[gmx-users] make error "Makefile:347: recipe for target `all-recursive' failed" for Gromacs-4.5.5

[Rashek Kazi]

I am currently attempting to install gromacs-4.5.5. on a winXP 32bit system
through Cygwin. I had previously installed gromacs-4.5.4 without any issue
but now I get an error during Make that reads like the following...

mv -f .deps/pthreads.Tpo .deps/pthreads.Plo
/bin/sh ../../../libtool --tag=CC    --mode=compile cc  -DHAVE_CONFIG_H -I.
-I..

                                            /../../src
-I/usr/include/libxml2  -I../../../include -I/usr/local/include  -O3


                                 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-lo


    ops -std=gnu99 -fexcess-precision=fast  -I./include -MT numa_malloc.lo
-MD -MP -

                                                MF .deps/numa_malloc.Tpo -c
-o numa_malloc.lo numa_malloc.c
 cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2
-I../../../include


 -I/usr/local/include -O3 -fomit-frame-pointer -finline-functions -Wall
-Wno-unu

                                                sed -msse2
-funroll-all-loops -std=gnu99 -fexcess-precision=fast -I./include -MT


                                 numa_malloc.lo -MD -MP -MF
.deps/numa_malloc.Tpo -c numa_malloc.c  -DPIC -o .li


                bs/numa_malloc.o
numa_malloc.c:117:73: error: expected ‘)’ before ‘Processor’
numa_malloc.c:118:78: error: expected ‘)’ before ‘ProcNumber’
numa_malloc.c:121:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ be

                                                          fore
‘smalloc_GetNumaProcessorNodeEx’
numa_malloc.c:122:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ be

                                                          fore
‘smalloc_GetCurrentProcessorNumberEx’
numa_malloc.c: In function ‘InitNumaHeapSupport’:
numa_malloc.c:151:5: error: ‘smalloc_GetCurrentProcessorNumberEx’
undeclared (fi

                                                      rst use in this
function)
numa_malloc.c:151:5: note: each undeclared identifier is reported only once
for

                                           each function it appears in
numa_malloc.c:151:44: error: ‘func_GetCurrentProcessorNumberEx_t’
undeclared (fi

                                                      rst use in this
function)
numa_malloc.c:151:79: error: expected ‘;’ before ‘GetProcAddress’
numa_malloc.c:152:5: error: ‘smalloc_GetNumaProcessorNodeEx’ undeclared
(first u

                                                se in this function)
numa_malloc.c:152:39: error: ‘func_GetNumaProcessorNodeEx_t’ undeclared
(first u

                                                se in this function)
numa_malloc.c:152:69: error: expected ‘;’ before ‘GetProcAddress’
numa_malloc.c: In function ‘ReturnHeapHandle’:
numa_malloc.c:246:5: error: ‘PROCESSOR_NUMBER’ undeclared (first use in
this fun

                                                ction)
numa_malloc.c:246:22: error: expected ‘;’ before ‘CurrentProcessorNumber’
numa_malloc.c:285:5: warning: implicit declaration of function
‘smalloc_GetCurre

                                                        ntProcessorNumberEx’
numa_malloc.c:285:42: error: ‘CurrentProcessorNumber’ undeclared (first use
in t

                                            his function)
numa_malloc.c:287:5: warning: implicit declaration of function
‘smalloc_GetNumaP

                                                        rocessorNodeEx’
numa_malloc.c:324:9: warning: implicit declaration of function
‘HeapSetInformati

                                                        on’
Makefile:332: recipe for target `numa_malloc.lo' failed
make[4]: *** [numa_malloc.lo] Error 1
make[4]: Leaving directory
`/home/Administrator/gromacs-4.5.5/src/gmxlib/thread_


                mpi'
Makefile:599: recipe for target `all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/Administrator/gromacs-4.5.5/src/gmxlib'
Makefile:302: recipe for target `all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/Administrator/gromacs-4.5.5/src'
Makefile:238: recipe for target `all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/Administrator/gromacs-4.5.5/src'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1


I have no idea why this is and how to fix it, below are all of the steps I
followed exactly as I did for 4.5.4.

I first uninstalled fftw and manually installed fftw-3.3 for single
precision with the following...

./configure --with-our-malloc16 --with-windows-f77-mangling --enable-shared
--disable-static --enable-
threads --with-combined-threads --enable-portable-binary --enable-float
--enable-sse
make
make install

I didn't see any glitches in there.

I cd-ed into the gromacs-4.5.5 folder and did the following:

export CPPFLAGS="-I/usr/local/include"
export LDFLAGS="-L/usr/local/lib"

./configure --enable-cpu-optimization --enable-largefile

make

and that's where I'm stuck. I tried re-installing 4.5.4 and was unable to
so I'm wondering if the updated fftw build is causing this. Any help would
be appreciated. I'm not a linux user so please spell out explanations for
me, sorry for the inconvenience. Thanks!

-- 
Rashek Kazi
GS 2
MSTP Candidate
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