install i2b2 using the quickstart method described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989048/

[Li Li]

Hi, all,

I am new to i2b2 and tried to install i2b2 using the quickstart method described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989048/ on centos 7. but I am getting this error:

[root@i2b2 ~]# git clone https://github.com/waghsk/i2b2-quickstart.git
Cloning into 'i2b2-quickstart'...
remote: Counting objects: 7476, done.
remote: Total 7476 (delta 0), reused 0 (delta 0), pack-reused 7476
Receiving objects: 100% (7476/7476), 122.85 MiB | 30.00 MiB/s, done.
Resolving deltas: 100% (3857/3857), done.
[root@i2b2 ~]# git checkout qspaper1.0
fatal: Not a git repository (or any of the parent directories): .git

Anyone has any suggestions or comments?

Thanks,

-Li

[Kavishwar Wagholikar]

Li,

That's an error in the script:

Can you try running the following?

sudo yum -y install git wget unzip patch bzip2 screen

export IP_ADDRESS=[external IP ADDRESS or hostname]

git clone  https://github.com/waghsk/i2b2-quickstart.git

cd i2b2-quickstart

git checkout tags/qspaper1.0

sudo sh scripts/install/centos_first_install.sh $IP_ADDRESS 2>&1|tee first.log

kavi

--
You received this message because you are subscribed to the Google Groups "i2b2 Install Help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to i2b2-install-h...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Li Li]

Hi Kavi,

Thanks for your quick response! That got past the "git checkout tags/qspaper1.0" step, however the last step ran into some issues, as shown below:

  xalan-j2.noarch 0:2.7.1-23.el7
  xerces-j2.noarch 0:2.11.0-17.el7_0
  xml-commons-apis.noarch 0:1.4.01-16.el7
  xml-commons-resolver.noarch 0:1.2-15.el7
  xorg-x11-font-utils.x86_64 1:7.5-20.el7
  xorg-x11-fonts-Type1.noarch 0:7.5-9.el7

Complete!
setenforce: SELinux is disabled
Redirecting to /bin/systemctl stop iptables.service
Failed to stop iptables.service: Unit iptables.service not loaded.
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: mirror.oss.ou.edu
 * extras: mirror.oss.ou.edu
 * updates: repos-tx.psychz.net
Package 1:java-1.8.0-openjdk-devel-1.8.0.181-3.b13.el7_5.x86_64 already installed and latest version
Nothing to do
sudo: unknown user: bash
sudo: unable to initialize policy plugin
Note: Forwarding request to 'systemctl enable httpd.service'.
Created symlink from /etc/systemd/system/multi-user.target.wants/httpd.service to /usr/lib/systemd/system/httpd.service.
Redirecting to /bin/systemctl start httpd.service
setsebool:  SELinux is disabled.
BASE_CORE:/root/i2b2-quickstart/unzipped_packages
 webclient source not found

Thanks for your help!

-Li

[Kavishwar Wagholikar]

Possibly the errors are due to missing packages in the centos7 installation:

Are you using centos7 instances in aws?

Some more details on the testing we did can be found at : https://github.com/waghsk/i2b2-quickstart/wiki/Installation-and-Test-Platforms

I would also recommend exploring i2b2-docker:

https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-018-0646-2

[Li Li]

Hi Kavi,

Thanks! I missed "sudo" in the final step of  "sudo sh scripts/install/centos_first_install.sh $IP_ADDRESS 2>&1|tee first.log". Once I did that, it was working! Do have a question: If I control+C and get out of my ssh session to the server, then when I go to http://hostname/webclient to login, I get a pop up window saying: "The PM Cell is down or the address in the properties file is incorrect". I tried screen and nohup with "sudo sh scripts/install/centos_first_install.sh $IP_ADDRESS 2>&1|tee first.log", neither kept the system up after my control + c.

Thanks,

-Li

[Kavishwar Wagholikar]

Just use screen and do not use nohup, and let me know if it works.

[Li Li]

Hi Kavi,

I tried screen, and it didn't work. My OS is Centos 7.5 if that matters.

Thanks,

-Li

[Kavishwar Wagholikar]

Do you run screen and obtain a command prompt, before running the install script commands?

After you ctrl-X your ssh screen:

1 open a new terminal 

2. run screen -ls, to find the id of the original screen, and

3. the reattach to it using screen -r [id]

[Li Li]

Yes, I did run "screen" before running the install script command. The problem appears to be "ctrl + c" stops the java process, as shown below:

1. I open 2 ssh sessions, 1st session, I run all your steps to get i2b2 installed, all appears to be working fine, and I can login to http://hostname/webclient

2. in my 2nd ssh session, I can see below:

[root@i2b2 ~]# screen -ls
There is a screen on:
        1353.pts-0.i2b2 (Attached)
1 Socket in /var/run/screen/S-root.
[root@i2b2 ~]# w
 15:46:16 up 40 min,  2 users,  load average: 0.09, 0.08, 0.21
USER     TTY      FROM             LOGIN@   IDLE   JCPU   PCPU WHAT
root     pts/1    li-vdi2:S.0      15:07   38:24   1:25  58.74s java -D[Standalone] -server -XX:+UseCompressedOops -server -XX:+UseCompressedOops -Xms64m -Xmx512m -XX:MaxPermSize=256m -Djava.net.preferIPv4Stack
root     pts/2    li-vdi2.net.ou.e 15:44    0.00s  0.04s  0.01s w
[root@i2b2 ~]#

3. Now from my 1st session, I do "ctrl + c", once I did that, I could NO LONGER login with webclient. then from my 2nd session, I saw the java process is gone:

[root@i2b2 ~]# w
 15:47:34 up 41 min,  2 users,  load average: 0.02, 0.06, 0.20
USER     TTY      FROM             LOGIN@   IDLE   JCPU   PCPU WHAT
root     pts/1    li-vdi2:S.0      15:07   39:42   0.01s  0.01s /bin/bash
root     pts/2    li-vdi2.net.ou.e 15:44    6.00s  0.04s  0.01s w

[Kavishwar Wagholikar]

Thats good news.

If the server is rebooted, the postgres, webserver and the wildfly processes need to be started.

For using i2b2 in production setting, do change the default passwords.

kavi

On Fri, Sep 14, 2018 at 9:29 AM Li Li <lit...@gmail.com> wrote:

Hi Kavi,

Ctrl-a d worked! Thanks for your all your help! It is greatly appreciated! One more question: If the i2b2 server gets rebooted, will all the service come back automatically? if no, how can I start everything back up?

Thanks,

-Li

On Thu, Sep 13, 2018 at 7:58 PM Kavishwar Wagholikar <wag...@gmail.com> wrote:

Does screen behave the same when you do use non i2b2 related scripts?

How about using Ctrl-a d? see https://support.suso.com/supki/Screen_tutorial

[Li Li]

Hi, Kavi,

Thanks! Is there a documentation about managing the i2b2 server such as stopping/starting all the services, etc? I am new to i2b2 and find it challenging to find information. On the i2b2 community wiki page: http://community.i2b2.org/wiki/dashboard.action, I couldn't find where to sign up for an account... how do I get an account so that I can login?

[Kavishwar Wagholikar]

On second thought:

when the server is rebooted, I expect the the postgres and webserver to restart on their own , as these are setup as services.

Wildfly can be started with:

sh $JBOSS_HOME/bin/standalone.sh

Let me know if this works for you.

[Li Li]

That worked! Thanks Kavi!