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2023_deploy_notes.md

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Things to keep track of for the upcoming production deploy

  1. Turn off/move the old httpd/djanog process on bioinf1
  2. Remove any portforwarding rules that the old system needed
  3. Installing s4pred
  4. bioinf3 update python and update the A_A virtualenv, and update commandRunner 8.12
  5. bm2 and bm3, update python and update the A_A virtualenvand update commandRunner 8.12 biopython expected
  6. hspred needs updated for cleanexpect changes
  7. dmpfold2 needs installing correctly with pip and rewrite the job/tasks. Monkey patch aa_env/lib/python3.9/site-packages/dmpfold/network.py at two locations w, v = torch.symeig(M.float(), eigenvectors=True) or w, v = torch.linalg.eigh(M.float())
  8. Update hhblits dbs and blast_cache
  9. Double check mogrify is working for dompred plot and add css rotation if needed
  10. Makes sure the timers for polling in results seq, results structure and model as set sensibly

//blast_cache

psipred_react

Fixing the repo list:

Yum repo list error https://stackoverflow.com/questions/60648390/how-to-remove-rpmdb-failed-release-provides

Cannot find a valid baseurl for repo: base/$releasever/x86_64

cat /etc/centos-release machine is on centos 7.9.2009 These repos @ http://vault.centos.org/7.9.2009 are archived.

Need to change to mirror.centos.org in /etc/yum.repos.d/CentOS-Vault.repo and /etc/yum.repos.d/CentOS-Sources.repo

  1. in CentOS-Base.repo swap mirrorlist for baseurl and set $releasever to 7.9.2009

Updating python

As root build and install python3.9 with shared libs

sudo su
yum install openssl-devel bzip2-devel libffi-devel
cd ~
wget https://www.python.org/ftp/python/3.9.17/Python-3.9.17.tgz 
tar -zxvf Python-3.9.17.tgz
cd Python-3.9.17/
./configure --prefix=/usr --enable-shared LDFLAGS="-Wl,-rpath /usr/lib"
make; make install
ldconfig

As the aa head user install the depenencies, probably comment out the mod-wsgi and mod-wsgi-httpd versions

cd /opt/aa_httpd
apachectl stop
su django_aa
pip3.9 install --upgrade virtualenv
cd ~
mv aa_env aa_env_old
virtualenv aa_env -p /bin/python3.9
source ~/aa_env/bin/activate
cd analytics_automated
pip install "setuptools<58.0.0"
vi requirements/base.txt
pip install -r requirements/staging.txt

As a worker install the bits probably comment out the mod-wsgi and mod-wsgi-httpd versions

Probably need to find all other pacakges that have a requirements.txt (merizo, s4pred, dmpfold2)

su django_worker
cd ~ 
source ~/aa_env/bin/activate
cd analytics_automated
celery multi stop_verify worker --pidfile=/home/django_worker/analytics_automated/celery.pid --logfile=/home/django_worker/analytics_automated/logs/ 
cd ../
deactivate
mv aa_env aa_env_old
virtualenv aa_env -p /bin/python3.9
source ~/aa_env/bin/activate
cd analytics_automated
pip install "setuptools<58.0.0"
vi requirements/base.txt
pip install -r requirements/staging.txt
celery --app=analytics_automated_project.celery:app worker --loglevel=INFO -Q low_localhost,localhost,high_localhost,celery,low_R,R,high_R,low_Python,Python,high_Python --pidfile=celery.pid --detach

s4pred - biopython dmpfold - scipy, numpy, torch merizo