User:Ppomorsk

Pawel Pomorski works for SHARCNET at the University of Waterloo.

FEniCS

For installation instructions, go to dedicated page: FEniCS

Instructions for installing version 1.9.4 Alpha

1. Download the 1.9.4 LATEST ALPHA tar file from http://www.ks.uiuc.edu/, selecting the LINUX_64 version (free registration is required).

2. Copy the file to the home directory of the cluster you wish to use.

3. Unpack the file with:

tar xvf vmd-1.9.4*.opengl.tar.gz

4. Enter the created directory by:

cd vmd-1.9.4*

5.

mkdir ~/vmd_install
mkdir ~/vmd_library

6. edit the configure file to read

# Directory where VMD startup script is installed, should be in users' paths.
$install_bin_dir="/home/your_user_name/vmd_install";

# Directory where VMD files and executables are installed
$install_library_dir="/home/your_user_name/vmd_library";

but replace your_user_name with your actual user name.

7. Run configure:

./configure

8. Run make

cd src
make install

9. Add the resulting executable to your path

export PATH=~/vmd_install:$PATH

If getting a blank window on a Mac, try:

defaults write org.macosforge.xquartz.X11 enable_iglx -bool true

Benchmarking NAMD

Efficiency is computed from (time with 1 core) / (N * (time with N cores) ).

# cores	Wall time (s) per step	Efficiency
1	0.8313	100%
2	0.4151	100%
4	0.1945	107%
8	0.0987	105%
16	0.0501	104%
32	0.0257	101%
64	0.0133	98%
128	0.0074	88%
256	0.0036	90%
512	0.0021	77%

# cores	#GPUs	Wall time (s) per step	Notes
4	1	0.0165	1 node, multicore
8	1	0.0088	1 node, multicore
16	1	0.0071	1 node, multicore
32	2	0.0045	1 node, multicore
64	4	0.0058	2 nodes, verbs-smp
128	8	0.0051	2 nodes, verbs-smp