Re: [AMBER-Developers] Recurring, non-reproducible NetCDF compile errors

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 25 Nov 2014 06:16:56 -0500

IIRC, the password was added to combat bots spamming the content, not to keep people out. Luckily bots are not nearly smart enough to try and mine it from email archives :). I'm pretty sure it's been written here before, too.

--
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
>>>>>> 
>>>>>> 
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>>>>> 
>>>>> 
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Received on Tue Nov 25 2014 - 03:30:03 PST
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