Computing Services

FAQ Regarding the Transition to RHEL7

ICDS has begun transitioning the Roar operating system from Red Hat Enterprise Linux (RHEL) version 6 to version 7.

We’ll update this page as new information becomes available, and as we compile helpful tips for users related to the transition.

What’s the best way to get help with any aspect of the RHEL7 upgrade?

Email iask@ics.psu.edu, submit a ticket at iask.aci.ics.psu.edu, or attend the i-ASK helpdesk “virtual office hours” devoted to questions and concerns about the transition. Use this Zoom link to attend any of the following sessions:


How do I access a RHEL7 login node?

Users can access a RHEL 7 login node with the hostname

submit.aci.ics.psu.edu

…using ssh. For example, if your username was “abc123” you would submit:

ssh abc123@submit.aci.ics.psu.edu


How do I run my job on a RHEL7 compute node?

Simply add “rhel7” to your job request directive in order to submit to a rhel7 node. If you don’t add this specification, your job will run on an rhel6 node, by default. For example, if you submit:

qsub -A open -l walltime=1:00:00 -l nodes=1:ppn=2 -I

…your job will run on a RHEL 6 node. But if you submit:

qsub -A open -l walltime=1:00:00 -l nodes=1:ppn=2 -l feature=rhel7 –I

…your job will run on a RHEL 7 node.

How can I confirm that my job is running on a RHEL7 node?

Run the following (replacing comp-XX-0000 with the node where your job is running):

pbsnodes -a comp-XX-0000 | grep rhel

The properties line should return “rhel7” and “opsys=rhel7” on the status line of all rhel7 nodes. If your job is running on rhel 6, the properties line will return “rhel6” instead.

What versions and point releases are available for software in the RHEL7 software stack?

The RHEL 7 software stack includes updated point releases of several popular software packages, while many of the oldest versions have been removed. The following point releases will not be included in the RHEL7 software stack. If your code references any of these retired versions or point releases, you’ll need to update your code accordingly with one of the alternative versions listed in parentheses.

  • abaqus/2017 (use abaqus/2018)
  • adf/2019.103 (use adf/2019.303)
  • afni/17.2.05 (use afni/20.2.11)
  • amber/14 (use amber/18)
  • ampl/20170731 (use ampl/20190529)
  • ansys/19.1 (use ansys/2019R3)
  • avizo/9.4.0 (use avizo/2020.1 OR avizo/9.7.0)
  • beast/1.15 (use beast/1.10.4 OR beast2/2.5.2)
  • bedtools/2.26.0 (use bedtools/2.27.1)
  • blat/36 (use blat/35)
  • boost/1.61.0 (use boost/1.63.0)
  • cmake/3.9.1 (use cmake/3.16.2)
  • comsol/5.3 (use comsol/5.4)
  • cplex/12.8.0 (use cplex/12.10.0)dl_poly/4.08 (use dl_poly/4.08)
  • ddt/7.1 & ddt/19.1.3 (use ddt/20.1.1)
  • fastqc/0.11.2 (use fastqc/0.11.7)
  • ffmpeg/3.1.1 & ffmpeg/3.3.3 (use ffmpeg/4.1.1)
  • freebayes/1.2.0 (use freebayes/1.1.0)
  • freesurfer/5.3.0 & freesurfer/6.0.0 (use freesurfer/7.1.1)
  • gams/24.8.5 (use gams/28.2.0)
  • gauss/19.2.0 (use gauss/20.0.4)
  • gaussian/g03e1 (use gaussian/g09c01)
  • gcc/5.3.1 & gcc/7.3.1 (use gcc/8.3.1 OR gcc/9.3.1)
  • gromacs/5.1.4 (use gromacs/2019.5)
  • hdf5/1.8.18 (use hdf5/1.10.7)
  • htslib/1.1 (use htslib/1.10.2)idl/8.5 (use idl/8.5)
  • impi/5.1.3 & impi/2019.5 (use impi/2019.8)
  • intel/16.0.3 & intel/19.0.5 (use intel/19.1.2)
  • jags/4.2.0 (use jags/4.3.0)
  • julia/0.6.0 (use julia/1.3.1)
  • kim-api/1.8.2 (use kim-api/2.1.3)
  • knitro/10.2.1 & knitro/12.0.0 (use knitro/12.2.2)
  • lammps/20150210 & lammps/20160827 (use lammps/20190807)
  • lmod/6.5.1 (use lmod/8.2.7)lsprepost/4.3 (use lsprepost/4.3)
  • mafft/7.310 (use mafft/7.453)
  • mathematica/11.0.1 (use mathematica/12.0.0)
  • matlab/R2017b & matlab/R2019a (matlab/R2019b)
  • mkl/11.3.3 & mkl/2019.5 (use mkl/2020.3)
  • muscle/3.8.31 (use muscle/3.8.1551)ncbi-blast/2.6.0 (use ncbi-rmblastn/2.9.0)
  • netcdf-cxx/4.3.0 (use netcdf-cxx/4.2)
  • openjdk/1.8.0 (use openjdk/11.0.6.10)
  • openmpi/1.10.1 (use openmpi/3.1.5)
  • parallel/20170522 (use parallel/20190222)
  • petsc/3.7.3 (use petsc/3.8.3)
  • pgi/16.4 & pgi/18.5 (use pgi/18.10)
  • picard/2.5.0 (use picard/2.20.8) ploticus/2.42 (use ploticus/2.42)
  • python/2.7.14-anaconda5.0.1 & python/3.6.3-anaconda5.0.1 (use anaconda3/2020.07 – *python now separate)
  • python/2.7.14-anaconda5.0.1 & python/3.6.3-anaconda5.0.1 (use python/2.7.5 OR python/3.6.8
  • samtools/0.1.19 (use samtools/1.5)
  • schrodinger/2016.4 (use schrodinger/2019.4)
  • spm/8 (use spm/12)
  • starccm/12.04.010 & starccm/14.04.011 (use starccm/14.04.011-R8)
  • stata/14.2 (use stata/16)
  • tbb/4.4.4 & tbb/2017 & tbb/2019.8 (use tbb/2020.8)
  • totalview/2017.1.21 (use totalview/2019.2.12)
  • trinity/2.2.0 (use trinity/2.6.6)
  • vasp/5.4.1.05Feb16 (use vasp/5.4.4)
  • vtune-amplifier/16.4 & vtune-amplifier/2018.1 (use vtune-amplifier/2020.3)
  • wgs/8.3 (use wgs/8.3rc2)xdrf/1.2 (use xdrf/1.2)vasp_vtst/5.4.1.05Feb16 (use vasp_vtst/5.4.4)

Is there a programmatic way to find out what software is available in the RHEL7 software stack?

Use the module spider.

Will my custom software or modules work in RHEL7?

If you compile your own software or build your own software from source, or install your own Python or R modules, then it’s likely that you’ll need to recompile or reinstall these elements for them to work properly in the new operating system. Procedures vary, so the best option is to consult user documentation for your software.
If you need help in making these updates, or if you’re concerned that you won’t be able to implement these changes in a timely manner, you can alert our support team here.

Will I lose connectivity to any of my Roar storage spaces when logged into a RHEL7 node?

No – All current storage will continue to be available on RHEL7.

How should I use Git on the new RHEL7 environment?

Git is now provided by the system on RHEL7 so there is no longer a need for a module file. Use the git command to use Git on Roar. For mor information, see this “cheat sheet” provided by Github.