VMD-L Mailing List

From: Strahs, Dr. Daniel Bernard (dstrahs_at_pace.edu)
Date: Sat Jul 30 2022 - 14:04:38 CDT

Hello all:

I just finished compiling VMD 1.9.3 under Ubuntu 22.04LTS. A couple of weeks ago I had downtime, and I thought this time would be appropriate for updating my laptop from Ubuntu 20.04LTS to 22.04LTS.

Some colleagues had expressed dissatisfaction with 22.04LTS so I had waited until I was between teaching semesters. For those of you who don't know, Ubuntu has transitioned some software applications/suites to SNAP. Among the apps transitioned include the C library. I'm also not a fan of snaps - some of the snaps are problematic, such as firefox.

VMD 1.93 from source didn't install correctly the 1st time. Many plugins were listed as missing. Investigation indicated that all of the missing plugins either were binaries compiled from source or such binaries as required packages.

I tracked down the issue to libdl.so which is used for dynamic loading; this library is included in the TCL calls for the LINUXAMD64 target of the plugin Make-arch files. Although libdl.so.2 is present, the generic alias libdl.so is not.

Since GCC 2.34, dynamic loading is accomplished in the C library. Ubuntu 22.04LTS uses GCC 2.35, and they're both downloaded snaps. My guess is that libdl is not being given enough consideration and may be on the way to obsolescence.

Once I removed "-ldl" from the Make-arch TCL call, the plugins build correctly and VMD starts with correct plugin loading.

Be well y'all!

Dan Strahs
Biology Department
Pace University, NYC