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Compiling Wannier90-2.1.0 with Intel-MPI 5.1.3

Compiling Wannier90-2.1.0 is quite straight-forward.

Step 1: Download the source code from Wannier.Org at http://www.wannier.org/download.html

Step 2: Untar the tar-ball

$ tar -zxvf wannier90-2.1.0.tar.gz

Step 3: Copy and Edit the make file

$ cd wannier90-2.1.0/config
$ cp make.inc.ifort ..
$ cd ..
$ mv make.inc.ifort make.inc
#=====================================================
# For Linux with intel version 11/12 on 64bit machines
#=====================================================
F90 = ifort
COMMS=mpi
MPIF90=mpiifort
FCOPTS=-O2
LDOPTS=-O2
#========================================================
# Intel mkl libraries. Set LIBPATH if not in default path
#========================================================
LIBDIR = /usr/local/RH6_apps/intel/mkl/lib/intel64
LIBS = -L$(LIBDIR) -lmkl_core -lmkl_intel_lp64 -lmkl_sequential -lpthread
#=======================
# ATLAS Blas and LAPACK
#=======================
#LIBDIR = /usr/local/lib
#LIBS = -L$(LIBDIR) -llapack -lf77blas -lcblas -latlas
$ make default -j 8
$ make lib
$ make w90chk2chk
$ make w90vdw
$ make w90pov
$ make test
$ make doc

IF you need to restart the compilation, you use the command

$ make veryclean

For more information, do take a look at

  1. http://www.wannier.org/doc/README.install
  2. http://www.wannier.org/

Compiling VTST Tools with VASP-5.3.5

Taken from VTST.Tools Installation Guide

The VTST•Tools has a fortran component which can be linked into the VASP code as well as a collection of scripts. Its CINEB has some improvement compared to the NEB method

Step 1: Download the VTST Code

Download the VTST Code (vtstcode.tgz) at http://theory.cm.utexas.edu/vtsttools/download.html 

Step 2: Download the files in vtsttools/source into your vasp source directory.

In my situation, I put it in /home/user1/vasp.5.3.5_impi_neb/vasp.5.3/

$ tar -zxvf vtstcode.gz
$ cd vtstcode-173
$ cp *.* ..

(Replace the chain.F with the new one)

Step 3: Edit main.F in the source file

Find and Replace

CALL CHAIN_FORCE(T_INFO%NIONS,DYN%POSION,TOTEN,TIFOR, &
LATT_CUR%A,LATT_CUR%B,IO%IU6)

with

CALL CHAIN_FORCE(T_INFO%NIONS,DYN%POSION,TOTEN,TIFOR, &
TSIF,LATT_CUR%A,LATT_CUR%B,IO%IU6)

Step 4: Edit the Makefile

To build the code, the VASP makefile needs to be changed. Find the variable SOURCE, which defines which objects will be built, and add the following objects before chain.o

bfgs.o dynmat.o instanton.o lbfgs.o sd.o cg.o dimer.o bbm.o fire.o lanczos.o neb.o qm.o opt.o \

Step 5: Change and compile the Makefile

Please follow Compiling VASP-5.2.12 with Intel MPI-5.0.3

References:

  1. VTST.Tools Installation Guide
  2. Compiling VASP-5.2.12 with Intel MPI-5.0.3

Testing the AD User Authentication with Centrify

Test 1: Test with SSH

The simplest way is to enable SSH and connect to it.

Test 2: Test with adinfo

# adinfo -A --user user1
Active Directory password:
Password for user "user1" is correct

Test 3: Test using kinit

# /usr/share/centrifydc/kerberos/bin/kinit user1
# /usr/share/centrifydc/kerberos/bin/klist
Ticket cache: FILE:/tmp/krb5cc_0
Default principal: user2@test.com
.....
.....
Valid starting       Expires           Service principal
.....
.....

References:

  1. Centrify is in connected mode but users are unable to login.

Resolving Unable to determine user account for execution

If you are facing this issue “Unable to determine user account for execution;”, it is likely casued by the fact that LSF cluster must be restarted if user authentication is switched from NIS to LDAP.

After user authentication method is switched from NIS to LDAP, all user jobs are pending with the pending reason: “Unable to determine user account for execution”.

If user authentication mode is changed, you have to restart LSF daemons on all LSF hosts for jobs to run successfully. On the LSF master master host do:

# lsadmin reconfig
# badmin mbdrestart
# badmin hrestart all

References:

  1. LSF cluster must be restarted if user authentication is switched from NIS to LDAP