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Bug 835604 - sci-chemistry/vmd-1.9.4_alpha55 - catdcd segfaults immediately
Summary: sci-chemistry/vmd-1.9.4_alpha55 - catdcd segfaults immediately
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: Normal major (vote)
Assignee: Alexey Shvetsov
Depends on:
Reported: 2022-03-18 22:55 UTC by Hypoon
Modified: 2022-06-01 18:02 UTC (History)
3 users (show)

See Also:
Package list:
Runtime testing required: ---


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Description Hypoon 2022-03-18 22:55:48 UTC
vmd ships with a tool, catdcd, which is very useful for converting molecular dynamics trajectories from one format to another. It would be nice to have catdcd added to the PATH, but that's not critically important. The problem is that catdcd segfaults immediately upon trying to run it.

I wonder if this is related in some way to the extra patches Gentoo bundles with vmd.

Reproducible: Always

Steps to Reproduce:
Run catdcd (with no arguments)
Actual Results:  
$ /usr/lib64/vmd/plugins/LINUX/bin/catdcd5.2/catdcd 
Segmentation fault

Expected Results:  
Print usage information

I tried recompiling with debugging info...

CFLAGS="-march=native -O2 -pipe -ggdb3" CXXFLAGS="${CFLAGS}" FEATURES="splitdebug compressdebug installsources" emerge -1 vmd

...and this is the result in gdb:

$ gdb -q /usr/lib64/vmd/plugins/LINUX/bin/catdcd5.2/catdcd
Reading symbols from /usr/lib64/vmd/plugins/LINUX/bin/catdcd5.2/catdcd...
Reading symbols from /usr/lib/debug//usr/lib64/vmd/plugins/LINUX/bin/catdcd5.2/catdcd.debug...
(gdb) r
Starting program: /usr/lib64/vmd/plugins/LINUX/bin/catdcd5.2/catdcd 

Program received signal SIGSEGV, Segmentation fault.
0x0000000000000001 in ?? ()
Comment 1 Sam James archtester Gentoo Infrastructure gentoo-dev Security 2022-03-18 23:00:00 UTC
Is there not more in the backtrace?
Comment 2 Hypoon 2022-03-18 23:39:56 UTC
Nope, that's all there is. Some googling suggested that this might happen when you try to execute a shared library, which makes me wonder if it's being linked incorrectly.
Comment 3 Pacho Ramos gentoo-dev 2022-05-16 10:51:28 UTC
It is the same issue even without applying the plugins patch :/
Comment 4 Hypoon 2022-05-26 08:49:42 UTC
This is still a problem in 1.9.4_alpha57
Comment 5 Hypoon 2022-06-01 18:02:34 UTC
I was playing with the plugins directory, and with a small change to remove the hardcoded tcl version, the plugins directory compiles fine on my system and catdcd runs without issues. So, the segfault is related to either the ebuild or the context of compiling the plugins as part of the overall VMD compilation.