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Configuring External libraries for R-Studio for CentOS 7

RStudio can be configured by adding entries to 2 configuration files. It may not exist by default and you may need to create

/etc/rstudio/rserver.conf
/etc/rstudio/rsession.conf

If you need to add additional libraries to the default LD_LIBRARY_PATH for R sessions. You have to add the parameters to the /etc/rstudio/rserver.conf

Step 1: Enter External Libraries settings
For example, you may want to add GCC-6.5 libraries

# Server Configuration File
rsession-ld-library-path=/usr/local/gcc-6.5.0/lib64:/usr/local/gcc-6.5.0/lib

Step 2a: Stop the R Server Services

# /usr/sbin/rstudio-server stop

Step 2b: Verify the Installation

# rstudio-server verify-installation

Step 2c: Start the R Server Services

# /usr/sbin/rstudio-server start
# /usr/sbin/rstudio-server status

(Make sure there is no error)

References:

  1. RStudio Server: Configuring the Server

 

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AlmaLinux Enterprise-Grade Server OS compatible with RHEL 8

What is AlmaLinux? According to the website https://almalinux.org/

AlmaLinux is an enterprise-grade server OS, a stable Linux distribution with regular releases that come with long support windows. You can rely on AlmaLinux to run you and your clients’ critical workloads.

  • Fedora-like distribution based on a precise RHEL clone
  • Production-ready and stable, matching RHEL features 1:1
  • Enjoy the predictability of a stable release issued in tandem with RHEL
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No-Cost, Self-Supported RHEL up to 16 systems under Individual Developer Subscription for RHEL

From RHEL, “No-cost RHEL for small production workloads and customer development teams”

We’re addressing this by expanding the terms of the Red Hat Developer program so that the Individual Developer subscription for RHEL can be
used in production for up to 16 systems. That’s exactly what it sounds like: for small production use cases, this is no-cost, self-supported RHEL.
You need only to sign in with a free Red Hat account (or via single sign-on through GitHub, Twitter, Facebook, and other accounts) to download
RHEL and receive updates. Nothing else is required. This isn’t a sales program and no sales representative will follow up. An option will exist within
the subscription to easily upgrade to full support, but that’s up to you.

……

The updated Individual Developer subscription for RHEL will be available no later than February 1, 2021.

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How to Install Intel® oneAPI Toolkits

In this four-minute video, Intel’s David Liu provides installation instructions for an offline/local installation of Intel’s oneAPI Toolkits. David shows you where to find the Intel oneAPI Toolkits, how to download the toolkits, and the various ways to install the toolkits: from the GUI or from the command line (a silent install without the GUI, an interactive install, or a custom install).

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Running Arrays on PBS Professional

If you are intending to run the same program with the different input files, it is best you use Jobs Array instead of creating separate programs for the input files which is tedious. It is very easy

Amending the Submission Scripts (Part 1)

To create an arrays jobs, you have to use the -J option on the PBS Scripts. For 10 sub-jobs, you do the following

#PBS -J 1-10

Amending the Submission Scripts (Part 2)

If your input files are concatenated with a running number. For example, if your input file is data1.gjf, data2.gjf, data3.gjf, data4.gjf, data5.gjf ….. data10.gjf

inputfile=data$PBS_ARRAY_INDEX.gjf

Submitting the Jobs

a. To submit the jobs, just

% qsub yoursubmissionscript.pbs

Checking Jobs

b. You will notice that after you qstat, you will notice that your jobs bas a “B”

% qstat -u user1
544198[].node1 Gaussian-09e user1 0 B q32

You have to do a “-t” or “-Jt”

% qstat -t 544198[]

% qstat -t 544198[]
Job id Name User Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
544198[].node1 Gaussian-09e user1 0 B q32
544198[54].node1 Gaussian-09e user1 00:40:21 R q32
544198[55].node1 Gaussian-09e user1 00:15:25 R q32

To delete the Sub Jobs

% qdel "544198[5]"