Month: June 2019

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Compile LATTE package for LAMMPS using Intel Compilers

Step 1: Download LATTE Source Code from Project

Download or clone the LATTE source code from https://github.com/lanl/LATTE. If you download a zipfile or tarball, unpack the tarball either in this /lib/latte directory or somewhere else on your system.

Step 2: Modify makefile.CHOICES

Modify the makefile.CHOICES according to your system architecture and compilers. Check that the MAKELIB flag is ON in makefile.CHOICES and finally, build the code via the make command

#
# Compilation and link flags for LATTE
#

# Precision - double or single
PRECISION = DOUBLE
#PRECISION = SINGLE

# Make the latte library
# AR and RUNLIB executable default path to compile
# latte as a library (change accordingly)
MAKELIB = ON
AR = /usr/bin/ar cq
RANLIB = /usr/bin/ranlib

# Use PROGRESS and BML libraries
PROGRESS = OFF
PROGRESS_PATH= $(HOME)/qmd-progress/install/lib
BML_PATH= $(HOME)/bml/install/lib

# Use METIS library for graph partitioning
METIS = OFF
METIS_PATH= $(HOME)/metis/metis-5.1.0/install

# GPU available - OFF or ON
GPUOPT = OFF

# Using DBCSR library from cp2k? OFF or ON
DBCSR_OPT = OFF

# Parallelizing over k-points?
MPIOPT = OFF

#
# CPU Fortran options
#

#For GNU compiler:
#FC = mpif90
FC = gfortran
FCL = $(FC)
FFLAGS = -O3 -fopenmp -cpp
#FFLAGS =  -fast -Mpreprocess -mp
LINKFLAG = -fopenmp

#For intel compiler:
FC = ifort
FCL = $(FC)
FFLAGS =  -O3 -fpp -qopenmp
LINKFLAG = -qopenmp
LIB = -mkl=parallel

#GNU BLAS/LAPACK libraries:
#LIB = -L/usr/local/lapack-3.8.0 -llapack -L/usr/local/blas-3.8.0/lib -lblas

#Intel MKL BLAS/LAPACK libraries:
LIB = -Wl,--no-as-needed -L${MKLROOT}/lib/intel64 \
 -lmkl_lapack95_lp64 -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core \
 -lmkl_gnu_thread -lmkl_core -ldl -lpthread -lm

#Alternative flags for MKL:
#LIB += -mkl=parallel

#Other BLAS/LAPACK vendors:
#LIB = -framework Accelerate
#LIB = -L/usr/projects/hpcsoft/toss2/common/acml/5.3.1/gfortran64/lib -lacml

# Uncomment for coverage
#CVR = OFF
ifeq ($(CVR), ON)
        FFLAGS += -fprofile-arcs -ftest-coverage
        LINKFLAG += -fprofile-arcs -ftest-coverage
endif

ifeq ($(PROGRESS), ON)
        LIB += -L$(PROGRESS_PATH) -lprogress -L$(BML_PATH) -lbml_fortran -lbml
        FFLAGS += -I$(BML_PATH)/../include -I$(PROGRESS_PATH)/../include
endif

ifeq ($(GRAPH), ON)
        LIB += -L$(METIS_PATH)/lib -lmetis
        FFLAGS += -I$(METIS_PATH)/include
endif

#DBCSR_LIB = -L/home/cawkwell/cp2k/lib/cawkwell/popt -lcp2k_dbcsr_lib
#DBCSR_MOD = -I/home/cawkwell/cp2k/obj/cawkwell/popt

#
# GPU options
#

GPU_CUDA_LIB = -L/usr/local/cuda-9.1/lib64 -lcublas -lcudart
GPU_ARCH = sm_20

# make

You should see liblatte.a file.

 

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Redirecting to another site in User Directory in APACHE

Sometimes your users may require you to redirect to their new site and even capture errors like 404, 401 in their old site and redirect to their new site. You can do it by doing the following.

Step 1: After clearing out all the old site, you may want to put in a redirection page. Can be a simple one line on a index.html

Step 2: To trap “missing or ghost directory and files” in the website of the user directory. For example the old site could be http://www.myoldsite.com/~me/

You may want to create a .conf file such as myoldsite.conf and placed it at /etc/httpd/conf.d and put in the following configuration.

Step 3: Update the httpd service.

For CentOS 7, it could be

# systemctl start httpd.service
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Unable to open a connection to your SSH authentication agent

If you are unable to have open a connection to your SSH public key could not be exchanged successfully, you may want to do the following

Remember to do the following SSH Login without Password

Evaluate that the agent is up

# eval `ssh-agent -s`
Agent pid 265652

Add your SSH private key to the ssh-agent.

# ssh-add ~/.ssh/id_rsa.pub

*If you are still using “Could not open a connection to your authentication agent.”

# exec ssh-agent bash

*If You are having the issue. The default is

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@ WARNING: UNPROTECTED PRIVATE KEY FILE! @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Permissions 0644 for 'id_rsa.pub' are too open.
It is required that your private key files are NOT accessible by others.
This private key will be ignored.
# chmod 600 id_rsa.pub

 

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Remove virbr0 Interfaces from CentOS 7

Step 1: Stop the libvirtd Service

# systemctl stop libvirtd.service

You should see something like this

● libvirtd.service - Virtualization daemon
Loaded: loaded (/usr/lib/systemd/system/libvirtd.service; enabled; vendor preset: enabled)
Active: inactive (dead) since Mon 2019-06-03 13:33:26 +08; 43s ago
Docs: man:libvirtd(8)
https://libvirt.org
Process: 28069 ExecStart=/usr/sbin/libvirtd $LIBVIRTD_ARGS (code=exited, status=0/SUCCESS)
Main PID: 28069 (code=exited, status=0/SUCCESS)
Tasks: 2 (limit: 32768)
Memory: 6.7M
CGroup: /system.slice/libvirtd.service
├─28896 /usr/sbin/dnsmasq --conf-file=/var/lib/libvirt/dnsmasq/default.conf --leasefile-ro --dhcp-script=/usr/libexec/libvirt_leaseshelper
└─28897 /usr/sbin/dnsmasq --conf-file=/var/lib/libvirt/dnsmasq/default.conf --leasefile-ro --dhcp-script=/usr/libexec/libvirt_leaseshelper

Step 2. Disable the service

# systemctl disable libvirtd.service

Step 3: Removing the virbr0 interfaces on machine

# brctl show
bridge name     bridge id               STP enabled     interfaces
docker0         8000.0242f3432864       no
virbr0          8000.525400d6fcaa       yes             virbr0-nic

Step 4: Down the Bridge Link

# ip link set virbr0 down

Step 5: Remove the Bridge

# brctl delbr virbr0

Step 6: Verify that the bridge has been removed.

# brtcl show
bridge name bridge id STP enabled interfaces
docker0 8000.0242f3432864 no