[gmx-users] Cmake instruction file of new gromacs version trouble?

[Christian Wagner]

Hello All,

I am trying to install gromacs on a Windows 7 computer. I downloaded the current (Dec 2013) gromacs-4.6.5.tar.gz file from the gromacs web server. Then I uncompressed using 7-zip. I use the graphical interface to Cmake 2.8.12.1 in order to generate the build files and I choose the Visual Studio 12 Express 64 bit compiler or I let Cmake generate Unix files. I have verified permissions to the diverse installation folders and changed their locations such that neither spaces nor other special characters interfere. I also installed Windows SDK 8.1.

I can generate the build files, but Cmake can then not perform the build and exits with an MSB6006 cmd.exe code 9009 error in fftwBuild.vcxproj. Similarly using Cmake on Cygwin also results in aborting the make indicating errors in fftwbuild.
I've listed the corresponding verbose below.

Could it be that there are some troubles with the Cmake instructions for the latest gromacs release?

Best regards,
Chris




Here here the log files for the VS12 compilation:

First step: set source ( C:\gromacs465src) and build (C:\gromacsbuild) directories and compiler (VS 11 Win 64)


The C compiler identification is MSVC 17.0.61030.0
Check for working C compiler using: Visual Studio 11 Win64
Check for working C compiler using: Visual Studio 11 Win64 -- works
Detecting C compiler ABI info
Detecting C compiler ABI info - done
Looking for NVIDIA GPUs present in the system
Could not detect NVIDIA GPUs
No compatible CUDA toolkit found (v3.2+), disabling native GPU acceleration
Checking for GCC x86 inline asm
Checking for GCC x86 inline asm - not supported
Detecting best acceleration for this CPU
Detected best acceleration for this CPU - AVX_256
Try OpenMP C flag = [/openmp]
Performing Test OpenMP_FLAG_DETECTED
Performing Test OpenMP_FLAG_DETECTED - Success
Found OpenMP: /openmp  
Performing Test CFLAGS_WARN
Performing Test CFLAGS_WARN - Success
Looking for include file string.h
Looking for include file string.h - found
Looking for include file math.h
Looking for include file math.h - found
Looking for include file limits.h
Looking for include file limits.h - found
Looking for include file memory.h
Looking for include file memory.h - found
Looking for include file unistd.h
Looking for include file unistd.h - not found
Looking for include file direct.h
Looking for include file direct.h - found
Looking for include file pwd.h
Looking for include file pwd.h - not found
Looking for include file stdint.h
Looking for include file stdint.h - found
Looking for include file stdlib.h
Looking for include file stdlib.h - found
Looking for include file pthread.h
Looking for include file pthread.h - not found
Looking for include file dirent.h
Looking for include file dirent.h - not found
Looking for include file inttypes.h
Looking for include file inttypes.h - not found
Looking for include file regex.h
Looking for include file regex.h - not found
Looking for include file sys/types.h
Looking for include file sys/types.h - found
Looking for include file sys/stat.h
Looking for include file sys/stat.h - found
Looking for include file sys/time.h
Looking for include file sys/time.h - not found
Looking for include file rpc/rpc.h
Looking for include file rpc/rpc.h - not found
Looking for include files rpc/rpc.h, rpc/xdr.h
Looking for include files rpc/rpc.h, rpc/xdr.h - not found
Looking for include file io.h
Looking for include file io.h - found
Looking for include file sched.h
Looking for include file sched.h - not found
Looking for strcasecmp
Looking for strcasecmp - not found
Looking for strdup
Looking for strdup - found
Looking for vprintf
Looking for vprintf - found
Looking for memcmp
Looking for memcmp - found
Looking for posix_memalign
Looking for posix_memalign - not found
Looking for memalign
Looking for memalign - not found
Looking for _aligned_malloc
Looking for _aligned_malloc - found
Looking for gettimeofday
Looking for gettimeofday - not found
Looking for isnan
Looking for isnan - not found
Looking for _isnan
Looking for _isnan - found
Looking for fsync
Looking for fsync - not found
Looking for _fileno
Looking for _fileno - found
Looking for fileno
Looking for fileno - found
Looking for _commit
Looking for _commit - found
Looking for sigaction
Looking for sigaction - not found
Looking for sysconf
Looking for sysconf - not found
Looking for sched_setaffinity
Looking for sched_setaffinity - not found
Looking for sched_getaffinity
Looking for sched_getaffinity - not found
Looking for rsqrt
Looking for rsqrt - not found
Looking for rsqrtf
Looking for rsqrtf - not found
Looking for sqrtf
Looking for sqrtf - found
Looking for sqrt in m
Looking for sqrt in m - not found
Looking for cbrt in m
Looking for cbrt in m - not found
Looking for stddef.h
Looking for stddef.h - found
Check size of bool
Check size of bool - failed
Check size of int
Check size of int - done
Check size of long int
Check size of long int - done
Check size of long long int
Check size of long long int - done
Check size of off_t
Check size of off_t - done
Check size of void *
Check size of void * - done
Check size of uid_t
Check size of uid_t - failed
Check size of gid_t
Check size of gid_t - failed
Check size of size_t
Check size of size_t - done
Check size of off_t
Check size of off_t - done
Check if the system is big endian
Searching 16 bit integer
Check size of unsigned short
Check size of unsigned short - done
Using unsigned short
Check if the system is big endian - little endian
Looking for include file pthread.h
Looking for include file pthread.h - not found
Found Threads: TRUE  
Atomic operations found
Setting build user/date/host/cpu information
Setting build user & time - not on Unix, using anonymous
Checking floating point format
Checking floating point format - IEEE754 (LE byte, LE word)
Checking for 64-bit off_t
Checking for 64-bit off_t - present with _fseeki64
Checking for fseeko/ftello
Checking for SIGUSR1
Checking for SIGUSR1 - not found
Checking for inline keyword
Checking for inline keyword - __inline
Checking for restrict keyword
Checking for restrict keyword - __restrict
Checking for pipe support
Checking for isfinite
Performing Test isfinite_compile_ok
Performing Test isfinite_compile_ok - Failed
Checking for isfinite - no
Checking for _isfinite
Performing Test _isfinite_compile_ok
Performing Test _isfinite_compile_ok - Failed
Checking for _isfinite - no
Checking for _finite
Performing Test _finite_compile_ok
Performing Test _finite_compile_ok - Success
Checking for _finite - yes
Checking for system XDR support
Checking for system XDR support - not present
Performing Test GNU_AVX_CFLAG
Performing Test GNU_AVX_CFLAG - Failed
Performing Test MSVC_AVX_CFLAG
Performing Test MSVC_AVX_CFLAG - Success
Looking for immintrin.h
Looking for immintrin.h - found
Looking for x86intrin.h
Looking for x86intrin.h - not found
Looking for intrin.h
Looking for intrin.h - found
Enabling 256-bit AVX Gromacs acceleration
Checking for gcc AVX maskload bug
Checking for gcc AVX maskload bug - not present
Could NOT find PkgConfig (missing:  PKG_CONFIG_EXECUTABLE) 
pkg-config could not detect fftw3f, trying generic detection
Could not find fftw3f library named libfftw3f, please specify its location in CMAKE_PREFIX_PATH or FFTWF_LIBRARY by hand (e.g. -DFFTWF_LIBRARY='/path/to/libfftw3f.so')
CMake Error at CMakeLists.txt:900 (MESSAGE):
  Cannot find FFTW 3 (with correct precision - libfftw3f for single-precision
  GROMACS or libfftw3 for double-precision GROMACS).  Either choose the right
  precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the
  advanced option to let GROMACS build FFTW 3 for you
  (-DGMX_BUILD_OWN_FFTW=ON) , or use the really slow GROMACS built-in fftpack
  library (-DGMX_FFT_LIBRARY=fftpack).


Configuring incomplete, errors occurred!
See also "C:/gromacsbuild/CMakeFiles/CMakeOutput.log".
See also "C:/gromacsbuild/CMakeFiles/CMakeError.log".







Then: I choose the GMX_Build_OWN_FFTW option
This allows to complete the configuration and generate the build files:







No compatible CUDA toolkit found (v3.2+), disabling native GPU acceleration
CMake Warning at src/contrib/fftw/CMakeLists.txt:35 (message):
  The GROMACS build will download FFTW 3.3.2 as requested, but it will not
  know the file it receives is correct.  GROMACS will build and link to FFTW
  anyway, but there is a possible security risk if you execute a GROMACS tool
  that calls this library.  You can use

  make gmxfftw

   to do the download and build, and then run

  md5sum src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz

  to see if it matches 6977ee770ed68c85698c7168ffa6e178.  If so, everything
  is OK and you should proceed with the rest of the GROMACS build.
  Alternatively, you can follow the GROMACS installation instructions to
  build FFTW yourself.


The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2
Using external FFT library - FFTW3
A BLAS library was not found by CMake in the paths available to it. Falling back on the GROMACS internal version of the BLAS library instead. This is fine for normal usage.
LAPACK requires BLAS
A LAPACK library was not found by CMake in the paths available to it. Falling back on the GROMACS internal version of the LAPACK library instead. This is fine for normal usage.
Found the ability to use plug-ins when building shared libaries, so will compile to use plug-ins (e.g. to read VMD-supported file formats).
Checking for suitable VMD version
VMD plugins not found. Path to VMD can be set with VMDDIR.
Using default binary suffix: ""
Using default library suffix: ""
Configuring done
Generating done








Then I launch cmake --build C:\gromacsbuild which aborts as follows:







c:\CMake2.8\bin>cmake --build C:\gromacsbuild
Microsoft (R) Build Engine version 4.0.30319.18408
[Microsoft .NET Framework, version 4.0.30319.18408]
Copyright (C) Microsoft Corporation. All rights reserved.

Build started 1/15/2014 11:16:52 AM.
Project "C:\gromacsbuild\ALL_BUILD.vcxproj" on node 1 (default targets).
Project "C:\gromacsbuild\ALL_BUILD.vcxproj" (1) is building "C:\gromacsbuild\ZER
O_CHECK.vcxproj" (2) on node 1 (default targets).
InitializeBuildStatus:
  Creating "x64\Debug\ZERO_CHECK\ZERO_CHECK.unsuccessfulbuild" because "AlwaysCr
eate" was specified.
FinalizeBuildStatus:
  Deleting file "x64\Debug\ZERO_CHECK\ZERO_CHECK.unsuccessfulbuild".
  Touching "x64\Debug\ZERO_CHECK\ZERO_CHECK.lastbuildstate".
Done Building Project "C:\gromacsbuild\ZERO_CHECK.vcxproj" (default targets).
Project "C:\gromacsbuild\ALL_BUILD.vcxproj" (1) is building "C:\gromacsbuild\src
\tools\do_dssp.vcxproj" (3) on node 1 (default targets).
Project "C:\gromacsbuild\src\tools\do_dssp.vcxproj" (3) is building "C:\gromacsb
uild\src\contrib\fftw\fftwBuild.vcxproj" (4) on node 1 (default targets).
InitializeBuildStatus:
  Touching "x64\Debug\fftwBuild\fftwBuild.unsuccessfulbuild".
CustomBuild:
  Building Custom Rule C:/gromacs465src/src/contrib/fftw/CMakeLists.txt
  CMake does not need to re-run because C:\gromacsbuild\src\contrib\fftw\CMakeFi
les\generate.stamp is up-to-date.
  Creating directories for 'fftwBuild'
  Performing download step (download, verify and extract) for 'fftwBuild'
  -- downloading...
       src='http://www.fftw.org/fftw-3.3.2.tar.gz'
       dst='C:/gromacsbuild/src/contrib/fftw/fftwBuild-prefix/src/fftw-3.3.2.tar
.gz'
       timeout='none'
  -- [download 0% complete]
  -- [download 1% complete]
  -- [download 6% complete]
  -- [download 12% complete]
  -- [download 18% complete]
  -- [download 23% complete]
  -- [download 29% complete]
  -- [download 35% complete]
  -- [download 41% complete]
  -- [download 48% complete]
  -- [download 55% complete]
  -- [download 62% complete]
  -- [download 69% complete]
  -- [download 78% complete]
  -- [download 86% complete]
  -- [download 95% complete]
  -- [download 100% complete]
  -- downloading... done
  -- verifying file...
       file='C:/gromacsbuild/src/contrib/fftw/fftwBuild-prefix/src/fftw-3.3.2.ta
r.gz'
CUSTOMBUILD : -- verifying file... warning : did not verify file - no URL_HASH s
pecified? [C:\gromacsbuild\src\contrib\fftw\fftwBuild.vcxproj]
  -- extracting...
       src='C:/gromacsbuild/src/contrib/fftw/fftwBuild-prefix/src/fftw-3.3.2.tar
.gz'
       dst='C:/gromacsbuild/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild'
  -- extracting... [tar xfz]
  -- extracting... [analysis]
  -- extracting... [rename]
  -- extracting... [clean up]
  -- extracting... done
  No update step for 'fftwBuild'
  No patch step for 'fftwBuild'
  Performing configure step for 'fftwBuild'
  'C:\gromacsbuild\src\contrib\fftw\fftwBuild-prefix\src\fftwBuild\configure' is
 not recognized as an internal or external command,
  operable program or batch file.
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V110\Microsoft.CppCommon.targe
ts(172,5): error MSB6006: "cmd.exe" exited with code 9009. [C:\gromacsbuild\src\
contrib\fftw\fftwBuild.vcxproj]
Done Building Project "C:\gromacsbuild\src\contrib\fftw\fftwBuild.vcxproj" (defa
ult targets) -- FAILED.
Done Building Project "C:\gromacsbuild\src\tools\do_dssp.vcxproj" (default targe
ts) -- FAILED.
Project "C:\gromacsbuild\ALL_BUILD.vcxproj" (1) is building "C:\gromacsbuild\sha
re\template\template.vcxproj" (98) on node 1 (default targets).
Project "C:\gromacsbuild\share\template\template.vcxproj" (98) is building "C:\g
romacsbuild\share\template\gromacs_include_links.vcxproj" (99) on node 1 (defaul
t targets).
InitializeBuildStatus:
  Creating "x64\Debug\gromacs_include_links\gromacs_include_links.unsuccessfulbu
ild" because "AlwaysCreate" was specified.
FinalizeBuildStatus:
  Deleting file "x64\Debug\gromacs_include_links\gromacs_include_links.unsuccess
fulbuild".
  Touching "x64\Debug\gromacs_include_links\gromacs_include_links.lastbuildstate
".
Done Building Project "C:\gromacsbuild\share\template\gromacs_include_links.vcxp
roj" (default targets).
Done Building Project "C:\gromacsbuild\share\template\template.vcxproj" (default
 targets) -- FAILED.
Done Building Project "C:\gromacsbuild\ALL_BUILD.vcxproj" (default targets) -- F
AILED.

Build FAILED.

"C:\gromacsbuild\ALL_BUILD.vcxproj" (default target) (1) ->
"C:\gromacsbuild\src\tools\do_dssp.vcxproj" (default target) (3) ->
"C:\gromacsbuild\src\contrib\fftw\fftwBuild.vcxproj" (default target) (4) ->
(CustomBuild target) ->
  CUSTOMBUILD : -- verifying file... warning : did not verify file - no URL_HASH
 specified? [C:\gromacsbuild\src\contrib\fftw\fftwBuild.vcxproj]


"C:\gromacsbuild\ALL_BUILD.vcxproj" (default target) (1) ->
"C:\gromacsbuild\src\tools\do_dssp.vcxproj" (default target) (3) ->
"C:\gromacsbuild\src\contrib\fftw\fftwBuild.vcxproj" (default target) (4) ->
(CustomBuild target) ->
  C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V110\Microsoft.CppCommon.tar
gets(172,5): error MSB6006: "cmd.exe" exited with code 9009. [C:\gromacsbuild\sr
c\contrib\fftw\fftwBuild.vcxproj]

    1 Warning(s)
    1 Error(s)

Time Elapsed 00:00:27.57

c:\CMake2.8\bin>











Here here the log files for the unix compilation:






The C compiler identification is GNU 4.5.2
Check for working C compiler: C:/MinGW32-xy/bin/gcc.exe
Check for working C compiler: C:/MinGW32-xy/bin/gcc.exe -- works
Detecting C compiler ABI info
Detecting C compiler ABI info - done
Looking for NVIDIA GPUs present in the system
Could not detect NVIDIA GPUs
No compatible CUDA toolkit found (v3.2+), disabling native GPU acceleration
Checking for GCC x86 inline asm
Checking for GCC x86 inline asm - supported
Detecting best acceleration for this CPU
Detected best acceleration for this CPU - AVX_256
Try OpenMP C flag = [-fopenmp]
Performing Test OpenMP_FLAG_DETECTED
Performing Test OpenMP_FLAG_DETECTED - Success
Found OpenMP: -fopenmp  
Performing Test CFLAGS_WARN
Performing Test CFLAGS_WARN - Success
Performing Test CFLAGS_WARN_EXTRA
Performing Test CFLAGS_WARN_EXTRA - Success
Performing Test CFLAGS_EXCESS_PREC
Performing Test CFLAGS_EXCESS_PREC - Success
Performing Test CFLAGS_COPT
Performing Test CFLAGS_COPT - Success
Performing Test CFLAGS_NOINLINE
Performing Test CFLAGS_NOINLINE - Success
Looking for include file string.h
Looking for include file string.h - found
Looking for include file math.h
Looking for include file math.h - found
Looking for include file limits.h
Looking for include file limits.h - found
Looking for include file memory.h
Looking for include file memory.h - found
Looking for include file unistd.h
Looking for include file unistd.h - found
Looking for include file direct.h
Looking for include file direct.h - found
Looking for include file pwd.h
Looking for include file pwd.h - not found
Looking for include file stdint.h
Looking for include file stdint.h - found
Looking for include file stdlib.h
Looking for include file stdlib.h - found
Looking for include file pthread.h
Looking for include file pthread.h - found
Looking for include file dirent.h
Looking for include file dirent.h - found
Looking for include file inttypes.h
Looking for include file inttypes.h - found
Looking for include file regex.h
Looking for include file regex.h - not found
Looking for include file sys/types.h
Looking for include file sys/types.h - found
Looking for include file sys/stat.h
Looking for include file sys/stat.h - found
Looking for include file sys/time.h
Looking for include file sys/time.h - found
Looking for include file rpc/rpc.h
Looking for include file rpc/rpc.h - not found
Looking for include files rpc/rpc.h, rpc/xdr.h
Looking for include files rpc/rpc.h, rpc/xdr.h - not found
Looking for include file io.h
Looking for include file io.h - found
Looking for include file sched.h
Looking for include file sched.h - found
Looking for strcasecmp
Looking for strcasecmp - found
Looking for strdup
Looking for strdup - found
Looking for vprintf
Looking for vprintf - found
Looking for memcmp
Looking for memcmp - found
Looking for posix_memalign
Looking for posix_memalign - not found
Looking for memalign
Looking for memalign - not found
Looking for _aligned_malloc
Looking for _aligned_malloc - found
Looking for gettimeofday
Looking for gettimeofday - found
Looking for isnan
Looking for isnan - found
Looking for _isnan
Looking for _isnan - found
Looking for fsync
Looking for fsync - not found
Looking for _fileno
Looking for _fileno - found
Looking for fileno
Looking for fileno - found
Looking for _commit
Looking for _commit - found
Looking for sigaction
Looking for sigaction - not found
Looking for sysconf
Looking for sysconf - not found
Looking for sched_setaffinity
Looking for sched_setaffinity - not found
Looking for sched_getaffinity
Looking for sched_getaffinity - not found
Looking for rsqrt
Looking for rsqrt - not found
Looking for rsqrtf
Looking for rsqrtf - not found
Looking for sqrtf
Looking for sqrtf - found
Looking for sqrt in m
Looking for sqrt in m - found
Looking for cbrt in m
Looking for cbrt in m - found
Looking for stddef.h
Looking for stddef.h - found
Check size of bool
Check size of bool - failed
Check size of int
Check size of int - done
Check size of long int
Check size of long int - done
Check size of long long int
Check size of long long int - done
Check size of off_t
Check size of off_t - done
Check size of void *
Check size of void * - done
Check size of uid_t
Check size of uid_t - failed
Check size of gid_t
Check size of gid_t - failed
Check size of size_t
Check size of size_t - done
Check size of off_t
Check size of off_t - done
Check if the system is big endian
Searching 16 bit integer
Check size of unsigned short
Check size of unsigned short - done
Using unsigned short
Check if the system is big endian - little endian
Looking for include file pthread.h
Looking for include file pthread.h - found
Looking for pthread_create
Looking for pthread_create - not found
Looking for pthread_create in pthreads
Looking for pthread_create in pthreads - not found
Looking for pthread_create in pthread
Looking for pthread_create in pthread - found
Found Threads: TRUE  
Atomic operations found
Performing Test PTHREAD_SETAFFINITY
Performing Test PTHREAD_SETAFFINITY - Failed
Setting build user/date/host/cpu information
Setting build user & time - not on Unix, using anonymous
Checking floating point format
Checking floating point format - IEEE754 (LE byte, LE word)
Checking for 64-bit off_t
Checking for 64-bit off_t - not present
Checking for fseeko/ftello - not found
Checking for SIGUSR1
Checking for SIGUSR1 - not found
Checking for inline keyword
Checking for inline keyword - __inline__
Checking for restrict keyword
Checking for restrict keyword - __restrict__
Checking for pipe support
Checking for isfinite
Performing Test isfinite_compile_ok
Performing Test isfinite_compile_ok - Success
Checking for isfinite - yes
Checking for _isfinite
Performing Test _isfinite_compile_ok
Performing Test _isfinite_compile_ok - Failed
Checking for _isfinite - no
Checking for _finite
Performing Test _finite_compile_ok
Performing Test _finite_compile_ok - Success
Checking for _finite - yes
Checking for system XDR support
Checking for system XDR support - not present
Performing Test GNU_AVX_CFLAG
Performing Test GNU_AVX_CFLAG - Success
Looking for immintrin.h
Looking for immintrin.h - found
Looking for x86intrin.h
Looking for x86intrin.h - not found
Looking for intrin.h
Looking for intrin.h - not found
Enabling 256-bit AVX Gromacs acceleration
Checking for gcc AVX maskload bug
Checking for gcc AVX maskload bug - found, will try to work around
Could NOT find PkgConfig (missing:  PKG_CONFIG_EXECUTABLE) 
pkg-config could not detect fftw3f, trying generic detection
Could not find fftw3f library named libfftw3f, please specify its location in CMAKE_PREFIX_PATH or FFTWF_LIBRARY by hand (e.g. -DFFTWF_LIBRARY='/path/to/libfftw3f.so')
CMake Error at CMakeLists.txt:900 (MESSAGE):
  Cannot find FFTW 3 (with correct precision - libfftw3f for single-precision
  GROMACS or libfftw3 for double-precision GROMACS).  Either choose the right
  precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the
  advanced option to let GROMACS build FFTW 3 for you
  (-DGMX_BUILD_OWN_FFTW=ON) , or use the really slow GROMACS built-in fftpack
  library (-DGMX_FFT_LIBRARY=fftpack).


Configuring incomplete, errors occurred!
See also "C:/gromacsbuild_unix/CMakeFiles/CMakeOutput.log".
See also "C:/gromacsbuild_unix/CMakeFiles/CMakeError.log".








Then I select the GMX_BUILD_OWN_FFTW and refonfigure, which gives the following output:







No compatible CUDA toolkit found (v3.2+), disabling native GPU acceleration
CMake Warning at src/contrib/fftw/CMakeLists.txt:35 (message):
  The GROMACS build will download FFTW 3.3.2 as requested, but it will not
  know the file it receives is correct.  GROMACS will build and link to FFTW
  anyway, but there is a possible security risk if you execute a GROMACS tool
  that calls this library.  You can use

  make gmxfftw

   to do the download and build, and then run

  md5sum src/contrib/fftw/gmxfftw-prefix/src/fftw-3.3.2.tar.gz

  to see if it matches 6977ee770ed68c85698c7168ffa6e178.  If so, everything
  is OK and you should proceed with the rest of the GROMACS build.
  Alternatively, you can follow the GROMACS installation instructions to
  build FFTW yourself.


The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2
Using external FFT library - FFTW3
A BLAS library was not found by CMake in the paths available to it. Falling back on the GROMACS internal version of the BLAS library instead. This is fine for normal usage.
LAPACK requires BLAS
A LAPACK library was not found by CMake in the paths available to it. Falling back on the GROMACS internal version of the LAPACK library instead. This is fine for normal usage.
Found the ability to use plug-ins when building shared libaries, so will compile to use plug-ins (e.g. to read VMD-supported file formats).
Checking for suitable VMD version
VMD plugins not found. Path to VMD can be set with VMDDIR.
Using default binary suffix: ""
Using default library suffix: ""
Configuring done
Generating done






And here the cygwin verbose when trying to use the above build instructions (gromacsbuild_unix holds the Cmake Unix build files):





c:\CMake2.8\bin>cd C:\gromacsbuild_unix

C:\gromacsbuild_unix>make
make[2]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/depend] Error 1
make[1]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
make: *** [all] Error 2