Custom Search
-- B. Lachele Foley, PhD '92,'02 Assistant Research Scientist Complex Carbohydrate Research Center, UGA 706-542-0263 lfoley.ccrc.uga.edu ----- Original Message ----- From: Jason Swails [mailto:jason.swails.gmail.com] To: AMBER Developers Mailing List [mailto:amber-developers.ambermd.org] Sent: Mon, 07 Dec 2009 16:50:17 -0500 Subject: Re: [AMBER-Developers] netcdf reference despite no netcdf config > If netcdf configure failed, and it was not actually built, should we be > passing -DBINTRAJ flag to the preprocessors? If netcdf is going to fail, > why not specify -nobintraj in the configure command? If you do that, does > it work? > > --Jason > > On Mon, Dec 7, 2009 at 4:17 PM, Lachele Foley <lfoley.ccrc.uga.edu> wrote: > > > I tried compiling it on an itanium system. The netcdf configure failed, > > which wasn't an issue for this location, and I did get a config.h file > > (yay!) from which I could delete compiler options as often required for > > ia64. > > > > But, I got the following. I'm guessing that if the netcdf config failed, > > then ptraj shouldn't be using netcdf stuff? I'm not asking for > significant > > ia64 support here if that's what's required. > > > > ranlib f2c.a > > mv f2c.a /usr/local/programs/amber/amber11_AT_20091207/lib > > make[2]: Leaving directory > > `/usr/local/programs/amber/amber11_AT_20091207/src/f2c' > > gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o main.o > > main.c > > In file included from ptraj.h:69, > > from main.c:114: > > utility.h:47:38: error: ../netcdf/include/netcdf.h: No such file or > > directory > > make[1]: *** [main.o] Error 1 > > make[1]: Leaving directory > > `/usr/local/programs/amber/amber11_AT_20091207/src/ptraj' > > make: *** [serial] Error 2 > > > > > > For the curious: > > > > Linux glycam.ccrc.uga.edu 2.6.9-42.0.3.EL #1 SMP Mon Sep 25 17:14:34 EDT > > 2006 ia64 ia64 ia64 GNU/Linux > > GNU Fortran (GCC) 4.3.1 > > gcc (GCC) 4.3.1 > > >From netcdf_config.log: > > " > > checking for /usr/bin/nm... /usr/bin/nm -B > > checking nm flags... > > checking for C-equivalent to Fortran routine "SUB"... configure: error: > > Could not compile conftest.f > > " > > > > And, from the config.h file, the following changes were required to get > > that far: > > > > #OCFLAGS=-O3 -mtune=generic -msse -mfpmath=sse -D_FILE_OFFSET_BITS=64 > > -D_LARGEFILE_SOURCE -DBINTRAJ $(AMBERBUILDFLAGS) > > OCFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ > > $(AMBERBUILDFLAGS) > > > > #FOPTFLAGS= -O3 -mtune=generic -msse -mfpmath=sse $(LOCALFLAGS) > > $(AMBERBUILDFLAGS) > > FOPTFLAGS= -O3 $(LOCALFLAGS) $(AMBERBUILDFLAGS) > > > > > > > > :-) Lachele > > -- > > B. Lachele Foley, PhD '92,'02 > > Assistant Research Scientist > > Complex Carbohydrate Research Center, UGA > > 706-542-0263 > > lfoley.ccrc.uga.edu > > > > > > ----- Original Message ----- > > From: case > > [mailto:case.biomaps.rutgers.edu] > > To: amber-developers.ambermd.org > > Sent: > > Mon, 07 Dec 2009 09:53:25 -0500 > > Subject: [AMBER-Developers] latest release > > candidate for AmberTools 1.3 > > > > > > > I have placed the current release candidate here: > > > > > > http://ambermd.org/downloads/AmberTools.04dec09.tar.bz2 > > > > > > I think we are getting close! As usual, it is like pulling teeth to get > > > anyone to look at and update the documentation. I may have to just lock > > > all developers in a room at the January meeting and require a certain > > number > > > of updates before allowing them out. But please make changes now if you > > > can. > > > As I have mentioned before, this is an excellent opportunity for > students > > > and post-docs to gain some recognition outside their own group by > > > contributing > > > to a common project. > > > > > > ...thx...dac > > > > > > > > > _______________________________________________ > > > 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 > > > > > > -- > --------------------------------------- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Graduate Student > 352-392-4032 > _______________________________________________ > 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 Mon Dec 07 2009 - 14:30:03 PST