Sam’s Notebook: Installation – Microsoft Machine Learning Server (Microsoft R Open) on Emu/Roadrunner R Studio Server


Steven recently saw an announcement that Microsoft R Open now handles multi-threaded processing (default R does not), so we were interested in trying it out. I installed MLR/MRO on Emu/Roadrunner (Apple Xserve; Ubuntu 16.04). Followed the Microsoft installation directions for Ubuntu. In retrospect, I think I could’ve just installed MRO, but this gets the job done as well and won’t hurt anything.

I’ve set both Emu & Roadrunner R Studio Server to use this installation of R by changing the /etc/restudio/rserver.conf file to the following:

  # Server Configuration File # Use Microsoft R Open instead of default R version. # Comment out and restart R Studio Server (sudo rstudio-server restart) # to restore default R version. rsession-which-r=/opt/microsoft/ropen/3.4.3/lib64/R/bin/R  

I have confirmed that R Studio Server on both machines starts up and is using MRO instead of the default version of R.

from Sam’s Notebook

Sam’s Notebook: Ubuntu – Fix “No Video Signal” Issue on Emu


An issue with Emu cropped up a few weeks ago that was seemingly caused by upgrading from Ubuntu 16.04 to 18.04.

However, the problems only seemed related to using Emu via the GUI; users could still use Emu as a headless computer via SSH.

Today, I was upgrading some packages and noticed two things:

  1. When initially logging in to Emu.
      sam@swoose:~$ ssh emu Welcome to Ubuntu 16.04.5 LTS (GNU/Linux 4.4.0-57-generic x86_64) * Documentation: * Management: * Support: 0 packages can be updated. 0 updates are security updates. New release '18.04.1 LTS' available. Run 'do-release-upgrade' to upgrade to it. You have mail. Last login: Tue Oct 2 07:30:32 2018 from  

    This is showing that Emu is still running Ubuntu 16.04, not 18.04 as presumed!

  2. An error in the GRUB config generation process when upgrading packages.
  run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-134-generic /boot/vmlinuz-4.4.0-134-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-137-generic Found initrd image: /boot/initrd.img-4.4.0-137-generic Found linux image: /boot/vmlinuz-4.4.0-135-generic Found initrd image: /boot/initrd.img-4.4.0-135-generic Found linux image: /boot/vmlinuz-4.4.0-57-generic Found initrd image: /boot/initrd.img-4.4.0-57-generic Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic error: syntax error. error: Incorrect command. error: syntax error. Syntax error at line 98 Syntax errors are detected in generated GRUB config file. Ensure that there are no errors in /etc/default/grub and /etc/grub.d/* files or please file a bug report with /boot/grub/ file attached. done Processing triggers for libc-bin (2.23-0ubuntu10) ...  

These two bits of information led me to believe the problem wasn’t that the system upgrade to 18.04 was incompatible with these old Apple Xserve hardware (since the upgrade didn’t actually get implemented) and instead was that the upgrade might have been initiated, but aborted, which modified the GRUB configuration file(s), breaking the GUI; much like the problem I previously addressed earlier this summer.

When I fixed the display/GUI issues with Emu and Roadrunner earlier this summer, I noted that the /etc/default/grub files on each of the computers were slightly different, despite the fact that these two computers should be identical. So, I replaced the /etc/default/grub file on Emu with the file from Roadrunner and rebooted Emu.

Contents of /etc/default/grub file on Emu/Roadrunner, for future reference:

  # If you change this file, run 'update-grub' afterwards to update # /boot/grub/grub.cfg. # For full documentation of the options in this file, see: # info -f grub -n 'Simple configuration' GRUB_DEFAULT=0 #GRUB_HIDDEN_TIMEOUT=0 GRUB_HIDDEN_TIMEOUT_QUIET=true GRUB_TIMEOUT=10 GRUB_DISTRIBUTOR=`lsb_release -i -s 2> /dev/null || echo Debian` GRUB_CMDLINE_LINUX_DEFAULT="quiet splash" GRUB_CMDLINE_LINUX="" # Uncomment to enable BadRAM filtering, modify to suit your needs # This works with Linux (no patch required) and with any kernel that obtains # the memory map information from GRUB (GNU Mach, kernel of FreeBSD ...) #GRUB_BADRAM="0x01234567,0xfefefefe,0x89abcdef,0xefefefef" # Uncomment to disable graphical terminal (grub-pc only) #GRUB_TERMINAL=console # The resolution used on graphical terminal # note that you can use only modes which your graphic card supports via VBE # you can see them in real GRUB with the command `vbeinfo' #GRUB_GFXMODE=640x480 # Uncomment if you don't want GRUB to pass "root=UUID=xxx" parameter to Linux #GRUB_DISABLE_LINUX_UUID=true # Uncomment to disable generation of recovery mode menu entries #GRUB_DISABLE_RECOVERY="true" # Uncomment to get a beep at grub start #GRUB_INIT_TUNE="480 440 1"  

Voila! Emu now has a functional display/GUI again!

from Sam’s Notebook

Yaamini’s Notebook: October 2018 Goals


September Goals Recap:


  • I finished addressing reviewer comments! The manuscript is almost finalized for resubmission.


  • I presented my preliminary results at PCSGA!
  • Worked on in compGO and DAVID, but my methods are most likely wrong
  • Didn’t make much headway writing because the gene enrichment stuff was confusing enough

Gigas Broodstock:

October Goals


  • Re-submit. That. Paper.


  • Address minor reviewer comments
  • Address major comments
  • Try using multivariate methods to explore relationship between environmental data and protein expression data
  • Upload proteomics data to online databases
  • Reformat the paper repository

Gigas Broodstock:

  • Finish extracting broodstock DNA
  • Identify sequencing protocol
  • Prepare samples for bisulfite sequencing


  • Rework bismark and methylKit to solidfy analysis parameters
  • Present more solid findings to Eastern oyster methylation project group
  • Update methods and results
  • Fix gene enrichment methods

// Please enable JavaScript to view the comments powered by Disqus.

from the responsible grad student