :
status = int(sys.argv[1])
print(status)

if len(sys.argv) <= 2 :
arg2 = 50
elif len(sys.argv) > 2 :
arg2 = int(sys.argv[2])
print(arg2)

if len(sys.argv) <= 3 :
arg3 = 80
elif len(sys.argv) > 3 :
arg3 = int(sys.argv[3])
print(arg3)

Then in one pbs script, we can ask to run several jobs

sleep 2
bin/ljbond_mc2 scripts/ex_polymer/polymer_expansion.py 0 40 50 &
sleep 2
bin/ljbond_mc2 scripts/ex_polymer/polymer_expansion.py 0 50 50 &
sleep 2
bin/ljbond_mc2 scripts/ex_polymer/polymer_expansion.py 0 60 50 &
wait

At the end of each command, '''&''' asks to continue to run the other commands. '''Wait''' asks to keep occupying the nodes and processes.

Saving the pbs file as 'scripts/ex_polymer/md++.pbs', we can submit the job by
qsub scripts/ex_polymer/md++.pbs
Since we run the job non-interactively, we need to comment out the interactive commands in the MD++ script, for example, openwindow(). Otherwise, the job will stop will errors.

We can check the status of the job by
qstat
If the state is '''Q''', the job is queued and waiting to start. If the state is '''R''', the job is running. We can delete the job by
qdel Job_ID
where Job_ID is the job's unique identifier and will be given when you submit the job.

More information about PBS can be found https://rcc.its.psu.edu/user_guides/system_utilities/pbs/.

==Stretch a polymer melt with MD++==

==Suggestions==

1. Add searching function in the manual website.
2. Add a comment to clear the variable input.

Submit MD++ Jobs to a Cluster

2015-03-18T01:03:03Z

Lihuajin: /* Submit MD++ to a cluster */

Submit MD++ Jobs to a Cluster

2015-03-18T01:02:34Z

Lihuajin: /* Submit MD++ to a cluster */

Submit MD++ Jobs to a Cluster

2015-03-18T01:01:58Z

Lihuajin: /* Submit MD++ to a cluster */

2015-03-18T00:05:38Z

Lihuajin:

Submit MD++ Jobs to a Cluster

2015-03-18T00:05:08Z

Lihuajin: Created page with "==Submit MD++ to a cluster== Besides running MD++ on your own computers, we can also submit MD++ job to clusters. Here take cluster mc2 as an example. Make a sub-directory ''..."

MD++ Manuals

2015-03-12T17:44:45Z

Lihuajin: Add a new page "Submit MD++ Jobs to a Cluster"

<H4>Manuals</H4>
<UL>
<LI> [http://micro.stanford.edu/MDpp/docs/list MD++ Documentation]
<LI>[[M01 Introduction to MD++]]
<LI>[[M02 Making a Perfect Crystal]]
<LI>[[M03 Equilibrium Lattice Constant and Bulk Modulus]]
<LI>[[M04 Energy Minimization of Vacancy]]
<LI>[[M05 Finite Temperature Simulation]]
<LI>[[M06 Visualization ]]
<LI>[[M07 Computing Elastic Constants | M07 Computing Elastic Constants at ''T'' = 0]]
<LI>[[M08 MD++ Powered by Tcl Language]]
<LI>[[M09 Computing Ideal Strength]]
<LI>[[M10 DisregistryAnalysis | M10 Visualize Disregistry vector]]
<LI>[[M11 MD++ Powered by Python]]
<LI>[http://micro.stanford.edu/~caiwei/me346/ Molecular Simulations Lecture Notes]
<LI>[[Comprehensive Nuclear Materials MD Case Studies | Case Studies of Crystals and Dislocations]]
<LI>[[MD++ An Example Script File | An Example Script File]]
<LI>[[MD++ An Example Tcl File | An Example Tcl File]]
</UL>

<H4>Technical details</H4>
<UL>
<LI>[[ MD++ QnA | MD++ FAQs]]
<LI>[[MD Potential Files]]
<LI>[[Making Amimations Using a MD++ Script File | Making Movies in MD++]]
<LI>[[Output File Formats in MD++]]
<LI>[[Running MD++ on Mac OS]]
<LI>[[Submit MD++ Jobs to a Cluster]]
</UL>

<H4>Advanced topics</H4>
<UL>
<LI>[[media:ewald_notes.pdf | Notes on Ewald Summation]]
<LI>[[Computing Melting Point by Free Energy Method]]
<LI>[[M04A Conjugate Gradient Method in MD++ | Conjugate Gradient Methods in MD++]]
<LI>[[Computing Elastic Constants 2 | Computing Elastic Constants at Finite Temperature]]
<LI>[[M10 Angular momentum is conserved or not | Conservation of Angular Momentum]]
<LI>[[Use MEAM in MD++]]
<LI>[[media:Day1_Ising_Demo.pdf | Monte Carlo Simulation of 2D Ising Model]]
<LI>[[Phonon dispersion relation | Phonon Dispersion Relation of Graphene]]
</UL>