Document scidas host at RENCI

Scidas host has IP address 152.54.3.214
Ann Loraine has a login.
To log into the host, you need to use a "jump" host, like:

ssh -J aloraine@hop.renci.org aloraine@lorainelab-quickload.scidas.org

Host info:

[root@lorainelab-quickload aloraine]# uname -a
Linux lorainelab-quickload.scidas.org 3.10.0-1160.108.1.el7.x86_64 #1 SMP Thu Jan 25 16:17:31 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

Web content is here:

/projects/igbquickload/lorainelab/www/main/htdocs
[aloraine@lorainelab-quickload htdocs]$ ls
aspb                 demo        IGBF-1385      rnaseq
autoindex_strapdown  dnaseq      IGBF-1423      saltyrice
bar                  eplant1     index.html     schallerlab
blueberry            flower      krizeklab      secureQuickloadTestSites
brokenQuickloads     genome.txt  krizek_review  smokeTestingQuickload
chess                HEADER.md   lorainelab     soyseq
chipseq              hotpollen   pollen         styling
cressexpress         IGBF-1362   quickload      workShop

Disk usage:

[root@lorainelab-quickload sites-available]# df -h
Filesystem                  Size  Used Avail Use% Mounted on
devtmpfs                    3.9G     0  3.9G   0% /dev
tmpfs                       3.9G     0  3.9G   0% /dev/shm
tmpfs                       3.9G   17M  3.9G   1% /run
tmpfs                       3.9G     0  3.9G   0% /sys/fs/cgroup
/dev/mapper/VGos-LVslash    5.9G  2.1G  3.8G  36% /
/dev/mapper/VGos-LVvar      5.9G  810M  5.1G  14% /var
/dev/mapper/VGos-LVhome     3.9G   38M  3.9G   1% /home
/dev/mapper/VGos-LVopt      3.9G  126M  3.8G   4% /opt
/dev/sda2                   497M  191M  306M  39% /boot
/dev/sda1                   200M   12M  189M   6% /boot/efi
172.25.8.100:/igbquickload  2.9T  2.6T  322G  89% /projects/igbquickload

Update:

• Testing to see if I can set up a new bioviz domain site on RENCI infrastructure - renci.bioviz.org.
• Doing this to see if we can host whatever domain we want on RENCI.
• Result: I added a new virtual host configuration for domain renci.bioviz.org. The IP address associated in DNS to lorainelab-quickload.scidas.org was then able to serve content for renci.bioviz.org. Looks like our RENCI host can indeed serve whatever domain we want it to.

Notes from recent trouble-shooting on their end, from previous problems with RENCI hosting:

This looks like DNS is resolving correctly:

nslookup
Show quoted text
Server: 172.28.0.4
Address: 172.28.0.4#53

Non-authoritative answer:
scidas.org nameserver = dns1.registrar-servers.com.
scidas.org nameserver = dns2.registrar-servers.com.

Authoritative answers can be found from:
Show quoted text
Server: 172.28.0.4
Address: 172.28.0.4#53

Non-authoritative answer:
Name: lorainelab-quickload.scidas.org
Address: 152.54.3.214

I restarted the apache service as it looks like it had crashed at some point. Let me know if it's still not working for you.

We need the flexibility to quickly re-assign our "quickload main" site to a new IP address if and when our RENCI or main campus hosting fails.

To make that work, I'd like to have a quickload main-specific domain name that I can easily re-assign to AWS infrastructure or other equally flexible hosting infrastructure when the need arises.

So, I'd like to create a new domain - igbquickload-main.bioviz.org, which would be associated with our main quickload site, the one that serves sequence data and reference annotations for our Quickload-supported genomes.

I made the above domain and assigned it to the scidas host.

If there are problems with the host in future, we can submit them to help.renci.org to get help.
However, if there are problems with logging in there, it might be because the user needs to have its password reset.
To do that, visit https://selfservice.renci.org to reset the password.