Er, doesn't the devlist get echoed onto a public web server?
In that case we just posted the password for the wiki online
Josh
On 24 November 2014 at 23:55, Andreas Goetz <agoetz.sdsc.edu> wrote:
> Thanks Jason. Gustavo, I added a paragraph. Thanks.
>
> All the best,
> Andy
>
> --
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
> On Nov 24, 2014, at 2:15 PM, Jason Swails wrote:
>
> > pakrules
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >> On Nov 24, 2014, at 5:10 PM, Andreas Goetz <agoetz.sdsc.edu> wrote:
> >>
> >> I just tried to edit the wiki but I forgot the password (and so did my
> web browser) ...
> >>
> >> Best,
> >> Andy
> >> --
> >> Dr. Andreas W. Goetz
> >> Assistant Project Scientist
> >> San Diego Supercomputer Center
> >> Tel : +1-858-822-4771
> >> Email: agoetz.sdsc.edu
> >> Web : www.awgoetz.de
> >>
> >>> On Nov 24, 2014, at 1:32 PM, Gustavo Seabra wrote:
> >>>
> >>> Hi guys,
> >>>
> >>> I've been (silently) following on this discussion. Would it be a good
> idea to put a note on this on the pmwiki?
> >>>
> >>> Gustavo Seabra
> >>>
> >>>
> >>>
> >>> Em 24/11/2014, à(s) 18:29, Andreas Goetz <agoetz.sdsc.edu> escreveu:
> >>>
> >>>> Dan, Jason, thanks for the quick response.
> >>>>
> >>>> Jason, you nailed it. It happens after 'git clean -d -f'. Adding '-x'
> solves the problem. This is reproducible. I checked again with my
> collaborator: it did not happen with a fresh clone (my misunderstanding)
> but after issuing 'git clean -d -f' using a non-clean repo with previous
> build.
> >>>>
> >>>> Thanks,
> >>>> Andy
> >>>>
> >>>> --
> >>>> Dr. Andreas W. Goetz
> >>>> Assistant Project Scientist
> >>>> San Diego Supercomputer Center
> >>>> Tel : +1-858-822-4771
> >>>> Email: agoetz.sdsc.edu
> >>>> Web : www.awgoetz.de
> >>>>
> >>>>> On Nov 24, 2014, at 8:01 AM, Jason Swails wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>>> On Nov 24, 2014, at 10:23 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >>>>>>
> >>>>>> Hi,
> >>>>>>
> >>>>>> I've never seen this before, and I build GIT amber all over the
> place
> >>>>>> (many systems, many compilers). You mentioned initially you see this
> >>>>>> after a git 'clean -d -f'.
> >>>>>
> >>>>> I didn't see this part of your post, Andy. And this could easily be
> the problem. The problem here is that you are not using the -x flag, which
> also gets rid of files masked by .gitignore. And we mask a lot of
> compilation intermediate files that could cause these errors you are seeing.
> >>>>>
> >>>>> So see if "git clean -fxd" fixes your issues. (FWIW I use this
> workflow all the time).
> >>>>>
> >>>>> All the best,
> >>>>> Jason
> >>>>>
> >>>>>
> >>>>>
> >>>>>> Do you *only* see it after this? This is a
> >>>>>> totally wild guess: the only thing I can think of is the '-d' flag
> >>>>>> causes removal of some directory that is generated by netcdf during
> an
> >>>>>> initial build, but for some reason is not re-created on subsequent
> >>>>>> builds. Do you ever see this with release code?
> >>>>>>
> >>>>>> -Dan
> >>>>>>
> >>>>>>
> >>>>>>> On Sun, Nov 23, 2014 at 9:17 PM, Andreas Goetz <agoetz.sdsc.edu>
> wrote:
> >>>>>>> Hi all,
> >>>>>>>
> >>>>>>> I have observed compile errors of the NetCDF C and Fortran
> interface during configure of either fresh amber git repo clones or after
> git clean -d -f. I first thought this was a problem with the file system I
> was working on but it happened more than once during the last few weeks and
> now a collaborator came across the same problem. Unfortunately, it happens
> only sometimes and thus is not reproducible. Has anybody else observed the
> following:
> >>>>>>>
> >>>>>>> Checking NetCDF...
> >>>>>>> Using bundled NetCDF library.
> >>>>>>> Starting NetCDF build.
> >>>>>>> Configuring NetCDF C interface (may be time-consuming)...
> >>>>>>> Compiling the NetCDF C interface (may be time-consuming)...
> >>>>>>> Configuring NetCDF Fortran interface (may be time-consuming)...
> >>>>>>> Compiling the NetCDF Fortran interface (may be time-consuming)...
> >>>>>>> Error: NetCDF Fortran compile failed.
> >>>>>>> Check
> /home/tpirojsi/amber-clone/amber-new/AmberTools/src/netcdf-fortran-4.2/netcdf.fortran.compile.log
> >>>>>>> for errors.
> >>>>>>>
> >>>>>>> When looking into
> /home/tpirojsi/amber-clone/amber-new/AmberTools/src/netcdf-fortran-4.2/netcdf.fortran.compile.log,
> I saw
> >>>>>>>
> >>>>>>> make[2]: Entering directory
> `/home/tpirojsi/amber-clone/amber-new/AmberTools/src/netcdf-fortran-4.2/fortran'
> >>>>>>> /bin/sh ../libtool --tag=FC --mode=link gfortran -fPIC -O3
> -mtune=native -version-number 5:3:1
> -L/home/tpirojsi/amber-clone/amber-new/lib -olibnetcdff.la -rpath
> /home/tpirojsi/amber-clone/amber-new/lib fort-attio.lo fort-control.lo
> fort-dim.lo fort-genatt.lo fort-geninq.lo fort-genvar.lo fort-lib.lo
> fort-misc.lo fort-v2compat.lo fort-vario.lo fort-var1io.lo fort-varaio.lo
> fort-varmio.lo fort-varsio.lo ../f90/libnetcdff90.la -lnetcdf
> >>>>>>> libtool: link: gfortran -shared .libs/fort-attio.o
> .libs/fort-control.o .libs/fort-dim.o .libs/fort-genatt.o
> .libs/fort-geninq.o .libs/fort-genvar.o .libs/fort-lib.o .libs/fort-misc.o
> .libs/fort-v2compat.o .libs/fort-vario.o .libs/fort-var1io.o
> .libs/fort-varaio.o .libs/fort-varmio.o .libs/fort-varsio.o
> -Wl,--whole-archive ../f90/.libs/libnetcdff90.a -Wl,--no-whole-archive
> -Wl,-rpath -Wl,/home/tpirojsi/amber-clone/amber-new/lib -Wl,-rpath
> -Wl,/home/tpirojsi/amber-clone/amber-new/lib
> -L/home/tpirojsi/amber-clone/amber-new/lib
> /home/tpirojsi/amber-clone/amber-new/lib/libnetcdf.so -lm -mtune=native
> -Wl,-soname -Wl,libnetcdff.so.5 -o .libs/libnetcdff.so.5.3.1
> >>>>>>> gfortran: .libs/fort-attio.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-control.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-dim.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-genatt.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-geninq.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-genvar.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-lib.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-misc.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-v2compat.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-vario.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-var1io.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-varaio.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-varmio.o: No such file or directory
> >>>>>>> gfortran: .libs/fort-varsio.o: No such file or directory
> >>>>>>> gfortran: ../f90/.libs/libnetcdff90.a: No such file or directory
> >>>>>>> make[2]: *** [libnetcdff.la] Error 1
> >>>>>>> make[2]: Leaving directory
> `/home/tpirojsi/amber-clone/amber-new/AmberTools/src/netcdf-fortran-4.2/fortran'
> >>>>>>> make[1]: *** [install] Error 2
> >>>>>>> make[1]: Leaving directory
> `/home/tpirojsi/amber-clone/amber-new/AmberTools/src/netcdf-fortran-4.2/fortran'
> >>>>>>> make: *** [install-recursive] Error 1
> >>>>>>>
> >>>>>>> I observed similar errors sometimes during the C and sometimes
> during the Fortran interface build. The .libs directory did not exist at
> the point the linker was trying to link. In all cases this could be
> resolved by repeatedly running the configure script - clearly not a good
> solution. I am using gnu 4.4.7-4 compilers on a RHEL 6.5 system. I have no
> idea what is going wrong here, comments are welcome.
> >>>>>>>
> >>>>>>> All the best,
> >>>>>>> Andy
> >>>>>>>
> >>>>>>> --
> >>>>>>> Dr. Andreas W. Goetz
> >>>>>>> Assistant Project Scientist
> >>>>>>> San Diego Supercomputer Center
> >>>>>>> Tel : +1-858-822-4771
> >>>>>>> Email: agoetz.sdsc.edu
> >>>>>>> Web : www.awgoetz.de
> >>>>>>>
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> AMBER-Developers mailing list
> >>>>>>> AMBER-Developers.ambermd.org
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> -------------------------
> >>>>>> Daniel R. Roe, PhD
> >>>>>> Department of Medicinal Chemistry
> >>>>>> University of Utah
> >>>>>> 30 South 2000 East, Room 307
> >>>>>> Salt Lake City, UT 84112-5820
> >>>>>> http://home.chpc.utah.edu/~cheatham/
> >>>>>> (801) 587-9652
> >>>>>> (801) 585-6208 (Fax)
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER-Developers mailing list
> >>>>>> AMBER-Developers.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Jason M. Swails
> >>>>> BioMaPS,
> >>>>> Rutgers University
> >>>>> Postdoctoral Researcher
> >>>>> _______________________________________________
> >>>>> AMBER-Developers mailing list
> >>>>> AMBER-Developers.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER-Developers mailing list
> >>>> AMBER-Developers.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER-Developers mailing list
> >>> AMBER-Developers.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
> >>
> >> _______________________________________________
> >> AMBER-Developers mailing list
> >> AMBER-Developers.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Tue Nov 25 2014 - 00:00:02 PST
