From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 16 2020 - 13:38:35 CDT

Hi,
  It never happened for us here just because our plugin builds get run
in automated scripts with a smaller CPU count that doesn't trigger
the race condition. The correction to the missing dependency is
committed and will show up in the publically accessible CVS tomorrow.

Best regards,
  John

On Wed, Sep 16, 2020 at 01:55:38PM -0400, Giacomo Fiorin wrote:
> 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 <[1]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
> [2]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
> [3]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [4]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
> [5]http://goo.gl/Q3TBQU
> [6]https://github.com/giacomofiorin
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:johns_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/~johns/
> 4. http://www.ks.uiuc.edu/Research/vmd/
> 5. http://goo.gl/Q3TBQU
> 6. https://github.com/giacomofiorin

-- 
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/