Prerequisites¶

Installing Java¶

Dataverse should run fine with only the Java Runtime Environment (JRE) installed, but installing the Java Development Kit (JDK) is recommended so that useful tools for troubleshooting production environments are available. We recommend using Oracle JDK or OpenJDK.

The Oracle JDK can be downloaded from http://www.oracle.com/technetwork/java/javase/downloads/index.html

On a RHEL/CentOS, install OpenJDK (devel version) using yum:

# yum install java-1.8.0-openjdk-devel

If you have multiple versions of Java installed, Java 8 should be the default when java is invoked from the command line. You can test this by running java -version.

On RHEL/CentOS you can make Java 8 the default with the alternatives command, having it prompt you to select the version of Java from a list:

# alternatives --config java

If you don’t want to be prompted, here is an example of the non-interactive invocation:

# alternatives --set java /usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java

Installing Payara¶

Note: The Dataverse installer need not be run as root, and it is recommended that Payara not run as root either. We suggest the creation of a “dataverse” service account for this purpose:

# useradd dataverse

• Download and install Payara (installed in /usr/local/payara5 in the example commands below):

  # wget https://github.com/payara/Payara/releases/download/payara-server-5.2020.2/payara-5.2020.2.zip
  # unzip payara-5.2020.2.zip
  # mv payara5 /usr/local
  

If you intend to install and run Payara under a service account (and we hope you do), chown -R the Payara hierarchy to root to protect it but give the service account access to the below directories:

• Set service account permissions:

  # chown -R root:root /usr/local/payara5
  # chown dataverse /usr/local/payara5/glassfish/lib
  # chown -R dataverse:dataverse /usr/local/payara5/glassfish/domains/domain1
  

After installation, you may chown the lib/ directory back to root; the installer only needs write access to copy the JDBC driver into that directory.

• Change from -client to -server under <jvm-options>-client</jvm-options>:

  # vim /usr/local/payara5/glassfish/domains/domain1/config/domain.xml
  

This recommendation comes from http://www.c2b2.co.uk/middleware-blog/glassfish-4-performance-tuning-monitoring-and-troubleshooting.php among other places.

Launching Payara on System Boot¶

The Dataverse installation script will start Payara if necessary, but you may find the following scripts helpful to launch Payara start automatically on boot. They were originally written for Glassfish but have been adjusted for Payara.

• This Systemd file may be serve as a reference for systems using Systemd (such as RHEL/CentOS 7 or Ubuntu 16+)
• This init script may be useful for RHEL/CentOS 6 or Ubuntu >= 14 if you’re using a Payara service account, or
• This Payara init script may be helpful if you’re just going to run Payara as root (not recommended).

It is not necessary for Payara to be running before you execute the Dataverse installation script; it will start Payara for you.

Please note that you must run Payara in an English locale. If you are using something like LANG=de_DE.UTF-8, ingest of tabular data will fail with the message “RoundRoutines:decimal separator no in right place”.

Also note that Payara may utilize more than the default number of file descriptors, especially when running batch jobs such as harvesting. We have increased ours by adding ulimit -n 32768 to our Payara init script. On operating systems which use systemd such as RHEL or CentOS 7, file descriptor limits may be increased by adding a line like LimitNOFILE=32768 to the systemd unit file. You may adjust the file descriptor limits on running processes by using the prlimit utility:

# sudo prlimit --pid pid --nofile=32768:32768

Installing PostgreSQL¶

Version 9.6 is strongly recommended because it is the version developers and QA test with:

# yum install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm
# yum makecache fast
# yum install -y postgresql96-server
# /usr/pgsql-9.6/bin/postgresql96-setup initdb
# /usr/bin/systemctl start postgresql-9.6
# /usr/bin/systemctl enable postgresql-9.6

The above steps are specific to RHEL/CentOS 7. For RHEL/CentOS 8 you must install Postgres 10 or higher:

# yum install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-8-x86_64/pgdg-redhat-repo-latest.noarch.rpm
# yum makecache fast
# yum install -y postgresql10-server
# /usr/pgsql-10/bin/postgresql-10-setup initdb
# systemctl start postgresql-10
# systemctl enable postgresql-10

Note that the Dataverse installer includes its own Postgres JDBC driver. If you choose to install the newest version of Postgres (12 as of this writing), you may need to grab a current JDBC driver from https://jdbc.postgresql.org/download.html before launching the install script.

Configuring Database Access for the Dataverse Application (and the Dataverse Installer)¶

• The application and the installer script will be connecting to PostgreSQL over TCP/IP, using password authentication. In this section we explain how to configure PostgreSQL to accept these connections.

• If PostgreSQL is running on the same server as Payara, find the localhost (127.0.0.1) entry that’s already in the pg_hba.conf and modify it to look like this:

  host all all 127.0.0.1/32 md5
  

  Once you are done with the prerequisites and run the installer script (documented here: Installation) it will ask you to enter the address of the Postgres server. Simply accept the default value 127.0.0.1 there.

• The Dataverse installer script will need to connect to PostgreSQL as the admin user, in order to create and set up the database that the Dataverse will be using. If for whatever reason it is failing to connect (for example, if you don’t know/remember what your Postgres admin password is), you may choose to temporarily disable all the access restrictions on localhost connections, by changing the above line to:

  host all all 127.0.0.1/32 trust
  

  Note that this rule opens access to the database server via localhost only. Still, in a production environment, this may constitute a security risk. So you will likely want to change it back to “md5” once the installer has finished.

• If the Dataverse application is running on a different server, you will need to add a new entry to the pg_hba.conf granting it access by its network address:

  host all all [ADDRESS]      255.255.255.255 md5
  

  Where [ADDRESS] is the numeric IP address of the Payara server. Enter this address when the installer asks for the PostgreSQL server address.

• In some distributions, PostgreSQL is pre-configured so that it doesn’t accept network connections at all. Check that the listen_address line in the configuration file postgresql.conf is not commented out and looks like this:

  listen_addresses='*'
  

  The file postgresql.conf will be located in the same directory as the pg_hba.conf above.

• Important: PostgreSQL must be restarted for the configuration changes to take effect! On RHEL/CentOS 7 and similar (provided you installed Postgres as instructed above):

  # systemctl restart postgresql-9.6
  

  On MacOS X a “Reload Configuration” icon is usually supplied in the PostgreSQL application folder. Or you could look up the process id of the PostgreSQL postmaster process, and send it the SIGHUP signal:

  kill -1 PROCESS_ID
  

Supported Versions¶

Dataverse has been tested with Solr version 7.7.2. Future releases in the 7.x series are likely to be compatible; however, this cannot be confirmed until they are officially tested. Major releases above 7.x (e.g. 8.x) are not supported.

Installing Solr¶

You should not run Solr as root. Create a user called solr and a directory to install Solr into:

useradd solr
mkdir /usr/local/solr
chown solr:solr /usr/local/solr

Become the solr user and then download and configure Solr:

su - solr
cd /usr/local/solr
wget https://archive.apache.org/dist/lucene/solr/7.7.2/solr-7.7.2.tgz
tar xvzf solr-7.7.2.tgz
cd solr-7.7.2
cp -r server/solr/configsets/_default server/solr/collection1

You should already have a “dvinstall.zip” file that you downloaded from https://github.com/IQSS/dataverse/releases . Unzip it into /tmp. Then copy the files into place:

cp /tmp/dvinstall/schema*.xml /usr/local/solr/solr-7.7.2/server/solr/collection1/conf
cp /tmp/dvinstall/solrconfig.xml /usr/local/solr/solr-7.7.2/server/solr/collection1/conf

Note: Dataverse has customized Solr to boost results that come from certain indexed elements inside Dataverse, for example prioritizing results from Dataverses over Datasets. If you would like to remove this, edit your solrconfig.xml and remove the <str name="qf"> element and its contents. If you have ideas about how this boosting could be improved, feel free to contact us through our Google Group https://groups.google.com/forum/#!forum/dataverse-dev .

Dataverse requires a change to the jetty.xml file that ships with Solr. Edit /usr/local/solr/solr-7.7.2/server/etc/jetty.xml , increasing requestHeaderSize from 8192 to 102400

Solr will warn about needing to increase the number of file descriptors and max processes in a production environment but will still run with defaults. We have increased these values to the recommended levels by adding ulimit -n 65000 to the init script, and the following to /etc/security/limits.conf:

solr soft nproc 65000
solr hard nproc 65000
solr soft nofile 65000
solr hard nofile 65000

On operating systems which use systemd such as RHEL or CentOS 7, you may then add a line like LimitNOFILE=65000 for the number of open file descriptors and a line with LimitNPROC=65000 for the max processes to the systemd unit file, or adjust the limits on a running process using the prlimit tool:

# sudo prlimit --pid pid --nofile=65000:65000

Solr launches asynchronously and attempts to use the lsof binary to watch for its own availability. Installation of this package isn’t required but will prevent a warning in the log at startup:

# yum install lsof

Finally, you need to tell Solr to create the core “collection1” on startup:

echo "name=collection1" > /usr/local/solr/solr-7.7.2/server/solr/collection1/core.properties

Solr Init Script¶

Please choose the right option for your underlying Linux operating system. It will not be necessary to execute both!

For systems running systemd (like CentOS/RedHat since 7, Debian since 9, Ubuntu since 15.04), as root, download solr.service and place it in /tmp. Then start Solr and configure it to start at boot with the following commands:

cp /tmp/solr.service /etc/systemd/system
systemctl daemon-reload
systemctl start solr.service
systemctl enable solr.service

For systems using init.d (like CentOS 6), download this Solr init script and place it in /tmp. Then start Solr and configure it to start at boot with the following commands:

cp /tmp/solr /etc/init.d
service start solr
chkconfig solr on

Securing Solr¶

Our sample init script and systemd service file linked above tell Solr to only listen on localhost (127.0.0.1). We strongly recommend that you also use a firewall to block access to the Solr port (8983) from outside networks, for added redundancy.

It is very important not to allow direct access to the Solr API from outside networks! Otherwise, any host that can reach the Solr port (8983 by default) can add or delete data, search unpublished data, and even reconfigure Solr. For more information, please see https://lucene.apache.org/solr/guide/7_3/securing-solr.html. A particularly serious security issue that has been identified recently allows a potential intruder to remotely execute arbitrary code on the system. See RCE in Solr via Velocity Template for more information.

If you’re running your Dataverse instance across multiple service hosts you’ll want to remove the jetty.host argument (-j jetty.host=127.0.0.1) from the startup command line, but make sure Solr is behind a firewall and only accessible by the Dataverse web application host(s), by specific ip address(es).

We additionally recommend that the Solr service account’s shell be disabled, as it isn’t necessary for daily operation:

# usermod -s /sbin/nologin solr

For Solr upgrades or further configuration you may temporarily re-enable the service account shell:

# usermod -s /bin/bash solr

or simply prepend each command you would run as the Solr user with “sudo -u solr”:

# sudo -u solr command

Finally, we would like to reiterate that it is simply never a good idea to run Solr as root! Running the process as a non-privileged user would substantially minimize any potential damage even in the event that the instance is compromised.

Installing jq¶

jq is a command line tool for parsing JSON output that is used by the Dataverse installation script. It is available in the EPEL repository:

# yum install epel-release
# yum install jq

or you may install it manually:

# cd /usr/bin
# wget http://stedolan.github.io/jq/download/linux64/jq
# chmod +x jq
# jq --version

Installing and configuring ImageMagick¶

On a Red Hat and similar Linux distributions, you can install ImageMagick with something like:

# yum install ImageMagick

(most RedHat systems will have it pre-installed). When installed using standard yum mechanism, above, the executable for the ImageMagick convert utility will be located at /usr/bin/convert. No further configuration steps will then be required.

On MacOS you can compile ImageMagick from sources, or use one of the popular installation frameworks, such as brew.

If the installed location of the convert executable is different from /usr/bin/convert, you will also need to specify it in your Payara configuration using the JVM option, below. For example:

<jvm-options>-Ddataverse.path.imagemagick.convert=/opt/local/bin/convert</jvm-options>

(see the Configuration section for more information on the JVM options)

Installing R¶

Can be installed with yum:

yum install R-core R-core-devel

EPEL distribution is strongly recommended. The version of R currently available from epel6 and epel7 is 3.5; it has been tested and is known to work on RedHat and CentOS versions 6 and 7.

If yum isn’t configured to use EPEL repositories ( https://fedoraproject.org/wiki/EPEL ):

RHEL/CentOS users can install the RPM epel-release. For RHEL/CentOS 7:

yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm

RHEL/CentOS users can install the RPM epel-release. For RHEL/CentOS 6:

yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-6.noarch.rpm

RHEL users will want to log in to their organization’s respective RHN interface, find the particular machine in question and:

• click on “Subscribed Channels: Alter Channel Subscriptions”
• enable EPEL, Server Extras, Server Optional

Installing the required R libraries¶

The following R packages (libraries) are required:

R2HTML
rjson
DescTools
Rserve
haven

Install them following the normal R package installation procedures. For example, with the following R commands:

install.packages("R2HTML", repos="https://cloud.r-project.org/", lib="/usr/lib64/R/library" )
install.packages("rjson", repos="https://cloud.r-project.org/", lib="/usr/lib64/R/library" )
install.packages("DescTools", repos="https://cloud.r-project.org/", lib="/usr/lib64/R/library" )
install.packages("Rserve", repos="https://cloud.r-project.org/", lib="/usr/lib64/R/library" )
install.packages("haven", repos="https://cloud.r-project.org/", lib="/usr/lib64/R/library" )

Rserve¶

Dataverse uses Rserve to communicate to R. Rserve is installed as a library package, as described in the step above. It runs as a daemon process on the server, accepting network connections on a dedicated port. This requires some extra configuration and we provide a script (scripts/r/rserve/rserve-setup.sh) for setting it up. Run the script as follows (as root):

cd <DATAVERSE SOURCE TREE>/scripts/r/rserve
./rserve-setup.sh

The setup script will create a system user rserve that will run the daemon process. It will install the startup script for the daemon (/etc/init.d/rserve), so that it gets started automatically when the system boots. This is an init.d-style startup file. If this is a RedHat/CentOS 7 system, you may want to use the rserve.service systemd unit file instead. Copy it into the /usr/lib/systemd/system/ directory, then:

# systemctl daemon-reload
# systemctl enable rserve
# systemctl start rserve

Note that the setup will also set the Rserve password to “rserve”. Rserve daemon runs under a non-privileged user id, so there’s not much potential for security damage through unauthorized access. It is however still a good idea to change the password. The password is specified in /etc/Rserv.pwd. You can consult Rserve documentation for more information on password encryption and access security.

You should already have the following 4 JVM options added to your domain.xml by the Dataverse installer:

<jvm-options>-Ddataverse.rserve.host=localhost</jvm-options>
<jvm-options>-Ddataverse.rserve.port=6311</jvm-options>
<jvm-options>-Ddataverse.rserve.user=rserve</jvm-options>
<jvm-options>-Ddataverse.rserve.password=rserve</jvm-options>

If you have changed the password, make sure it is correctly specified in the dataverse.rserve.password option above. If Rserve is running on a host that’s different from your Dataverse server, change the dataverse.rserve.host option above as well (and make sure the port 6311 on the Rserve host is not firewalled from your Dataverse host).

Installing Counter Processor¶

Counter Processor has only been tested on el7 (see “Linux” above). Please note that a scripted installation using Ansible is mentioned in the Make Data Count section of the Developer Guide.

As root, download and install Counter Processor:

cd /usr/local
wget https://github.com/CDLUC3/counter-processor/archive/v0.0.1.tar.gz
tar xvfz v0.0.1.tar.gz

As root, change to the Counter Processor directory you just created, download the GeoLite2-Country tarball, untar it, and copy the geoip database into place:

cd /usr/local/counter-processor-0.0.1
wget https://geolite.maxmind.com/download/geoip/database/GeoLite2-Country.tar.gz
tar xvfz GeoLite2-Country.tar.gz
cp GeoLite2-Country_*/GeoLite2-Country.mmdb maxmind_geoip

As root, create a “counter” user and change ownership of Counter Processor directory to this new user:

useradd counter
chown -R counter:counter /usr/local/counter-processor-0.0.1

Installing Counter Processor Python Requirements¶

Counter Processor requires Python 3.6.4 or higher. The following commands are intended to be run as root but we are aware that Pythonistas might prefer fancy virtualenv or similar setups. Pull requests are welcome to improve these steps!

Enable the EPEL repo if you haven’t already:

yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm

Install Python 3.6:

yum install python36

Install Counter Processor Python requirements:

python3.6 -m ensurepip
cd /usr/local/counter-processor-0.0.1
pip3 install -r requirements.txt

See the Make Data Count section of the Admin Guide for how to configure and run Counter Processor.