Year: 2018

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Setting up NTP in CentOS 7

Prerequisites Step 1: Endure you are in the correct time zone

# timedatectl
      Local time: Wed 2018-09-12 13:48:31 +08
  Universal time: Wed 2018-09-12 05:48:31 UTC
        RTC time: Wed 2018-09-12 05:48:31
       Time zone: Asia/Singapore (+08, +0800)
     NTP enabled: yes
NTP synchronized: yes
 RTC in local TZ: no
      DST active: n/a

Prerequisites Step 2: List Time Zone

# timedatectl list-timezones
.....
Asia/Singapore
.....

Prerequisites Step 3: Set Time Zone

# timedatectl set-timezone Asia/Singapore

 

Step 1: Yum Install

NTP can be installed from the CentOS repositories with yum

# yum install ntp

Step 2: Edit the Public Time Servers

Once you have installed ntp package, go to official NTP Public Pool Time Servers . For Singapore, you can use this specific pool zone, add the following to your ntp.conf file:

server 0.sg.pool.ntp.org iburst
server 1.sg.pool.ntp.org iburst
server 2.sg.pool.ntp.org iburst
server 3.sg.pool.ntp.org iburst

Step 3: Allow the clients from the network to sync with this server

Restrict which clients from which network is allowed to query and sync time

restrict 192.168.5.0 netmask 255.255.224.0 nomodify notrap

Step 4: Record all NTP server issues into one dedicated log file. Edit /etc/ntp.conf

logfile /var/log/ntp.log

Step 5: Add Firewall Rule and Start Services

# firewall-cmd --add-service=ntp --permanent
# firewall-cmd --reload
# systemctl start ntpd
# systemctl enable ntpd
# systemctl status ntpd

Step 6: Verify Time Sync

# ntpq -p
# date -R

Or query or synchronize against a selected pool of time servers

# ntpdate -q 0.sg.pool.ntp.org

References:

  1. Setting Up “NTP (Network Time Protocol) Server” in RHEL/CentOS 7 (by Tecmint.com)
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Set hostname using hostnamectl for CentOS 7

1. Listing hostname using “hostnamectl” or “hostnamectl status”

[root@localhost ~]# hostnamectl
Static hostname: helloworld.com
Icon name: computer-server
Chassis: server
Machine ID: aaaaaaaaaaaaa
Boot ID: ddddddddddd
Operating System: CentOS Linux 7 (Core)
CPE OS Name: cpe:/o:centos:centos:7
Kernel: Linux 3.10.0-327.el7.x86_64
Architecture: x86-64

2.Setting static host-name using hostnamectl

# hostnamectl set-hostname "helloworld.com" --static

3. Delete static host-nameusing hostnamectl

# hostnamectl set-hostname "" --static
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IBM Spectrum Scale Development Blogs for (Q1 2018)

Here are list of development blogs in the this quarter (Q1 2018). As discussed in User Groups, passing it along:

GDPR Compliance and Unstructured Data Storage
https://developer.ibm.com/storage/2018/03/27/gdpr-compliance-unstructure-data-storage/

IBM Spectrum Scale for Linux on IBM Z ? Release 5.0 features and highlights
https://developer.ibm.com/storage/2018/03/09/ibm-spectrum-scale-linux-ibm-z-release-5-0-features-highlights/

Management GUI enhancements in IBM Spectrum Scale release 5.0.0
https://developer.ibm.com/storage/2018/01/18/gui-enhancements-in-spectrum-scale-release-5-0-0/

IBM Spectrum Scale 5.0.0 ? What?s new in NFS?
https://developer.ibm.com/storage/2018/01/18/ibm-spectrum-scale-5-0-0-whats-new-nfs/

Benefits and implementation of Spectrum Scale sudo wrappers
https://developer.ibm.com/storage/2018/01/15/benefits-implementation-spectrum-scale-sudo-wrappers/

IBM Spectrum Scale: Big Data and Analytics Solution Brief
https://developer.ibm.com/storage/2018/01/15/ibm-spectrum-scale-big-data-analytics-solution-brief/

Variant Sub-blocks in Spectrum Scale 5.0
https://developer.ibm.com/storage/2018/01/11/spectrum-scale-variant-sub-blocks/

Compression support in Spectrum Scale 5.0.0
https://developer.ibm.com/storage/2018/01/11/compression-support-spectrum-scale-5-0-0/

IBM Spectrum Scale Versus Apache Hadoop HDFS
https://developer.ibm.com/storage/2018/01/10/spectrumscale_vs_hdfs/

ESS Fault Tolerance
https://developer.ibm.com/storage/2018/01/09/ess-fault-tolerance/

Genomic Workloads ? How To Get it Right From Infrastructure Point Of View.
https://developer.ibm.com/storage/2018/01/06/genomic-workloads-get-right-infrastructure-point-view/

IBM Spectrum Scale On AWS Cloud: This video explains how to deploy IBM Spectrum Scale on AWS. This solution helps the users who require highly available access to a shared name space across multiple instances with good performance, without requiring an in-depth knowledge of IBM Spectrum Scale.

Detailed Demo : https://www.youtube.com/watch?v=6j5Xj_d0bh4
Brief Demo : https://www.youtube.com/watch?v=-aMQKPW_RfY

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Fixing out of memory Issues in Rsync

If you are doing rsync and you encountered this error like rsync out of memory, you may want to take a look.a this article (Rsync out of memory? Try this…). Need to add an additional parameter (–no-inc-recursive) to the rsync commands.

According to the article, the the out of memory failure occured when  rsync attempts to load all the filenames and info in to RAM at startup.

# rsync -lH -rva --no-inc-recursive --progress gromacs remote_server:/usr/local
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Compiling VASP-5.4.4 with Intel MPI-5.0.3

Details Information can be taken from Installing VASP from VASPwiki. This for CPU Compilation

Activate the Intel Compilers/ Intel MPI Environment. In your .bashrc

source /usr/local/intel_2015/parallel_studio_xe_2015/bin/psxevars.sh intel64
source /usr/local/intel_2015/impi/5.0.3.049/bin64/mpivars.sh intel64
source /usr/local/intel_2015/composerxe/bin/compilervars.sh intel64
source /usr/local/intel_2015/mkl/bin/mklvars.sh intel64
MKLROOT=/usr/local/intel_2015/mkl

At the installation base of vasp.5.4.4 base

# cp arch/makefile.include.linux_intel ./makefile.include

For Linking against Intel-MPI Libraries. Edit makefile.include.linux_intel

# vim makefile.include.linux_intel
MKL_PATH = $(MKLROOT)/lib/intel64
BLACS = -lmkl_blacs_intelmpi_lp64
SCALAPACK = $(MKL_PATH)/libmkl_scalapack_lp64.a $(BLACS)
LLIBS = $(SCALAPACK) $(LAPACK) $(BLAS)

For Linking Intel MKL Wrapper of fftw at makefile.include.linux_intel

OBJECTS= fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o \
         $(MKLROOT)/interfaces/fftw3xf/libfftw3xf_intel.a
INCS=-I$(MKLROOT)/include/fftw

Make the files

# make all

If you wish to build the standard, gamma, non-collinear individually, you should make as below

# make std
# make gam
# make ncl

The vasp binary of standard, gamma-only, and non-collinear version of VASP can be found in the bin folder of vasp

vasp_gam vasp_ncl vasp_std
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Making ISO using mkisofs

mkisofs is a wonderful utility to generate ISO images. To generate a compatible ISO images on a disc which are readable everywhere, consider the following commands

# mkisofs -rdlJ -o disc_directory_image.iso directory/

-r : “Rock Ridge” format is enabled to allow long filenames on UNIX systems
-J : allow long filenames on Windows Systems
-l : Allow full 31-character filenames.
-d : Do not append a period to files that do not have one which violate ISO9660

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Dealing with The compiler /usr/bin/c++ has no C++11 support for CentOS 6

If you compiling using cmake and you make encounter error like this. This is despite the fact that you use the latest compiler like GNU-5.2.0. But somehow the cmake is still looking at the older gnu that comes with CentOS 6

[user1@node1 build]$ cmake ..
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
CMake Error at CMakeLists.txt:24 (message):
The compiler /usr/bin/c++ has no C++11 support. Aborting.

To resolve this, you have to be more explicit in the cmake parameter point to the corrcet g++, gcc

[user1@node1 build]$ cmake .. -DCMAKE_CXX_COMPILER=/usr/local/gcc-5.2.0/bin/g++ -DCMAKE_C_COMPILER=/usr/local/gcc-5.2.0/bin/gcc