Tuesday, June 28, 2016

ntpdate failing to synchronise clock.

My client timing was ahead of the NTP Server by 15 hours. When I did a
# ntpdate -q 0.centos.pool.ntp.org

The synchronization did not work.

To force the client to synchronise no matter how absurd the time differences, you have to use a "-b" parameter.

# ntpdate -b 0.centos.pool.ntp.org

Tuesday, June 14, 2016

Compiling LAMMPS-14May16 with Intel-15.0.6 and Intel-MPI-5.0.3

Step 1: Remember to initialise Intel Environment. In your .bashrc
source /usr/local/intel/bin/compilervars.sh intel64
Step 2: Untar LAMMPS
# tar -zxvf lammps-stable.tar.gz
Step 3: Prepare libraries for lammps 3a. lib/reax
# make -f Makefile.gfortran
3b. lib/meam
# make -f Makefile.ifort
3c. lib/poems
# make -f Makefile.icc
Step 4: Compile required the packages. Go to src directory
# cd src
4a. Check which packages are included
# make package-status
Installed YES: package ASPHERE
Installed YES: package BODY
Installed YES: package CLASS2
Installed YES: package COLLOID
Installed YES: package COMPRESS
Installed YES: package CORESHELL
Installed YES: package DIPOLE
Installed YES: package FLD
Installed  NO: package GPU
Installed YES: package GRANULAR
Installed  NO: package KIM
Installed YES: package KOKKOS
  src/pair_lj_sdk_kokkos.cpp does not exist
  src/pair_lj_sdk_kokkos.h does not exist
Installed YES: package KSPACE
Installed YES: package MANYBODY
Installed YES: package MC
Installed YES: package MEAM
Installed YES: package MISC
Installed YES: package MOLECULE
Installed YES: package MPIIO
Installed YES: package OPT
Installed YES: package PERI
Installed YES: package POEMS
Installed YES: package PYTHON
Installed YES: package QEQ
Installed YES: package REAX
Installed YES: package REPLICA
Installed YES: package RIGID
Installed YES: package SHOCK
Installed YES: package SNAP
Installed YES: package SRD
Installed  NO: package VORONOI
Installed YES: package XTC
4b. Choose all the standard
# make yes-standard
4c. Exclude packages that are not required
# make no-voronoi
# make no-kim
# make no-gpu
# make no-kokkos
Step 5: Install User-Contributed Intel Optimised Package (user-intel) and User-Contributed OpenMP Packages (user-omp)
# make yes-user-intel
# make yes-user-omp
Step 6: Compile LAMMPS Check make options. Go to src
# make intel_cpu_intelmpi -j 16
Step 6a: If in the midst of compilation you land yourself in this error ld: unable to to locate -lompstub. This is due to Intel 2015 using depreciating ompstub to ompistub5. Just go to the Intel Directory
# cd /usr/local/intel_2015/composerxe/lib/intel64
# ln -s  libiompstubs5.so libompstub.so
Step 7: Create a /usr/local/lammps-7Dec15 and copy libraries. Go to lammps root directory
# cp -Rv bench /usr/local/lammps-14May16
# cp -Rv doc /usr/local/lammps-14May16
# cp -Rv examples /usr/local/lammps-14May16
# cp -Rv potentials /usr/local/lammps-14May16
# cp README /usr/local/lammps-14May16
# cp -Rv tools /usr/local/lammps-14May16
# cp -Rv lib /usr/local/lammps-14May16
# cp lmp_intel_cpu_intelmpi /usr/local/lammps-14May16/bin
7a. Create a softlinks
# ln -s /usr/local/lammps-7Dec15/bin/lmp_intel_cpu_intelmpi lammps
  1. Quick install guide for LAMMPS on Linux cluster
  2. LAMMPS Optimized for Intel on Quad Socket Xeon

Monday, June 6, 2016

New features and Enhancements of NetApp OnTap 9

Primary ONTAP Features
  1. Leading enterprise-class data services • Unified management across flash, disk, and cloud, as well as SAN and NAS protocols
  2. High performance for all-flash solutions • Nondisruptive operations
  3. Scaling up to 24-nodes
  4. Storage efficiency and inline data reduction 
  5. NetApp Integrated Data Protection 
  6. NetApp OnCommand® management software
 New Features: ONTAP 9 
  1. Simplified AFF deployments in <10 li="" microsoft="" minutes="" racle="" server="" sql="" vdi="" vmware="">
  2. Up to 60% more IOPS than with ONTAP 8.3.1 
  3. ONTAP Select (for SDS) and ONTAP Cloud 
  4. Support for 15TB SSD 
  5. Inline data compaction works with compression and deduplication for greater data reduction
  6. SnapLock® software for data compliance 
  7. RAID-TEC triple-parity protection 
  8. Headroom for visibility of performance capacity 
  9. MetroCluster enhancements (lower TCO,  8-node NAS configurations) 
  10. Onboard key manager 
  11. Inline deduplication and compression 
  12. MetroCluster 2-node solutions and improved distance (300km), performance, and deployment
  13. Storage virtual machine disaster recovery  
  14. Foreign LUN import enhancements
  1. NetApp ONTAP 9 Datasheet