VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Sep 16 2020 - 12:55:38 CDT

Hi John, I can confirm that this happens when compiling the plugins, using
a similar number of processes, which probably triggers the race condition
due to some of the plugins needing molfile to be built first. I don't
remember which one at the moment, I worked around it by using ccache
anyway, at which point the non-parallel make is fast enough.

Giacomo

On Wed, Sep 16, 2020 at 1:12 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> Thanks for reporting this. This is the first I've heard of this issue.
> I'm happy to apply the tiny patch. Let me know if you know of any other
> similar issues that I can help iron out.
>
> Best regards,
> John Stone
> johns_at_ks.uiuc.edu
>
> On Wed, Sep 16, 2020 at 01:32:59PM +0200, Francisco Ramos wrote:
> > Hello,
> >
> > Some people are hitting a build failure when using high -j make options
> like
> > -j18:
> > make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/vmd-
> > 1.9.4_alpha43/work/plugins/bossconvert'
> > make[2]: Entering directory '/var/tmp/portage/sci-chemistry/vmd-
> > 1.9.4_alpha43/work/plugins/catdcd'
> > mkdir -p ../compile/lib_LINUX/bin/catdcd5.2
> > x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -I. -I../include
> > -I../compile/lib_LINUX/molfile -c ./hash.c -fPIC -o
> > ./compile/lib_LINUX/bin/catdcd5.2/hash.o
> > x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -I. -I../include
> > -I../compile/lib_LINUX/molfile -c ./catdcd.c -fPIC -o
> > ./compile/lib_LINUX/bin/catdcd5.2/catdcd.o
> > make[2]: *** No rule to make target
> > '../compile/lib_LINUX/molfile/libmolfile_plugin.a', needed by
> > '../compile/lib_LINUX/bin/catdcd5.2/catdcd'. Stop.
> > make[2]: *** Waiting for unfinished jobs....
> > ./catdcd.c:17:10: fatal error: libmolfile_plugin.h: No such file or
> directory
> > 17 | #include "libmolfile_plugin.h"
> > | ^~~~~~~~~~~~~~~~~~~~~
> > compilation terminated.
> > make[2]: *** [Makefile:54: ../compile/lib_LINUX/bin/catdcd5.2/catdcd.o]
> Error 1
> > make[2]: Leaving directory '/var/tmp/portage/sci-chemistry/vmd-
> > 1.9.4_alpha43/work/plugins/catdcd'
> > make[1]: *** [Makefile:177: bins] Error 1
> > make[1]: *** Waiting for unfinished jobs....
> >
> > In Gentoo we were applying a patch to fix it for 1.9.3... but it looks
> to be
> > still needed for 1.9.4aX. This one is the updated version that works for
> > 1.9.4a43:
> >
> > --- a/plugins/Makefile
> > +++ b/plugins/Makefile
> > @@ -173,7 +173,7 @@
> > win32staticlibs: win32molfilelibs
> > for dir in $(BUILDDIRS); do cd $$dir && $(MAKE) win32staticlibs
> && cd
> > . || exit 1 ; done
> >
> > -bins:
> > +bins: molfilelibs
> > for dir in molfile_plugin $(BUILDDIRS); do cd $$dir && $(MAKE)
> bins &&
> > cd .. || exit 1 ; done
> >
> > win32bins:
> >
> > Maybe it could be upstreamed finally
> >
> > Thanks a lot
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin