Git at simple

Git a simple system for version control system, with a basic steps is possible to install or compile git and start using.

 


 
After a simple apt-get install git or a ./configure, make and make install the software is ready to run. To create the repository:

mkdir gitrepo
cd gitrepo (with the code)
git init #init repository
git config –global user.name “user”
git config –global user.email “user@user.com”
git commit -m ‘initial commit’
git push master
git config core.bare true

The workflow:
git status #shows the changed files
git add -u #add changed files or git add -u
git commit #inform the changes
git push #send the files

Molecular dynamics motion equation integrator

Molecular dynamics (MD) are based on a algorithm,  the figure below shows the basic molecular dynamics steps:

For each MD step (lines 3, 4 and 5), is necessary to integrate the Newton’s motions equation, the Verlet algorithm is widely use for this task.  However, there is a important issue to tackle, the Delta T has to be small (on 1 fs order) to minimize the error and result on a correct simulation. To solve this issue is possible to use accelerated molecular dynamics.

Infiniband for HPC

Which is the minimum hardware for InfiniBand for HPC ?

–  InfiniBand Adapter Card, Single-Port QSFP QDR IB (40Gb/s)  ($495 ~ R$ 4000)
–  Mellanox Passive Copper Cable, IB QDR/FDR10, 40Gb/s, QSFP, ($134 ~R$1200)
– Switch QDR 36-Port Managed InfiniBand ($10000 ~ R$50000)

For 10 computer nodes 10 x $495 (adpter card) + 10 x $134 Copper Cable + $10000 (switch) = $16290  ~ R$102000

For software, RocksCluster is very suitably solution.