install.notes

# install R

R packages are available in the EPEL repositories. If you don’t have EPEL repository installed on your machine you can do it by typing:

sudo yum install epel-release

Copy

You will be prompted to accept the repository GPG key, type y and hit Enter.

Once the repository is added, install R by typing:

sudo yum install R

Copy

R is a meta package that contains all the necessary R components.

Verify the installation by typing the following command which will print the R version:

R --version

Copy

R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
http://www.gnu.org/licenses/.

# install spacy
python -m pip install -U socketIO-client
installs: socketIO-client requests six websocket-client idna certifi chardet urllib3

# neo4j - via standalone tarball

download latest at https://neo4j.com/download-center/
Extract the contents of the archive, using tar -xf <filename>
Refer to the top-level extracted directory as: NEO4J_HOME
Change directory to: $NEO4J_HOME
Run ./bin/neo4j console

open localhost:7474 in browser
connect to db with ":server connect" using neo4j/neo4j as user/password (uses
bolt:7687 to access dbms functions like login, new users, etc)
will prompt to change default password

CALL dbms.security.createUser("root", "NGA", false)
to create new root user

test nodejs connect with "node flex.js F1".  Log should reflect good proxy.
# neo4j - via 
yum
First, you'll want our key:

cd /tmp
wget http://debian.neo4j.org/neotechnology.gpg.key
rpm --import neotechnology.gpg.key

Then, you'll want to add our yum repo to /etc/yum.repos.d/neo4j.repo:

cat <<EOF>  /etc/yum.repos.d/neo4j.repo
[neo4j]
name=Neo4j Yum Repo
baseurl=http://yum.neo4j.org/stable
enabled=1
gpgcheck=1
EOF

Finally, install a package

yum install neo4j

# start neo4j

2.2.3.2. Starting the service automatically on system start

If you installed the RPM package and want Neo4j to start automatically on system boot then you need to enable the service. On Debian-based distributions this is done for you at installation time.

systemctl enable neo4j

2.2.3.3. Controlling the service

System services are controlled with the systemctl command. It accepts a number of commands:

systemctl {start|stop|restart} neo4j

Service customizations can be placed in a service override file. To edit your specific options, do the following command which will open up an editor of the appropriate file:

systemctl edit neo4j

Then place any customizations under a [Service] section. The following example lists default values which may be interesting to change for some users:

[Service]
# The user and group which the service runs as.
User=neo4j
Group=neo4j
# If it takes longer than this then the shutdown is considered to have failed.
# This may need to be increased if the system serves long-running transactions.
TimeoutSec=120

You can print the effective service, including possible overrides, with:

systemctl cat neo4j

Remember to restart neo4j if you change any settings.

systemctl restart neo4j

### set intial password
rm /var/lib/neo4j/data/dbms/auth
neo4j-admin set-initial-password XXXX

# install docker

Step 1 — Installing Docker

First, install Docker if you haven't already. The quickest way to install Docker is to download and install their installation script (you'll be prompted for a sudo password).

    wget -qO- https://get.docker.com/ | sh

The above command downloads and executes a small installation script written by the Docker team. If you don't trust third party scripts or want more details about what the script is doing check out the instructions in the DigitalOcean Docker tutorial or Docker's own installation documentation.

Working with Docker is a pain if your user is not configured correctly, so add your user to the docker group with the following command.

sudo usermod -aG docker $(whoami)

Log out and log in from your server to activate your new groups.

Set Docker to start automatically at boot time:

    sudo systemctl enable docker.service

Finally, start the Docker service:

    sudo systemctl start docker.service

# docker compose install
sudo curl -L https://github.com/docker/compose/releases/download/1.22.0-rc1/docker-compose-$(uname -s)-$(uname -m) -o /usr/local/bin/docker-compose

# PKI certs
## converting pfx to crt-key
openssl pkcs12 -in keyStore.pfx -out keyStore.crt -nodes --nokeys
openssl pkcs12 -in keyStore.pfx -out keyStore.key -nodes --nocerts

# check that crt-key match
openssl x509 -noout -modulus -in certificate.crt | openssl md5
openssl rsa -noout -modulus -in privateKey.key | openssl md5

# notepadqq
wget -O /etc/yum.repos.d/sea-devel.repo "http://sea.fedorapeople.org/sea-devel.repo"
yum install notepadqq
# must explictly add epel repo and update for centos7.7 before qq install 
yum install -y epel-release
yum -y update

######
> move from node5 to node8

> npm install lwip fails due to izlib issue https://github.com/EyalAr/lwip/issues/297
> change zlib VERNUM to 0x1280 (from 0x12b0) in ~/.node-gyp/8.9.4/include/node/zlib.h and reinstall lwip
> also installed jimp as potential lwip replacement

> socket.io-clusterhub wont install due to "inherits super constructor" problem.
> removed include from totem

> rebuilt all node_modules.  integrated graceful_lwip into lwip.  Added jimp.  

> socket.io-clusterhub fails to be required due to misuse of util.inherits.  Changed lib/store/store.js
under socket.io/clusterhub to "var EventEmitter = require("events").EventEmitter" vs "process.EventEmitter".

> moved sqldb under local and updated my.cnf

>> installed toobusy-js to replace toobusy

######

# initial setup
git config --global user.name "DEBE"
git config --global user.email "g5120089@trbvm.com"
git remote add origin git@git.geointapps.org:ACME/sigma.git
cd sigma
git init
git touch README.md
git add README.md
git commit -m "first commit"
git push -u origin master

# commit changes to local repo
git commit -am "sigma 36 extjs5 themes charts ui fixes"

# push local repo to master branch at gitlab service
git push -u origin master

# pull master branch at gitlab service into local repo
git pull origin master

# forget all changes and reprime codebase
git reset --hard HEAD
git clean -f
git pull origin master

# make git stop tracking files that are now ignored
git rm -r --caced .
git add .
git commit -am "Remove ignoed files"

# initial stuff (if not installied  in base centos - doubt we need - only need cmake)
yum groupinstall "Development Tools"  --setopt=group_package_types=mandatory,default,optional  # centos 7.x
yum groupinstall "Development Tools"  # centos 6.x
yum install cmake
yum install libaio  # centos 6.x

# service iptables start  		# not sure why i noted this here

interface with git repo (end product name DEBE now known as geonode)
git config --global user.name "DEBE"
git config --global user.email "g500xxx@trbvm.com"
git remote add origin git@git.geointapps.org:ACME/sigma.git
git pull
.ssh/id_rsa shoould contain private key corresponding to git public key uploaded into https://git.geointapps.org

##### Folllowing gdal stuff never fully worked.  gdal and OSSIM used to orthorectify images

determining fastest mirrors
 * base: centos.mbni.med.umich.edu
 * extras: mirrors.lga7.us.voxel.net
 * updates: mirror.trouble-free.net
base                                                                           | 3.7 kB     00:00     
elgis                                                                          | 3.4 kB     00:00     
elgis/primary_db                                                               |  85 kB     00:00     
extras                                                                         | 3.4 kB     00:00     
updates                                                                        | 3.4 kB     00:00     
updates/primary_db                                                             | 2.5 MB     00:04   

yum list gdal*  
Loaded plugins: fastestmirror, refresh-packagekit, security
Determining fastest mirrors
 * base: mirror.raystedman.net
 * extras: mirrors.lga7.us.voxel.net
 * updates: mirror.trouble-free.net
Available Packages
gdal.i386                                          1.8.1-1_0.el6                                 elgis
gdal.i686                                          1.9.2-4.el6                                   elgis
gdal-devel.i386                                    1.8.1-1_0.el6                                 elgis
gdal-devel.i686                                    1.9.2-4.el6                                   elgis
gdal-doc.i386                                      1.8.1-1_0.el6                                 elgis
gdal-doc.noarch                                    1.9.2-4.el6                                   elgis
gdal-java.i386                                     1.8.1-1_0.el6                                 elgis
gdal-java.i686                                     1.9.2-4.el6                                   elgis
gdal-javadoc.noarch                                1.9.2-4.el6                                   elgis
gdal-libs.i686                                     1.9.2-4.el6                                   elgis
gdal-perl.i386                                     1.8.1-1_0.el6                                 elgis
gdal-perl.i686                                     1.9.2-4.el6                                   elgis
gdal-python.i386                                   1.8.1-1_0.el6                                 elgis
gdal-python.i686                                   1.9.2-4.el6                                   elgis
gdal-ruby.i386                                     1.8.1-1_0.el6                                 elgis
gdal-ruby.i686                                     1.9.2-4.el6                                   elgis
gdal-static.i386                                   1.8.1-1_0.el6                                 elgis


yum install gdal gdal-devel [gdal-java gdal-perl gdal-python] 

yum --enablerepo=rpmforge install gdal

#### end gdal

## Getting Started - eg on how client d3/topojson is used

    Include D3.js and Topojson on your page
    Include Datamaps.js on your page
    Add a container, set the height and width and position to relative
    Create a new Datamaps(options), passing in at least an element option

Example:

<script src="//cdnjs.cloudflare.com/ajax/libs/d3/3.5.3/d3.min.js"></script>
<script src="//cdnjs.cloudflare.com/ajax/libs/topojson/1.6.9/topojson.min.js"></script>
<script src="/datamaps.world.min.js"></script>
<div id="container" style="position: relative; width: 500px; height: 300px;"></div>
<script>
    var map = new Datamap({element: document.getElementById('container')});
</script>


#ruby etc - used for extjs sas custom css themes
yum install ruby rubygems ruby-devel
gem install compass

######## Start legacy - not used anymore)
mv newbuild ~/opencv
cp -r include/* ~/opencv/include
cp -r modules/core  ~/opencv/modules

# legacy - for mergevec util - but dont need this util 
#setup pkg config for compiler
export PKG_CONFIG_PATH=/home/jamesdb/opencv/unix-install/

pkg-config --cflags opencv # produces ...
	-I/home/jamesdb/opencv/include/opencv -I/home/jamesdb/opencv/include  

pkg-config --libs opencv  # produces ...
	-L/home/jamesdb/opencv/lib -lopencv_core -lopencv_imgproc -lopencv_highgui -lopencv_ml -lopencv_video -lopencv_features2d -lopencv_calib3d -lopencv_objdetect -lopencv_contrib -lopencv_legacy -lopencv_flann	

# to compile mergevec utility ... 
cd ~/opencv/modules/haartraining
cp ~/sigma/opencv_util/mergevec.cpp .
g++ `pkg-config --cflags opencv` `pkg-config --libs opencv` -o mergevec mergevec.cpp cvboost.o cvcommon.o cvsamples.o cvhaarclassifier.o cvhaartraining.o  #note .o (not .cpp) 

####### end legacy

# for gtk support for opencv (needed for graphical/console functions)
sudo yum install gtk+-devel gtk2-devel

####### install mysql cluster 

# tar xvf mysql cluster (7.3.6, 7.4.8, 7.5.5) from generic linux install package (not the .el versions)

# add missing english errmsg.sys
cd [mysql]
mkdir bin/share
cp share/english/errmsg.sys bin/share

# optional but advised to add a mysql user in a mysql group
groupadd mysql
useradd -g mysql mysql  # ok if /home/mysql does not get created

# revise my.cnf as follows
cd [mysql]
vi my.cnf
[mysqld_safe]
datadir=/local/service/sqldb
basedir=/local/mysql/bin
socket=/tmp/mysql.sock
symbolic-links=0
log-error=/local/service/sqldb/mysqld.log
pid-file=/local/service/sqldb/mysqld.pid
sql-mode=""   # ignored so spec on startup

# create / initialize the sqldb 
cd [mysql]
# for >=7.5
./bin/mysqld --initialize-insecure --defaults-file=my.cnf
./bin/mysqld_safe --defaults-file=my.cnf &
./bin/mysql -u root --skip-password
alter user "root"@"localhost" identified by "new password" # instead of using mysqladmin
set global sql_mode = ""  # if preferred over mysql_safe startup 

# for <=7.4
./scripts/mysql_install_db --user=mysql --datadir=/local/service/sqldb

# to start service (7.5+ needs sql-mode="" to revert to traditional error checking)
cd [mysql]
./bin/mysqld_safe --defaults-file=my.cnf --sql-mode="" &

# follow instructions to change password
cd [mysql]
./bin/mysqladmin -u root password 'newpassword'

# secure the database following the usual "secure initial database" procedure
mysql -u root -p 'password'
select user,host,password from mysql.user;
update mysql.user set password=password('newpassword');

# add 
# prime the database ...
create database openv;
create database app1;

cd sigma/admins/db
mysql -uroot -ppass openv <openv.sql
mysql -uroot -ppass app1 <app1.sql
mysql -uroot -ppass app1 <funcs.sql

# install pdftk
wget https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/pdftk-2.02-1.el6.x86_64.rpm
sudo yum install libgcj
sudo rpm -i pdftk*.rpm

sudo yum install libgcj
sudo rpm -i pdftk-2.02-1.*.rpm

####### end mysql

####### LEGACY atlas install
bunzip2 -c ~/dload/atlas3.10.0.tar.bz2 | tar xfm -
cd ATLAS 
mkdir build
cd build
# do not use doc example: 
../configure -b 64 -D c -DPentiumCPS=2400 --prefix=/home/jamesdb/atlas-3.10
# instead, use:
../configure -b 64 --prefix=/home/jamesdb/atlas-3.10 --shared
make build
make check
make ptcheck
make time
make install
####### atlas

# centos vbox home
# to access dns server from arcade, add 
	[Resolve]
	DNS1=82.163.142.7
	DNS2=95.211.158.134

to  /etc/systems/resolved.conf.  When rebooted this will be reflected
in the /etc/resolv.conf, and there should then be connectivity.  The
DNS addressed are discoveron the Windows via Startup | Control Panel | Network Setting | The Dom Site Guest Bridge | IPv4 | properties.

# system update
sudo yum -y update 
sudo yum -y groupinstall "Development Tools"
sudo yum -y install kernel-devel kernel-headers dkms cmake

# legacy - nvidia gpu drivers  (use cuda.run 2nd pass install only drivers)

yum install kernel-devel-$(uname -r) kernel-headers-$(uname -r)

lspci -vnn | grep VGA -A 12
# www.binarytides.com/linux-get-gpu-information
VGA compatible controller [0300]: InnoTek Systemberatung GmbH VirtualBox Graphics Adapter [80ee:beef] (prog-if 00 [VGA controller])
	Flags: bus master, fast devsel, latency 0, IRQ 11
	Memory at e0000000 (32-bit, prefetchable) [size=16M]
	Expansion ROM at <unassigned> [disabled]
	
	[80ee = vedor, beef = pci id]

# ****>>> use the -noopengl switch when installing the driver 
# to prevent desktop gnome from getting clobbered. Also
# skip the "update x11 driver" at end


sudo dmidecode -t baseboard | grep -i 'Product'

glxinfo | grep OpenGL
OpenGL vendor string: Mesa Project
OpenGL renderer string: Software Rasterizer
OpenGL version string: 2.1 Mesa 9.2.0-devel
OpenGL shading language version string: 1.20
OpenGL extensions:

modinfo nvidia

# do not do this ...
lsmod | grep -i nouveau  # these drivers are the ones we will be deleteing
sudo rpm --import https://www.elrepo.org/RPM-GPG-KEY-elrepo.org
sudo rpm -Uvh http://www.elrepo.org/elrepo-release-7.0-2.el7.elrepo.noarch.rpm
echo -e "\nblacklist nouveau\noptions nouveau modeset=0" | sudo tee -a /etc/modprobe.d/blacklist.conf

# some say this is advised:
#sudo mv -v /boot/initramfs-$(uname -r).img /boot/initramfs-$(uname -r).img.bak
#sudo dracut -v /boot/initramfs-$(uname -r).img $(uname -r)
#sudo systemctl disable gdm   # if gnome was installed 

# reboot

# dont do this ...
sudo yum install kmod-nvidia    # will take 10mins
# reboot

lsmod | grep -i nvidia     # tada

############## can install desktop (but wont work with nvidia)
#### this no longer needed if -noopengl used
sudo nvidia-xconfig
vi /etc/X11/xorg.conf
# add 'Load "glx"' to 'Section "Module"'
sudo yum install tigervnc xrdp
sudo yum group install "X Window System" "gnome desktop"
sudo systemctl enable gdm
sudo systemctl set-default graphical.target
sudo yum install tigervnc-server
sudo rpm -Uvh https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
sudo systemctl enable xrdp.service
vi /etc/systemd/system/vncserver@:1.service
# replace 2 <USER> tokens with <account> name
# ExecStart = /sbin/runuser -l <account> -c "/usr/bin/vncserver %i -geometry"
sudo systemctl start vncserver@:1.service

vi /etc/xrdp/xrdp.init
# ip = 127.0.0.1
# port = 5901
sudo systemctl start xrdp

echo -e "\nhald_enable='YES'\ndbus_enable='YES'" | sudo tee -a /etc/rc.conf
##################

#### selinux if installed
sestatus  # get status
setenforce 0  # temp disable - did not work - had to perm disable
vi /etc/sysconfig/selinux   # perm disable - set "enforcing" to "disabled"

# docker
sudo yum -y install docker docker-registry 
sudo systemctl enable docker.service  # start auto on boot
sudo systemctl start docker.service
sudo systemctl status docker.service
sudo docker pull centos
usermod -aG docker $(whoami)

# docker compose
sudo yum install epel-release  
sudo yum install -y python-pip

systemctl start docker  # starts

### dont know why i kept this
# move install rpms, zips etc to installs folder via winscp eg

####### cuda install

# cuda-nvidia compatibility: https://developer.nvidia.com/cuda-gpus
# K5000 compatibile with cuda 5.0 +

sudo sh cuda_X.X.run  # X.X=7.5 or 8.0 dont install the nvidia drivers - only the toolkit

########### nvidia install
#sudo sh cuda_X.X.run # run again - this time install only the drivers - no. instead ...
#download latest .sh nvidia drivers and install

cd /cuda/samples
make    # will take 20mins 
cd bin/x86_64/linux/release
./deviceQuery   # better work
./bandwidthTest	 # insightful info
########### end nvidia

####### end cuda

####### opencv install
# on centos 6.x we need to install opencv-2.x globally (as setting caffe Makefile.config includes/libs does not work):
# sudo yum install opencv-devel
#cp lib/libopencv* /usr/lib64   # on centos 6.x, caffe needs these copied here (despite explict override of its Makefile.config LIBRARY_DIRS)

# on centos 7.x we install opencv-3.x from downdload
cd opencv-3.x

# make sure cuda-8.0 installed as opencv defaults to these
# follow opencv.org standard install process
cd opencv
mkdir newbuild
cd newbuild
cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/local/opencv ..
make   # may get 2 errors re gpu/cuda support - ignore them - wont use these modules yet
sudo make install  # should install w/o errors - likely because it includes its own cuda drivers


######## end opencv

######## caffe install

# install caffe dependencies

sudo yum install protobuf-devel leveldb-devel snappy-devel boost-devel hdf5-devel gflags-devel glog-devel lmdb-devel python-devel


cd /local
# repack protobuf
mkdir protobuf
mkdir protobuf/include
mkdir protobuf/lib64
cd protobuf
cp -r /usr/include/google include
cp /usr/lib64/libproto* lib64

# repack boost
mkdir boost
mkdir boost/include
mkdir boost/lib64
cd boost
cp -r /usr/include/boost include
cp /usr/lib64/libboost* lib64

# repack hdf5
mkdir hdf5
mkdir hdf5/include
mkdir hdf5/lib64
mkdir hdf5/bin
cd hdf5
cp -r /usr/include/hdf5* include
cp -r /usr/include/H5* include
cp /usr/lib64/libhdf5* lib64
cp /usr/bin/h5* bin

# repack leveldb
mkdir leveldb
mkdir leveldb/include
mkdir leveldb/lib64
cd leveldb
cp /usr/include/leveldb/* include
cp /usr/lib64/libleveldb* lib64

# repack lmdb
mkdir lmdb
mkdir lmdb/include
mkdir lmdb/lib64
cd lmdb
cp /usr/include/lmdb* include
cp /usr/lib64/liblmdb* lib64

# repack glog
mkdir glog
mkdir glog/include
mkdir glog/lib64
cd glog
cp -r /usr/include/glog include
cp /usr/lib64/libglog* lib64

# repack gflags
mkdir gflags
mkdir gflags/include
mkdir gflags/lib64
cd gflags
cp -r /usr/include/gflags include
cp /usr/lib64/libgflags* lib64

# repack snappy
mkdir snappy
mkdir snappy/include
mkdir snappy/lib64
cd snappy
cp -r /usr/include/snappy* include
cp /usr/lib64/libsnappy* lib64

# atlas install
sudo yum install atlas-devel 
# centos 7.x renamed libs (cblas -> satlas and atlas -> tatlas) so need to revise caffe Makefile

# blas install centos 6.x only
# sudo yum install blas-devel
 
# repack atlas
mkdir atlas
mkdir atlas/include
mkdir atlas/lib64
cd atlas
cp -r /usr/include/atlas include   # dont think we need the x68_64 stuff
cp /usr/include/cblas* include
cp /usr/include/clapack* include
cp /usr/lib64/atlas/* lib64

# cuDNN install
unzip cuDNN-x.x  # could cp lib64/* and include/* to /usr/lib64 and /usr/include but, instead, I chose to ref these in caffe Makefile.conf via its LIBs and INCLUDEs

# setup symbolic links in /local/include and /local/lib64 for atlas, opencv, etc, for example:
cd /local/include
ln -s /local/atlas/include atlas

# caffe install
tar xvf caffe-master
mv caffe-master caffe
cd caffe
cp Makefile.config.example Makefile.config
vi Makefile.config   # adjust ...
   > CPU_ONLY := 0 # 1 if gpu-less laptop
   > USE_OPENCV := 1
   > USE_CUDNN := 1
   > USE_LMDB := 1
   > USE_LEVELD := 1
   > CUDA_DIR := /local/cuda
   > OPENCV_VERSION := 3
   > ANACONDA_HOME := $(CONDA)
   > PYTHON_LIB := $(CONDA)/lib
   > BLAS_INCLUDE := /local/atlas/include and BLAS_LIB=/local/atlas/lib64

vi Makefile # replace cblas -> satlas and altas -> tatlas on all LIBRARIES += lines

# setup paths
export BASE=/local
export CONDA=/local/anaconda
export LIB=/local/lib64

make clean
make all   # some glog and boost warnings generated
make test  # may get a few 'undefined ref to regexec'
make runtest     

# note during the make, INCLUDE_DIRS should look something like /local/atlas/include:/local/anaconda/bin:/local/include/python:/local/oxygen/bin:/opt/cmake:/local/anaconda/bin:/local/include/python:/local/oxygen/bin:/opt/cmake:/local/mysql/bin:/local/bin:/usr/bin:/local/sbin:/usr/sbin:/usr/local/share/gems/gems/jsduck-5.3.4/bin:/local/nodejs/bin:/local/include/opencv:/local/opencv/bin:/local/nodejs/bin:/local/include/opencv:/local/opencv/bin

# python interface
cd /local/caffe
make pycaffe

# we need python protobuf too (undocumented reqt)
cd /local/anaconda/bin
./pip install protobuf    # use conda's version so it installs to conda's site pkgs

# most of this may not be needed as it is provided by anaconda
cd caffe/python
for req in $(cat requirements.txt); do pip install $req; done    # some errors are generated
######## end caffe install

######## python code minifier
pip install pyminifier # --index-url= ..... (see gitadv)
# need to revise the pyminifier to reseed rvs so same var names produced. add to pyminifier the following:
# from random import seed
# seed(1234)

######## python connector for centos 7.x

#sudo rpm -Uvh mysql-connector-python-2.1.x.rpm
pip install mysql-connector-python   # better (works on 1.9.1 anaconda but not on 4.3.1 - used ver from 1.9.1)
#sudo cp -r /usr/lib/python2.7/site-packages/mysql $CONDA/lib/python2.7/site-packages
######## end python connector

# python re-direct
#cd /usr/lib
#mv python2.7 _python2.7
#ln -s /local/anaconda/lib/python2.7 python2.7
cd /local/lib64
ln -s /local/anaconda/lib/python2.7 python

# docker nvidia image
sudo usermod -aG docker jamesdb

docker run -it $VOL docker.io/centos
yum update
yum install kmod-nvidia   # see above for rpm setup.  blacklisting nouveau not needed.

# base link to /usr/local

ln -s /usr/local /local
ln -s /usr/lib64 /local/caffe/lib

# git
# install per notes-git.txt
ssh-agent  # allow service to push git cahnges w/o passwords
ssh-add ~/.ssh/id_rsa 

# putty and putty gen

wget http://pkgs.repoforge.org/rpmforge-release/rpmforge-release-0.5.3-1.el6.rf.x86_64.rpm
rpm --import http://apt.sw.be/RPM-GPG-KEY.dag.txt
sudo rpm -ivh rpmforge-release-0.5.3-1.el6.rf.x86_64.rpm
sudo yum --enablerepo=rpmforge install putty

# get putty source tar from www.chiark.greenend.org.uk/~sgtatham/putty/download.html
# is used "release" vs "develop" source.  Dev src may be better but Im ok with just fixing puttgen
# download cmdgen patch from www.itefix.net
# unpack src tar, cd into it
# following patch to add -N option "works", but does not circumvent prompt for load passphrase
# so must ssh-genkey with no passphrase, then use pathced puttygen with -N passphrase

patch cmdgen.c < cmdgen.option-N.patch
./configure
make
mv puttygen /usr/bin

# general dev tools
# yum groupinstall "Development Tools"
# service iptables start
# yum install cmake
# yum install libaio

# git install
# git config --global user.name "DEBE"
# git config --global user.email "g500xxx@trbvm.com"
# git remote add origin git@git.geointapps.org:ACME/sigma.git
# git config --global http.sslverify false
# git pull
# .ssh/id_rsa should contain private key corresponding to git public key uploaded into https://git.geointapps.org

# npm config set strict-ssl false -g   # needs to be set globally
# curl --insecure <url>

# find cert info for exmaple.com site that is failing with unsigne cert message
# openssl s_client -showcerts -connect example.com:443 < /dev/null
# then copy stuff bewteen BEGIN - END to a .crt that will get moved to /etc/ca-trust/source/anchores/exampleSite
# then sudo update-ca-trust 
#
##############
# smop matlab to python compiler
# download smop-master.zip
unzip smop-master
cd smop-master
python setup.py install --user
# to test
cd smop
python main.py smop solver.m

############
# add users to vbox share
usermod -G  vboxsf admin

# add epl to yum repo
sudo yum install epel-release

General dependencies

sudo yum install protobuf-devel leveldb-devel snappy-devel opencv-devel boost-devel hdf5-devel

Remaining dependencies, recent OS

sudo yum install gflags-devel glog-devel lmdb-devel

Remaining dependencies, if not found

# glog
wget https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/google-glog/glog-0.3.3.tar.gz
tar zxvf glog-0.3.3.tar.gz
cd glog-0.3.3
./configure
make && make install
# gflags
wget https://github.com/schuhschuh/gflags/archive/master.zip
unzip master.zip
cd gflags-master
mkdir build && cd build
export CXXFLAGS="-fPIC" && cmake .. && make VERBOSE=1
make && make install
# lmdb
git clone https://github.com/LMDB/lmdb
cd lmdb/libraries/liblmdb
make && make install

Note that glog does not compile with the most recent gflags version (2.1), so before that is resolved you will need to build with glog first.

CUDA: Install via the NVIDIA package instead of yum to be certain of the library and driver versions. Install the library and latest driver separately; the driver bundled with the library is usually out-of-date. + CentOS/RHEL/Fedora:

BLAS: install ATLAS by sudo yum install atlas-devel or install OpenBLAS or MKL for better CPU performance. For the Makefile build, uncomment and set BLAS_LIB accordingly as ATLAS is usually installed under /usr/lib[64]/atlas).

Python (optional): if you use the default Python you will need to sudo yum install the python-devel package to have the Python headers for building the pycaffe wrapper.

############ anaconda
bash ..../Anaconda-xxxx.sh
# place install at /local/anaconda-xxxx
# cd /local
# ln -s anaconda anaconda-xxxx
conda init   # post install init
conda install -c plotly plotly  # install plotly etc packages