create and use a service certificate for oasis cron job


cosg16:marki:marki> openssl x509 -in /etc/grid-security/hostcert.pem -subject -issuer -dates -noout
subject= /DC=org/DC=opensciencegrid/O=Open Science Grid/OU=Services/
issuer= /DC=org/DC=cilogon/C=US/O=CILogon/CN=CILogon OSG CA 1
notBefore=Mar 21 17:36:19 2017 GMT
notAfter=Apr 20 17:41:19 2018 GMT




OSG related notes

Running cronjob by hand succeeds where running from cron fails with proxy not generated.

  • GOC stands for Grid Operations Center
  • GOC ticket is a help request to the GOC

To install my personal grid certificate into Firefox 52.3.0:

  • preferences > advanced >view certificates > your certificates > import
  • choose “user_certificate_and_key.U228.p12”
  • enter certificate password


Possibly useful command for rsync’ing Oasis

find /group/halld/Software/builds/Linux_CentOS7-x86_64-gcc4.8.5/ -maxdepth 5 -type d \( -name lib -o -name bin \) > /scratch/marki/dirs.txt 
rsync -ruvt --delete /group/halld/Software/ /scratch/marki/group/halld/Software/ --exclude ExternalPackages/ --exclude \*\*/.git/\*\* --exclude \*\*/Linux_CentOS6\*/ --exclude \*\*/Linux_RHEL\*/ --exclude \*\*/\*.tar.gz
awk -e '{print "mkdir -p /scratch/marki" $1 " ; rsync -ruvt --delete --exclude \\*\\*/.git/\\*\\* " $1 " /scratch/marki" $1}' < /scratch/marki/dirs.txt > e.tmp

Notes on singularity and gluex software

July 29, 2017

Things to do:

  • Figure out how to copy files to oasis
  • Figure out how to copy containers to singlularity cvmfs

Useful commands:

singularity expand centos7.img
sudo /usr/local/bin/singularity shell --writable centos7.img
/usr/local/bin/singularity shell --bind /group/halld:/group/halld centos7.img

Getting mysql shared library to be seen by container:

> eval ` -l /home/marki/lib`
> -l /home/marki/lib
> ls /home/marki/lib
> cp /usr/lib64/mysql/ /u/scratch/marki

Try to find where the non-standard library is coming from, on ifarm1401:

> repoquery -f /usr/lib64/mysql/
> repoquery -i mysql-community-libs-0:5.7.15-1.el7.x86_64

Name        : mysql-community-libs
Version     : 5.7.15
Release     : 1.el7
Architecture: x86_64
Size        : 9898444
Packager    : MySQL Release Engineering <>
Group       : Applications/Databases
URL         :
Repository  : mysql
Summary     : Shared libraries for MySQL database client applications
Source      : mysql-community-5.7.15-1.el7.src.rpm
Description :
This package contains the shared libraries for MySQL client

Tracking down the mysql shared library needed:

In CentOS7 Singularity container:

> mysql --version
mysql Ver 15.1 Distrib 5.5.52-MariaDB, for Linux (x86_64) using readline 5.1

On ifarm1402:

> mysql --version
mysql Ver 14.14 Distrib 5.7.15, for Linux (x86_64) using EditLine wrapper
> ldd `which hd_root` | grep mysql => /usr/lib64/mysql/ (0x00007f670896c000)

On lorentz:

> mysql --version
mysql Ver 15.1 Distrib 5.5.52-MariaDB, for Linux (x86_64) using readline 5.1
> ldd `which hd_root` | grep mysql => /usr/lib64/mysql/ (0x00007f09a0cfd000)

Special repo on ifarm:

> pushd /etc/yum.repos.d
/etc/yum.repos.d /u/scratch/marki
ifarm1402:marki:yum.repos.d> ls
core72.repo epel-testing.repo.bak mysql.repo scicomp-extras.repo
epel.repo eple.repo.bak2 salt.repo
ifarm1402:marki:yum.repos.d> cat mysql.repo
# mysql rhel7 mirror
name = MySQL Community

GlueX and the Open Science Grid

  • at JLab
    • submit host installed: for submitting jobs to the OSG
    • SciComp did installation in consultation with OSG experts
    • log-in with CUE credentials for authorized users
    • JLab users submit jobs to the OSG with the installed software
  • at Collaborating Institutions
    • meeting was held with (different) set of OSG personnel to discuss contribute of University-based clusters to OSG infrastructure
    • makes these nodes available for general GlueX computing
    • UConn, NU already contributing
    • prospective contributions from CMU, IU, FIU, FSU