Hi,
The c9x complex failures were caused by Russ Brown's NAB/solaris work.
Ive been planning to re-fix this, but havent gotten to it.
The bad news is that Gustavo is apparently the first (except for nightly
testing) to build amber tools since Wed, 30 Jul 2008.
The more we developers use it, the better it becomes.
Scott
On Sat, 6 Sep 2008, Gustavo Seabra wrote:
> Hi All,
>
> I noticed some issues when trying to compile ambertools under Cygwin:
>
> I have cygwin with gcc, tcsh and g95 installed, and created the
> comfig.h file with the command './configure_at -cygwin'. Configuration
> runs nicely. When I try to compile it, compilation dies with the
> following message:
>
> $ make -f Makefile_at clean
> $ make -f Makefile_at
> [...]
> gcc -c -O3 -DCYGWIN -m32 nmode.c
> nmode.c:8:23: complex.h: No such file or directory
> nmode.c: In function `lnorm':
> nmode.c:1160: error: syntax error before "lambda"
> nmode.c:1161: error: syntax error before "piki"
> nmode.c:1172: error: `lambda' undeclared (first use in this function)
> nmode.c:1172: error: (Each undeclared identifier is reported only once
> nmode.c:1172: error: for each function it appears in.)
> nmode.c:1172: error: `I' undeclared (first use in this function)
> nmode.c:1179: error: `sum' undeclared (first use in this function)
> nmode.c:1184: error: `piki' undeclared (first use in this function)
> nmode.c:1188: error: `pili' undeclared (first use in this function)
> nmode.c:1200: error: `cons' undeclared (first use in this function)
> nmode.c:1210: error: `elki' undeclared (first use in this function)
> make[1]: *** [nmode.o] Error 1
> make[1]: Leaving directory `/cygdrive/c/Documents and
> Settings/seabra/My Documents/Work/Programs/amber11/src/nab'
> make: *** [install] Error 2
>
> As I was only interested in ptraj, I tried adding the "-" sign in the
> nab and antechamber lines in Makefile_at, so the compilation would
> ignore any errors and pass that point. However, I then have a
> different error:
>
> $ make -f Makefile_at clean
> $ make -f Makefile_at
> [...]
> gcc -c -DCYGWIN -m32 -DBINTRAJ -o clusterLib.o clusterLib.c
> gcc -o rdparm.exe main.o rdparm.o dispatch.o help.o utility.o second.o io.o
> trajectory.o evec.o torsion.o mask.o rms.o display.o interface.o
> energy.o experimental.o
> ptraj.o actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o
> /home/seabra/work/Programs/amber11/lib/libpdb.a
> /home/seabra/work/Programs/amber11/lib/libsym.a
> /home/seabra/work/Programs/amber11/lib/arpack.a
> /home/seabra/work/Programs/amber11/lib/lapack.a
> /home/seabra/work/Programs/amber11/lib/blas.a
> /home/seabra/work/Programs/amber11/lib/f2c.a
> /home/seabra/work/Programs/amber11/lib/libmc.a
> ../netcdf/lib/libnetcdf.a
> gcc: /home/seabra/work/Programs/amber11/lib/libsym.a: No such file or directory
> make[1]: *** [rdparm.exe] Error 1
> make[1]: Leaving directory `/cygdrive/c/Documents and
> Settings/seabra/My Documents/Work/Programs/amber11/src/ptraj'
> make: *** [install] Error 2
>
> So, it looks like ptraj needs libsym.a to compile, this is compiled in
> the 'nss' directory. I tried to force its compilation:
>
> $ cd nss
> $ make libsym.a
> /home/seabra/work/Programs/amber11/bin/nab -c symop.nab
> make: /home/seabra/work/Programs/amber11/bin/nab: Command not found
> make: *** [symop.o] Error 127
>
> So, ptraj needs libsym.a, which in turn needs nab, which doesn't
> compile (at least in my cygwin installation) because 'nmode.c' cannot
> find 'complex.h'. So, (finally :-) ) I want to ask:
> 1. I understand that I may be missing something in my cygwin
> installation, but what?
> 2. Aren't those compilations supposed to be independent?
> I mean, should I not be able to install only ptraj if that's all I need?
>
> Anyways, I did find a workaround. It is documented *only in nmode.c
> source file*, not in any config file. After the error, I can compile
> only nmode.c with:
>
> $ cd nab
> $ gcc -c -O3 -DCYGWIN -m32 -DUSE_AMBER_C9XCOMPLEX -DBINTRAJ nmode.c
>
> After that, everything else compiles just fine:
>
> $ cd ..
> $ make -f Makefile_at
> [...] (plus a bunch of warnings from gleap)
> Completed installation of AmberTools, version 1.2
>
> There's no documentation about the use of '-DUSE_AMBER_C9XCOMPLEX'
> anywhere. However, I'm not really convinced it should be necessary,
> but I can't identify what I'm missing here. Any ideas?
>
> Thanks,
> Gustavo.
>
Received on Sun Sep 07 2008 - 06:08:09 PDT
