On Tue, 2015-09-08 at 13:16 +0000, Nigel Palmer wrote:
> Hi All
>
> I am attempting to compile Amber15 on Windows using Cygwin but I am getting an compiler error during the 'make install' stage.
>
> My Cygwin is setup as described in http://ambermd.org/mswindows.html and I am using the following commands to build Amber.
> ./configure -cygwin -noX11 gnu
> source amber.sh
> make install
>
> After compiling for some time it gives the following errors
>
> gcc -O3 -fPIC -DCYGWIN -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN \
> -o /home/nigel/amber15/amber14/bin/mdgx.exe CompFrc.o BSpline.o Grid.o Random.o mdgxVector.o Matrix.o ChargeMap.o pmeRecip.o mleRecip.o pmeDirect.o CrdManip.o CellManip.o Topology.o Trajectory.o SpecialMath.o Nonbonded.o Bonded.o Parse.o Command.o Constraints.o Thermostats.o Barostats.o Integrator.o Timings.o Manual.o VirtualSites.o Buckingham.o ThermoDyn.o ChargeFit.o ParamOut.o ParamRead.o ParamFit.o IPolQ.o Restraints.o Debug.o BroadcastCommand.o MPIMap.o MPITypeCast.o ptrajmask.o AmberNetcdf.o mdgx.o -L/home/nigel/amber15/amber14/lib -lfftw3 /home/nigel/amber15/amber14/lib/libnetcdf.a
> gcc -c -fPIC -O3 -fPIC -DCYGWIN -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -I/home/nigel/amber15/amber14/include -I/home/nigel/amber15/amber14/include -o Wrappers.o Wrappers.c
> Wrappers.c:1:0: warning: -fPIC ignored for target (all code is position independent)
> #include <stdlib.h>
> ^
> gcc -shared -o /home/nigel/amber15/amber14/lib/libmdgx.so -fPIC -DCYGWIN -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -O3 -L/home/nigel/amber15/amber14/lib -larpack -llapack -lblas \
> -lfftw3 /home/nigel/amber15/amber14/lib/libnetcdf.a CompFrc.o BSpline.o Grid.o Random.o mdgxVector.o Matrix.o ChargeMap.o pmeRecip.o mleRecip.o pmeDirect.o CrdManip.o CellManip.o Topology.o Trajectory.o SpecialMath.o Nonbonded.o Bonded.o Parse.o Command.o Constraints.o Thermostats.o Barostats.o Integrator.o Timings.o Manual.o VirtualSites.o Buckingham.o ThermoDyn.o ChargeFit.o ParamOut.o ParamRead.o ParamFit.o IPolQ.o Restraints.o Debug.o BroadcastCommand.o MPIMap.o MPITypeCast.o ptrajmask.o AmberNetcdf.o mdgx.o Wrappers.o
> pmeRecip.o:pmeRecip.c:(.text+0x742): undefined reference to `fftw_plan_dft_r2c_3d'
> pmeRecip.o:pmeRecip.c:(.text+0x770): undefined reference to `fftw_plan_dft_c2r_3d'
> pmeRecip.o:pmeRecip.c:(.text+0x1087): undefined reference to `fftw_destroy_plan'
[snip]
> AmberNetcdf.o:AmberNetcdf.c:(.text+0x17): undefined reference to `nc_strerror'
> AmberNetcdf.o:AmberNetcdf.c:(.text+0xd0): undefined reference to `nc_inq'
> AmberNetcdf.o:AmberNetcdf.c:(.text+0x1d5): undefined reference to `nc_inq_varname'
> AmberNetcdf.o:AmberNetcdf.c:(.text+0x384): undefined reference to `nc_open'
[snip]
> collect2: error: ld returned 1 exit status
> Makefile:163: recipe for target '/home/nigel/amber15/amber14/lib/libmdgx.so' failed
> make[2]: *** [/home/nigel/amber15/amber14/lib/libmdgx.so] Error 1
> make[2]: Leaving directory '/home/nigel/amber15/amber14/AmberTools/src/mdgx'
> Makefile:16: recipe for target 'serial' failed
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory '/home/nigel/amber15/amber14/AmberTools/src'
> Makefile:7: recipe for target 'install' failed
> make: *** [install] Error 2
>
> Thank you for any help.
For whatever reason, libfftw3 and libnetcdf are not being found
correctly. Do you see a "libfftw3.so" or "libnetcdf.a" in
$AMBERHOME/lib?
I don't personally have a Windows machine to test this on, so I'm not
positive that Windows/Cygwin will necessarily work...
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 08 2015 - 07:00:04 PDT
