NetDRMS Installation » History » Version 212

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Pablo Alingery, 07/06/2016 14:52

Table of contents
NetDRMS Installation

NetDRMS Installation¶

Requirements¶

Configuring production environment¶

Adding user production (en root)

# adduser production
# addgroup ias
# adduser production ias

Configure /home/production/.profile¶

Adding environment variables

#Modif Herve.B Pablo.A 12/05/2016

PATH="/usr/local/netdrms_current/bin/linux_x86_64:$PATH" 
PATH="/usr/local/netdrms_current/scripts:$PATH" 
PATH="/usr/local/jmd/bin:$PATH" 
PATH="/usr/local/jmd/scripts:$PATH" 
#The following is not needed as installed with 'apt-get install' 
#PATH="/usr/local/pgsql/bin:$PATH" 
PATH="/usr/local/netdrms-tools/scripts:$PATH" 
#2014-12-17 Avec Herve et Pablo on pense que la ligne suivante est intutile as it is f.. install in /usr/local/lib
PATH="/usr/local/cfitsio:$PATH" 
#Done

DERBY_HOME=/usr/local/jmd/databases/derby/derbyBD
export DERBY_HOME

export CVSROOT=:pserver:anonymous@solarch.tuc.noao.edu:2401/vtarc1/vso/cvsroot

Configure /varl/lib/postgres/.profile¶

Add to $PATH so postgres can exeute command like initdb

#Modif Herve.B Pablo.A 19/05/2016
PATH="/usr/lib/postgresql/9.4/bin:$PATH"

Setting privileges for SUMS_MANAGER¶

Please modify file /etc/sudoers so user 'production' will be able to execute 'sum_chown' that we will locate in the dir : /usr/local/bin . See below
Add to /etc/sudoers the following line :
production host=NOPASSWD:/usr/local/bin/sum_chmown

Set passwords file for db postgres¶

Please create file .pgpass with the following information for user 'production" so he will be able to connect without password as 'production' or 'postgres' to 2 db that we will create later ias_sdo and ias_sdo_sums.

.pgpass content :

    #hostname:5432:ias_sdo:production: 
    #hostname:5434:ias_sdo_sums:production: 
    #hostname:5432:ias_sdo:postgres: 
    #hostname:5434:ias_sdo_sums:postgres

where #hostname is the name of your server

WARNING : change hostname when migrate sdo-new to sdo

Install missing libraries¶

• libreadline-dev (but already installed with postgresql)
• libssl-dev
• libpam0g-dev
• libperl-dev

NB : Already done in Debian 8.4 Jessy

# apt-get install $library_name

where
$library_name is the name of library

Then to update path on libraries, please type :

# ldconfig

Reconfigure locale¶

# dpkg-reconfigure locales

select fr_FR.UTF8 UTF8 and unselect en_US.UTF-8

localedef -i en_US -f UTF-8 en_US.UTF-8

(see here : [[http://www.thomas-krenn.com/en/wiki/Perl_warning_Setting_locale_failed_in_Debian]])

Install gfortran packages¶

# apt-get install gfortran swig

Installation of cfitsio library¶

In /usr/local dir

Version 3.39 (currently on sdo : 3.24)

# wget ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/cfitsio3390.tar.gz

Untar and decompression

# tar -xzvf cfitsio3390.tar.gz

Go into /usr/local and type

su - root and :

# ./configure --prefix=/usr/local
# make 
# make install

Installation of apache2 and lib perl¶

# apt-get install apache2

# apt-get install libjson-perl

# apt-get install libapache2-mod-perl2

Installation of postgresql¶

Into 'root'

apt-get install postgresql-9.4 postgresql-client-9.4

Installation python3¶

Into 'root'

apt-get install python3

Add some modules psycopg2 (postgres connector) and pySmartDL (Download manager)

apt-get install python3-psycopg2

apt-get install python3-psycopg2

Add python3-pip for modules within python3

apt-get install python3-pip

pip3 install pySmartDL

NetDRMS databases¶

into /var/lib/postgresql (hard mount point separated, 7 disks 15000 tr/min in raid5 in order to distribute read and write)

# cd /var/lib/postgresql
# mkdir data  data_sums data_monitor
# chown -R postgres:postgres *

Initialize 3 servers data, data_sums, data_monitor¶

Into postgres

# su - postgres

$ initdb --locale=C -D data -A md5 -W
(no password)

Success. You can now start the database server using:

    postgres -D data
or
    pg_ctl -D data -l logfile start

$ initdb --locale=C -D data_sums -A md5 -W
(no password)

Success. You can now start the database server using:

    postgres -D data_sums
or
    pg_ctl -D data_sums -l logfile start

$ initdb --locale=C -D data_monitor -A md5 -W
(no password)

Success. You can now start the database server using:

    postgres -D data_monitor
or
    pg_ctl -D data_monitor -l logfile start

Edition des fichiers postgresql.conf pour configurer les bons ports d'écoute :
listen_addresses = '*'
data -> port 5432
data_sums -> port 5434
data_monitor -> port 5436

Edit files data*/pg_hba.conf : replace 'md5' by 'trust'

#"local" 
local   all             all                                     trust
#"IPv4" 
host   all             all                                     trust

Tunning postgres¶

In file postgres.conf ( according to https://www.qwant.com/?q=Tunning+postgres+server+9.4+&client=firefox )

shared_buffer=4096MB So 1/12 of the total RAM memory available

work_mem = 24MB

maintenance_work_mem = 4096MB

wal_buffers = 16MB

checkpoint_segments = 32

checkpoint_completion_target = 0.9

random_page_cost = 1.0

effective_cache_size = 16384MB so 1/4 of the max memory

#log
logging_collector = on
log_directory = 'pg_log'
log_filename = 'postgresql-%Y-%m-%d_%H%M%S.log' # log file name pattern,
log_truncate_on_rotation = on # If on, an existing log file with the
log_rotation_age = 1d # Automatic rotation of logfiles will
client_min_messages = error
log_min_messages = error
log_min_duration_statement = 0

log_connections = on
log_disconnections = on
log_duration = off
log_hostname = on
log_line_prefix = '%t [%p]: %u@%h - %d :'

track_counts = on
autovacuum = on

extra_float_digits = 3

Start the 3 databases :¶

# su - postgres
$ cd /var/lib/postgresql
$ pg_ctl -D data  start
$ pg_ctl -D data_sums start
$ pg_ctl -D data_monitor start

Create the 3 databases :¶

Into user 'postgres'

createdb --locale C -E LATIN1 -T template0 ias_sdo
createdb --locale C -E LATIN1 -T template0 -p 5434 ias_sdo_sums
createdb --locale C -E LATIN1 -T template0 -p 5436 ias_sdo_monitor

Automatic startup¶

Add following lines in the /etc/rc.local file :

su -l -c "/usr/lib/postgresql/9.4/bin/pg_ctl -D /var/lib/postgresql/data start" postgres
su -l -c "/usr/lib/postgresql/9.4/bin/pg_ctl -D /var/lib/postgresql/data_sums start" postgres
su -l -c "/usr/lib/postgresql/9.4/bin/pg_ctl -D /var/lib/postgresql/data_monitor start" postgres

System tuning¶

Current configuration :

# sysctl -a

In the following file :

# vi /etc/sysctl.conf

we change some values (default values are commented with '#')

(resources links here)

# Semaphore is a object that is used to control utilization of a particular process.
# kernel.sem = SEMMSL SEMMNS SEMOPM SEMMNI
# SEMMSL maximum number of semaphores per array (min 128)
# SEMMNS maximum semaphores system-wide
# SEMOPM maximum operations per semop call
# SEMMNI maximum arrays
#semop incresed from 32 (default value)operation to 100 (3rd value )
# kernel.sem = 250 32000 32 128
kernel.sem = 250 32000 100 128

In order to apply changes :#This sets the OS receive buffer size for all types of connections (default value 212992)
#net.core.rmem_default = 212992
#net.core.rmem_max = 212992
net.core.rmem_default = 33554432
net.core.rmem_max = 33554432

#This is the OS send buffer size for all types of connections (212992 default value)
#net.core.wmem_default = 212992
#net.core.wmem_max = 212992
net.core.wmem_default = 33554432
net.core.wmem_max = 33554432

#TCP Autotuning setting. "The first value tells the kernel the minimum receive buffer for each TCP connection, and this buffer is always
# allocated to a TCP socket, even under high pressure on the system. ... The second value specified tells the kernel the default receive
# buffer allocated for each TCP socket. This value overrides the /proc/sys/net/core/rmem_default value used by other protocols. ...
# The third and last value specified in this variable specifies the maximum receive buffer that can be allocated for a TCP socket."
#net.ipv4.tcp_rmem = 4096 87380 6291456
net.ipv4.tcp_rmem = 10240 87380 33554432

#TCP Autotuning setting. "This variable takes 3 different values which holds information on how much TCP sendbuffer memory space
# each TCP socket has to use. Every TCP socket has this much buffer space to use before the buffer is filled up. Each of the three
#values are used under different conditions. ... The first value in this variable tells the minimum TCP send buffer space available
# for a single TCP socket. ... The second value in the variable tells us the default buffer space allowed for a single TCP socket to use. ...
#The third value tells the kernel the maximum TCP send buffer space."
#net.ipv4.tcp_wmem = 4096 16384 4194304
net.ipv4.tcp_wmem = 10240 87380 33554432

#Disable cache metrics so the initial conditions of the closed connections will not be saved to be used in near future connections
#net.ipv4.tcp_no_metrics_save = 0
net.ipv4.tcp_no_metrics_save = 1

# Increase number of incoming connections backlog
# net.core.netdev_max_backlog = 1000
net.core.netdev_max_backlog = 5000

# The tcp_mem variable defines how the TCP stack should behave when it comes to memory usage. ...
#The first value specified in the tcp_mem variable tells the kernel the low threshold.
#Below this point, the TCP stack do not bother at all about putting any pressure on the memory usage by different TCP sockets. ...
#The second value tells the kernel at which point to start pressuring memory usage down. ... The final value tells the kernel how many
# memory pages it may use maximally
# net.ipv4.tcp_mem = 1543347 2057796 3086694
net.ipv4.tcp_mem = 786432 1048576 26777216

# local port range that is used by TCP and UDP traffic to choose the local port. You will see in the parameters of this file two numbers:
# The first number is the first local port allowed for TCP and UDP traffic on the server, the second is the last local port number.
# net.ipv4.ip_local_port_range = 32768 61000
net.ipv4.ip_local_port_range = 1024 65535

# maximum number of sockets in TIME-WAIT to be held simultaneously.
# net.ipv4.tcp_max_tw_buckets = 262144
net.ipv4.tcp_max_tw_buckets = 360000

Then we run the following command to make our change take effect:

# sysctl -p

NetDRMS tool Install¶

The following installed is based on : [[http://inf-redmine.ias.u-psud.fr/redmine/attachments/download/114/Netdrms_First_Install.odt]]

The sources are in : http://jsoc.stanford.edu/netdrms/dist/
Locally on sdo-new in : /home/production/sources

Symbolic link created 'netdrms_current' that corresponds to the last release
ln -s netdrms_8.10/ netdrms_current

Edit file config.local

cp config.local.template config.local

Warning WEB_DBUSER apache We think that it should value www maybe , to be checked testing the cgi
So check the cgi to figure out which user is used to connect to bd

Create 2 followings dirs :

mkdir /usr/local/netdrms_8.10/logs/SUM
mkdir /usr/local/netdrms_8.10/logs/slony

Warning config.local from line 150 =>222 Remote config to provide data, series to externals
To be checked for PLATO

Création d'un alias netdrms dans /root/.bashrc

alias netdrms='cd /usr/local/netdrms_current'

In config.local we are at line 223
------------------------------------------------------------------------------------------------------------------

Modification du fichier /usr/local/netdrms_current/configure (Not Applied in NetDrms_8.10)¶

# The system configuration for configure script
set PERLBIN = "/usr/bin/perl" 
set PYBIN = "/usr/bin/python"

Compilation problem due to uncorrect variable types¶

Art (art.amezcua@stanford.edu) purpose us a workaround and send us 2 files with correct declaration :

SUMLIB_RmDo.pgc (diff with original file : diff_SUMLIB_RmDo.pgc)
SUMLIB_RmDoX.pgc (diff with original file : diff_SUMLIB_RmDoX.pgc)

Dans le répertoire base/sums/libs/pg renommer les anciens en *.orig et placer les nouveau fichiers SUMLIB_RmDo.pgc et SUMLIB_RmDoX.pgc

# wget http://jsoc.stanford.edu/~arta/SUMLIB_RmDo.pgc
# wget http://jsoc.stanford.edu/~arta/SUMLIB_RmDoX.pgc

Modification du fichier /usr/local/netdrms_current/build/jsoc_machine.csh¶

ligne 28 :

  case "x86_64":
      echo linux_x86_64
      breaksw

Overwriting the existing files in the right place (base/sums/libs/pg) & modif in jsoc_machine.csh
=> the command 'make' works well.

But there is still problem with 'make sums'

Workaround to solve make sums problem¶

Modify sum_rpc.h in order to match the type of some variables

Copier /usr/local/netdrms_2.4_release/base/drms/apps/serverdefs.h dans /usr/local/netdrms_current/base/drms/apps (not applied in NetDrms_8.10)¶

Modification du fichier /usr/local/netdrms_current/configure (not applied in NetDrms_8.10)¶

au lieu de $? en csh on va mettre plutot $status

ligne 110 :

  if ($status==0)

et ligne 123 :

  if ($status==0)

Lancement :

./configure

Installation des libraries libtar-dev, libcurl3-dev et libecpg-dev¶

apt-get install libtar libtar-dev

apt-get install libcurl3-dev

apt-get install libecpg-dev

#H4ck 2 Malade #PabloR0cks# (Not Applied in NetDrm_8.10)¶

Modification du fichier /usr/include/stdint.h

ligne 55 : long int remplacé par long long int

#if __WORDSIZE == 64
typedef unsigned long int       uint64_t; --> ici long long int
#else
__extension__
typedef unsigned long long int  uint64_t;
#endif

"Allo Linus ?!?.."

Compilation¶

# make
# make sums
# make jsoc_fetch

NB : lib64 does not exist on debian 8. so ln -s /usr/lib lib64

make sums KO (Not applied in NetDrms_8.10)¶

Solution found : Take old lib libcrypto instead libssl

dans le fichier base/sums/apps/Rules.mk ligne 51
replace -lssl by -lcrypto LD flag

NetDRMS replication¶

# cd base/drms/replication/etc
# scp production@sdo:/usr/local/netdrms/install-config-files/ias.subscribe_list.cfg  .
# scp production@sdo:/usr/local/netdrms/install-config-files/ias.repclient.cfg  .
WRONG !!!!!
To be done cp repclient.template.cfg into ias.subscribe_list.cfg because new field in config file can't appear 
Correct that step in NetDrms doc 
The existing ias.repclient.cfg can be used tough to fill params

Create tmp dir in netdrms working directory (/usr/local/netdrms_current)

# mkdir tmp

Prevent from deleting files

cd logs/SUM ; scp production@sdo:/usr/local/netdrms/install-config-files/sum_rm.cfg .

JMD installation¶

Donwnload new JMD package build by Niles Oien 2016-04-07 following thoses actions :

cd /urs/local

[oien@spsc-nso19-12 ~]$ ftp gong2.nso.edu
Name (gong2.nso.edu:oien): anonymous
Password: <---------------- use your email as the password
ftp> cd outgoing/oien
ftp> get pablo_jmd.tar.gz
ftp> quit

Install new JMD package following thoses actions

[oien@spsc-nso19-12 ~]$ gunzip -vf pablo_jmd.tar.gz
pablo_jmd.tar.gz:      8.3% -- replaced with pablo_jmd.tar
[oien@spsc-nso19-12 ~]$ tar xf pablo_jmd.tar
[oien@spsc-nso19-12 ~]$ cd pablo_jmd
[oien@spsc-nso19-12 pablo_jmd]$ less PABLO_README.txt
cd ..
mv jmd jmd_old
mv pablo_jmd jmd

JMD Configuration¶

Configure webserver to request jsoc_fetch
(following the mail from nilesoien@gmail.com)

config d 'apache2 fichier sdo3.ias.u-psud.fr


<VirtualHost *:80>
        ServerName sdo3.ias.u-psud.fr
        ServerAdmin pablo.alingery@ias.u-psud.fr
        #ErrorLog /var/log/apache2/error.log
        DocumentRoot /var/www

        # Possible values include: debug, info, notice, warn, error, crit,
        # alert, emerg.
        LogLevel debug

        #CustomLog /var/log/apache2/VSO/access.log combined

        Alias /VSO/DRMS/cgi-bin/ "/home/production/netdrms-tools/scripts/cgi-bin/" 

        <Location /VSO/DRMS/cgi-bin>
                SetHandler perl-script
                PerlResponseHandler ModPerl::Registry
                PerlOptions +ParseHeaders
                Options +ExecCGI
                Order allow,deny
                Allow from all
        </Location>
</VirtualHost>

Execution test cgi with URL :
http://sdo3.ias.u-psud.fr/ VSO/DRMS/cgi-bin/vso_jsoc_fetch.cgi

expected result :

{
   "wait" : 0,
   "requestid" : "",
   "data" : {},
   "method" : "url_quick",
   "size" : 0,
   "errormsg" : "Empty query",
   "protocol" : "as-is",
   "status" : 1,
   "space_ratio" : 0.1,
   "load_ratio" : 0.066875,
   "dir" : "",
   "count" : 0
}

NetDRMS Start script¶

sum_start.NetDRMS

Database repair (from Art)¶

On ias_sdo

delete from admin.ns where name = 'lm_jps';
delete from admin.ns where name = 'aia_test';

Private key Public key generation¶

ssh-keygen -t rsa

Not necessary cause we recover the ssh keys of the current server.

However, we have to retrieve the private key of production account on sdo3

From sdo :

rsync -av id_rsa production@sdo3:/home/production/.ssh/

Node definition¶

file : /usr/local/netdrms_current/base/drms/replication/etc/ias.repclient.cfg

node=IAStest

show_series and delete_series binaries¶

Remark : these 2 sources are not compiled during installation
Issue : in netdrms_current 8.10 , do :
$ make delete_series
$ make show_series

SSH-HPN install¶

Intallation de openssh 6.3p1 car le dernier patch hpn dispo est 6.3hpn13.V6

web site for open ssh : http://ftp2.fr.openbsd.org/pub/OpenBSD/OpenSSH/portable/openssh-6.3p1.tar.gz
patch hpn : http://www.psc.edu/index.php/hpn-ssh-patches/hpn-14-kitchen-sink-patches/viewdownload/24-hpn-14-kitchen-sink-patches/102-openssh-6-3p1-hpnssh14v2-kitchen-sink-patch

# tar -xzvf openssh-6.3p1.tar.gz
# gunzip openssh-6.3p1-hpnssh14v2.diff.gz
# cd openssh-6.3p1
# zcat ../openssh-6.3p1-hpnssh14v2.diff.gz | patch -p1
# ./configure --prefix=/usr/local/hpn-ssh --with-pam --with-md5-passwords --without-zlib-version-check --with-tcp-wrappers
# make
# make install

Depuis sdo :

# cd /usr/local/hpn-ssh/etc/
# rsync -av *key* netadm@sdo3:/home/netadm/

Sur sdo3 :

rsync -av /home/netadm/*key* /usr/local/hpn-ssh/etc/

We have to configure the port number to 55000

# vi ssh_config

and add :

#Port 22
Port 55000

We configure also the server hpn (even we don't use it yet)

# vi sshd_config

and add :

#Port 22
Port 55000

#PidFile /var/run/sshd.pid
PidFile /var/run/sshd.55000.pid

# allow the use of the none cipher
#NoneEnabled no
NoneEnabled yes

Correction¶

Modification du fichier ias.repclient.cfg¶

Copier le template existant repclient.template.cfg dans le répertoire [netdrms_current]/base/drms/replication/etc

production@sdo3:/usr/local/netdrms_current/base/drms/replication/etc$ cp repclient.template.cfg ias.repclient.cfg

Nouveau / netdrms2.4

# Apps
kRSPerl=<path to Perl binary to use when Perl scripts are executed>

Subscription test¶

Librairies manquantes¶

Errors

Failure to apply SQL file 'IAStest.subscribe_series.sql' from server: ABORTING!
Can't locate DBI.pm 
.
.
.
Failure to apply SQL file 'IAStest.subscribe_series.sql' from server: ABORTING!
Can't locate DBD/Pg.pm

root@sdo3:/usr/local/netdrms_8.10/base/drms/replication/subscribe_series# apt-get install libdbi-perl 
root@sdo3:/usr/local/netdrms_8.10/base/drms/replication/subscribe_series# apt-get install libdbd-pg-perl

Series souscrites¶

hmi.sharp_720s_nrt
hmi.mharp_720s_nrt
hmi.bharp_720s_nrt

production@sdo3:~$ show_info -s hmi.sharp_720s_nrt
First Record: hmi.sharp_720s_nrt[476][2012.09.14_02:12:00_TAI], Recnum = 829707
Last Record:  hmi.sharp_720s_nrt[4943][2016.03.22_18:24:00_TAI], Recnum = 2015202
Last Recnum:  2015202
Has shadow table: no

Lancement de jetty¶

$ jetty.sh start

Test recuperation de meta data¶

librairies manquantes
apt-get install libnet-ssh-perl
apt-get install libstring-shellquote-perl

TO BE DONE FURTHER¶

configure sytem nbr de fichier ouvert en meme temps

configure sytem taille buffer

swap désactivé ? discussion Stephane et Gilles

Modification du fichir config.local pour la souscription au jsoc¶

# NetDRMS users can request subdirectories from the Stanford proj directories 
# (e.g., JSOC/proj/util). These users will need to contact Stanford and obtain
# the source subdirectories desired. They will then place these subdirectories
# in the JSOC/proj directory of their NetDRMS release. To properly build 
# targets in these subdirectories, using the JSOC make system, the user needs
# to add entries to this configuration file - one entry for each subdirectory
# that contains source code to be compiled. Each entry is a space-separated pair
# of strings: the string "PROJDIR" followed by a subdirectory (of the proj 
# directory).  For example:
#
# PROJDIR     util/apps
# PROJDIR     util/libs
# 
# NOTE: It is not sufficient to list only a parent directory, like util. Source code
# in child directories will not automatically be compiled.

Python library for multi-threaded SUMS¶

Installation de la librairie python3.4m

Files

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