Tutorial Materials

Full list: http://www.ks.uiuc.edu/Training/Tutorials/

Recommended tutorials:

• QwikMD - best for those not comfortable preparing simulations for NAMD.
• NAMD Tutorial - extensive on the general use of NAMD, but one can skip sections.
• Tutorial on Adaptive Biasing Force Calculations - introductory tutorial on Adaptive Biasing Force Calculations in NAMD
• Stretching Deca-Alanine tutorial - introductory tutorial on Potential of Mean Force in NAMD
• Tutorial on Alchemical Free Energy Perturbation Calculations - introductory tutorial on Alchemical Free Energy Perturbation Calculations in NAMD
• Molecular Dynamics Flexible Fitting (MDFF) - introductory tutorial on MDFF in NAMD and VMD
• Self-guided scaling studies on Beskow - see directions below (compiling optional)

Recommended tutorial materials, from any PDC system:

/afs/pdc.kth.se/home/j/joao2/Public/

Commands for Running QwikMD Tutorial

VMD 1.9.4 should be pre-installed on the lab workstations for your use.

This tutorial runs completely on the lab workstation (or your laptop) and does not use Beskow or Tegner.

( cd /tmp; tar xzf /afs/pdc.kth.se/home/j/joao2/Public/qwikmd_tutorial/qwikmd-tutorial-files.tar.gz )

Running pre-compiled binaries on Beskow

The following commands submit simple batch jobs

~joao2/Public/NAMD_scripts/runbatch

(Notes: To prepare files for running on Beskow, Do not check out the "Live View" option in QwikMD)

This script requires three arguments:

• NAMD input file
• NAMD log file
• number of nodes (number of cores / 32)
• processes per node (1, 2, 4, 31, 32; defaults to 1, ignored for cuda)
• queue (defaults to "regular", other options are "test" and "low")
• replica or other args (optional)

Files need to be available on compute nodes, substitute your initial and username below.

ln -s /cfs/klemming/nobackup/y/youruser ~/work

cd ~/work

(The following are available at www.ks.uiuc.edu/Research/namd/utilities/)

tar xzf /afs/pdc.kth.se/home/j/joao2/Public/apoa1.tar.gz

The following commands will run NAMD in a variety of configurations on 4 nodes.

The "test" queue just sets the runtime to 30 minutes so the job might start earlier.

NAMD (Charm++) options in the generated batch job are:

• +ppn 31 31 worker threads per node
• +pemap 1-31 worker threads on cpus 1-31
• +commap 0 smp build communication thread on cpu 0

To understand the sbatch and aprun options in the submitted scripts see https://www.pdc.kth.se/resources/computers/beskow/how-to/run or "man aprun"

~joao2/Public/NAMD_scripts/runbatch apoa1/apoa1.namd apoa1_4_default.log 4 test

~joao2/Public/NAMD_scripts/runbatch apoa1/apoa1.namd apoa1_4_1.log 4 1 test

~joao2/Public/NAMD_scripts/runbatch apoa1/apoa1.namd apoa1_4_2.log 4 2 test

~joao2/Public/NAMD_scripts/runbatch apoa1/apoa1.namd apoa1_4_4.log 4 4 test

~joao2/Public/NAMD_scripts/runbatch apoa1/apoa1.namd apoa1_4_31.log 4 31 test

~joao2/Public/NAMD_scripts/runbatch apoa1/apoa1.namd apoa1_4_32.log 4 32 test

squeue -u $USER

When jobs have finished running, check performance with "grep time: *.log", the "Benchmark time:" lines are after load balancing and should represent the performance of a long run.

Compiling Charm++ and NAMD on Beskow

Libraries available from www.ks.uiuc.edu/Research/namd/libraries/

(Patch for Cray is www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-crayxe-tclUnixInit.patch)

cd

tar xzf /afs/pdc.kth.se/home/j/joao2/Public/tcl8.5.9-crayxe-threaded.tar.gz

tar xzf /afs/pdc.kth.se/home/j/joao2/Public/tcl8.5.9-crayxe.tar.gz

ln -s tcl8.5.9-crayxe-threaded tcl-threaded

ln -s tcl8.5.9-crayxe tcl

module swap PrgEnv-cray PrgEnv-intel

module load fftw

module load rca

module load craype-hugepages8M

module load intel/17.0.5.239

module load gcc/6.1.0

module list

Files need to be available on compute nodes, substitute your initial and username below.

ln -s /cfs/klemming/nobackup/y/youruser ~/work

cd ~/work

(Normally you would download NAMD source from www.ks.uiuc.edu/Research/namd/)

tar xzf /afs/pdc.kth.se/home/j/joao2/Public/NAMD_2.13_Source.tar.gz

cd NAMD_2.13_Source

tar xf charm-6.8.2.tar

cd charm-6.8.2

./build charm++ gni-crayxc persistent --no-build-shared --with-production

cd gni-crayxc-persistent/tests/charm++/megatest

make pgm

mv pgm ../../../bin/megatest

cd ../../converse/megacon

make pgm

mv pgm ../../../bin/megacon

cd ../../..

ldd bin/megatest bin/megacon

cd ..

./build charm++ gni-crayxc persistent smp --no-build-shared --with-production

cd gni-crayxc-persistent-smp/tests/charm++/megatest

make pgm

mv pgm ../../../bin/megatest

cd ../../converse/megacon

make pgm

mv pgm ../../../bin/megacon

cd ../../..

ldd bin/megatest bin/megacon

cd ..

cd ..

./config CRAY-XC-intel --with-fftw3 --charm-arch gni-crayxc-persistent

./config CRAY-XC-intel.smp --with-fftw3 --charm-arch gni-crayxc-persistent-smp

cd CRAY-XC-intel

make release

cd ../CRAY-XC-intel.smp

make release