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'
pmeRecip.o:pmeRecip.c:(.text+0x1307): undefined reference to `fftw_destroy_plan'
pmeRecip.o:pmeRecip.c:(.text+0x1318): undefined reference to `fftw_destroy_plan'
pmeRecip.o:pmeRecip.c:(.text+0x14f2): undefined reference to `fftw_execute'
pmeRecip.o:pmeRecip.c:(.text+0x17ea): undefined reference to `fftw_execute'
pmeRecip.o:pmeRecip.c:(.text+0x1a12): undefined reference to `fftw_execute'
pmeRecip.o:pmeRecip.c:(.text+0x1d63): undefined reference to `fftw_execute'
pmeRecip.o:pmeRecip.c:(.text+0x1fce): undefined reference to `fftw_execute'
pmeRecip.o:pmeRecip.c:(.text+0x232f): more undefined references to `fftw_execute' follow
pmeRecip.o:pmeRecip.c:(.text+0x1097): undefined reference to `fftw_destroy_plan'
mleRecip.o:mleRecip.c:(.text+0xf71): undefined reference to `fftw_plan_dft_r2c_3d'
mleRecip.o:mleRecip.c:(.text+0xfbc): undefined reference to `fftw_plan_dft_c2r_3d'
mleRecip.o:mleRecip.c:(.text+0x13c0): undefined reference to `fftw_plan_dft_r2c_3d'
mleRecip.o:mleRecip.c:(.text+0x1512): undefined reference to `fftw_execute'
mleRecip.o:mleRecip.c:(.text+0x151a): undefined reference to `fftw_destroy_plan'
mleRecip.o:mleRecip.c:(.text+0x1978): undefined reference to `fftw_execute'
mleRecip.o:mleRecip.c:(.text+0x1a24): undefined reference to `fftw_execute'
Restraints.o:Restraints.c:(.text+0x1e42): undefined reference to `fftw_plan_dft_r2c_3d'
Restraints.o:Restraints.c:(.text+0x1e87): undefined reference to `fftw_plan_dft_r2c_3d'
Restraints.o:Restraints.c:(.text+0x1ecc): undefined reference to `fftw_plan_dft_c2r_3d'
Restraints.o:Restraints.c:(.text+0x1ed6): undefined reference to `fftw_execute'
Restraints.o:Restraints.c:(.text+0x1ede): undefined reference to `fftw_execute'
Restraints.o:Restraints.c:(.text+0x1f4f): undefined reference to `fftw_execute'
Restraints.o:Restraints.c:(.text+0x1f57): undefined reference to `fftw_destroy_plan'
Restraints.o:Restraints.c:(.text+0x1f5f): undefined reference to `fftw_destroy_plan'
Restraints.o:Restraints.c:(.text+0x1f67): undefined reference to `fftw_destroy_plan'
Restraints.o:Restraints.c:(.text+0x2343): undefined reference to `fftw_plan_dft_r2c_3d'
Restraints.o:Restraints.c:(.text+0x2388): undefined reference to `fftw_plan_dft_r2c_3d'
Restraints.o:Restraints.c:(.text+0x23cd): undefined reference to `fftw_plan_dft_c2r_3d'
Restraints.o:Restraints.c:(.text+0x23d7): undefined reference to `fftw_execute'
Restraints.o:Restraints.c:(.text+0x23df): undefined reference to `fftw_execute'
Restraints.o:Restraints.c:(.text+0x2466): undefined reference to `fftw_execute'
Restraints.o:Restraints.c:(.text+0x246e): undefined reference to `fftw_destroy_plan'
Restraints.o:Restraints.c:(.text+0x2476): undefined reference to `fftw_destroy_plan'
Restraints.o:Restraints.c:(.text+0x247e): undefined reference to `fftw_destroy_plan'
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'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x3bf): undefined reference to `nc_inq_attlen'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x40c): undefined reference to `nc_get_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x494): undefined reference to `nc_inq_dimid'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x4c8): undefined reference to `nc_inq_dimlen'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x51f): undefined reference to `nc_inq_varid'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x55c): undefined reference to `nc_inq_varid'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x5a5): undefined reference to `nc_inq_varid'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x5cb): undefined reference to `nc_inq_attlen'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x614): undefined reference to `nc_get_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x68e): undefined reference to `nc_get_var_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x6c0): undefined reference to `nc_inq_varid'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x6f0): undefined reference to `nc_inq_varid'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x796): undefined reference to `nc_inq_dimid'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x7ca): undefined reference to `nc_inq_dimlen'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x879): undefined reference to `nc_inq_varid'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x96c): undefined reference to `nc_close'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xbe2): undefined reference to `nc_create'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xc70): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xcb3): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xcf2): undefined reference to `nc_def_dim'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xd4b): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xd97): undefined reference to `nc_def_dim'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xdfe): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xe45): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xe9e): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xee5): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xf34): undefined reference to `nc_put_att_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xf73): undefined reference to `nc_def_dim'
AmberNetcdf.o:AmberNetcdf.c:(.text+0xfcc): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x100b): undefined reference to `nc_def_dim'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x104a): undefined reference to `nc_def_dim'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x10b1): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1118): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x115f): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x11b8): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x11ff): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x125b): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x12a7): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x12eb): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x132f): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1373): more undefined references to `nc_put_att_text' follow
AmberNetcdf.o:AmberNetcdf.c:(.text+0x141e): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1465): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1495): undefined reference to `nc_set_fill'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x14b9): undefined reference to `nc_enddef'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x151f): undefined reference to `nc_put_vara_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1569): undefined reference to `nc_put_vara_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x15c8): undefined reference to `nc_put_vara_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x162d): undefined reference to `nc_put_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1679): undefined reference to `nc_put_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x16d9): undefined reference to `nc_put_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x171e): undefined reference to `nc_put_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1769): undefined reference to `nc_put_var_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x17b0): undefined reference to `nc_put_var_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x17d4): undefined reference to `nc_sync'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x17e0): undefined reference to `nc_close'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x19ae): undefined reference to `nc_create'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x19fe): undefined reference to `nc_def_dim'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1a4b): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1a8d): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1ac7): undefined reference to `nc_def_dim'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1b14): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1b51): undefined reference to `nc_def_dim'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1bbc): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1bfe): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1c38): undefined reference to `nc_def_dim'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1c85): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1cbf): undefined reference to `nc_def_dim'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1cf9): undefined reference to `nc_def_dim'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1d4d): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1daf): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1df1): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1e3e): undefined reference to `nc_def_var'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1e80): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1edd): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1f77): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1fba): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x1ffd): undefined reference to `nc_put_att_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2040): more undefined references to `nc_put_att_text' follow
AmberNetcdf.o:AmberNetcdf.c:(.text+0x20b2): undefined reference to `nc_set_fill'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x20d5): undefined reference to `nc_enddef'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2136): undefined reference to `nc_put_vara_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x217b): undefined reference to `nc_put_vara_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x21d5): undefined reference to `nc_put_vara_text'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2293): undefined reference to `nc_get_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2337): undefined reference to `nc_get_vara_float'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2544): undefined reference to `nc_get_var_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x25a1): undefined reference to `nc_get_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x25fc): undefined reference to `nc_get_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x269e): undefined reference to `nc_get_vara_float'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2721): undefined reference to `nc_get_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2784): undefined reference to `nc_get_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x27c5): undefined reference to `nc_get_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x294b): undefined reference to `nc_get_var_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x29a8): undefined reference to `nc_get_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2a03): undefined reference to `nc_get_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2a9e): undefined reference to `nc_get_vara_float'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2b21): undefined reference to `nc_get_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2b84): undefined reference to `nc_get_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2bc5): undefined reference to `nc_get_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2d7b): undefined reference to `nc_put_vara_float'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2e47): undefined reference to `nc_put_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2e84): undefined reference to `nc_put_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x2eaf): undefined reference to `nc_sync'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x305b): undefined reference to `nc_put_vara_float'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x3123): undefined reference to `nc_put_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x3164): undefined reference to `nc_put_vara_double'
AmberNetcdf.o:AmberNetcdf.c:(.text+0x31a2): undefined reference to `nc_sync'
mdgx.o:mdgx.c:(.text.startup+0x1102): undefined reference to `fftw_cleanup'
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.
Regards
Nigel
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Received on Tue Sep 08 2015 - 06:30:03 PDT
