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
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>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Mon Nov 24 2014 - 14:00:04 PST
