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 ?? ()
Is there not more in the backtrace?
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.
It is the same issue even without applying the plugins patch :/
This is still a problem in 1.9.4_alpha57
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.
(In reply to Hypoon from comment #2) > 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. You were right! If we drop all the "-shared" from the ebuild, it works fine (I don't know why we are forcing that)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8762ad972d826ad2be59344e68b67b1bbfefe760 commit 8762ad972d826ad2be59344e68b67b1bbfefe760 Author: Pacho Ramos <pacho@gentoo.org> AuthorDate: 2024-07-11 11:39:53 +0000 Commit: Pacho Ramos <pacho@gentoo.org> CommitDate: 2024-07-11 11:42:13 +0000 sci-chemistry/vmd: Fix compat with numpy-2 and don't mess with linking Ebuild forcing linking flags break some utils, point to new location for numpy2 include files Closes: https://bugs.gentoo.org/929763 Thanks-to: he.ousia Closes: https://bugs.gentoo.org/835604 Thanks-to: Hypoon Signed-off-by: Pacho Ramos <pacho@gentoo.org> sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild | 263 ++++++++++++++++++++++++++ 1 file changed, 263 insertions(+)
