On 31/12/2011 3:13 AM, Rashek Kazi wrote:
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...
Yep. See
http://lists.gromacs.org/pipermail/gmx-users/2011-November/065886.html
for explanation and work-around for 4.5.5.
Mark
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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