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 - 06:08:08 PDT
