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-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher > On Nov 25, 2014, at 2:46 AM, Josh Berryman <the.real.josh.berryman.gmail.com> wrote: > > 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 _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Tue Nov 25 2014 - 03:30:03 PST