On 11/01/2012 12:32 AM, Sylwia Chmielewska wrote:
Hello,
Thanks for the advice. For one moment everything was ok, but at some point
appeared an error.
Use "make distclean" before configure if you have already configured and
built and need to change stuff. Else things can get confused sometimes.
Mark
$ cd gromacs-4.5.5
./configure --disable-threads
make
.libs/xlate.o:xlate.c:(.text+0x774): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0x7a0): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0x7da): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0x801): more undefined references to `_save_free'
follow
.libs/xlate.o:xlate.c:(.text+0x9d5): undefined reference to
`_gmx_residuetype_is_rna'
.libs/xlate.o:xlate.c:(.text+0xa9b): undefined reference to `_put_symtab'
.libs/xlate.o:xlate.c:(.text+0xb3a): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xba6): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xc0d): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xc6d): undefined reference to `_save_free'
.libs/xlate.o:xlate.c:(.text+0xc99): undefined reference to `_save_free'
collect2: ld returned 1 exit status
Makefile:459: recipe for target `libgmxpreprocess.la' failed
make[3]: *** [libgmxpreprocess.la] Error 1
make[3]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/kernel'
Makefile:302: recipe for target `all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:238: recipe for target `all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1
What have I done now?
Sylwia Chmielewska
----- Oryginalna wiadomość -----
Od: "Mark Abraham"<mark.abra...@anu.edu.au>
Do: "Discussion list for GROMACS users"<gmx-users@gromacs.org>
Wysłane: niedziela, 8 styczeń 2012 23:37:42
Temat: Re: [gmx-users] problem with gromacs
On 9/01/2012 3:44 AM, Sylwia Chmielewska wrote:
Hello
Folder with the program GROMACS save in a folder cygwin / home / Sylwia.
then:
$ cd gromacs-4.5.5
./configure --enable-sse --enable-float
no errors occurred only at the end:
configure: WARNING: unrecognized options: - enable-sse
You'll note that
http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO does
not recommend --enable-sse for this part of the procedure.
make
no errors occurred only at the end:
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__’
before ‘smalloc_GetNumaProcessorNodeEx’
numa_malloc.c:122:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘smalloc_GetCurrentProcessorNumberEx’
numa_malloc.c: In function ‘InitNumaHeapSupport’:
numa_malloc.c:151:5: error: ‘smalloc_GetCurrentProcessorNumberEx’ undeclared
(first 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
(first use in this function)
numa_malloc.c:151:79: error: expected ‘;’ before ‘GetProcAddress’
numa_malloc.c:152:5: error: ‘smalloc_GetNumaProcessorNodeEx’ undeclared (first
use in this function)
numa_malloc.c:152:39: error: ‘func_GetNumaProcessorNodeEx_t’ undeclared (first
use 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
function)
numa_malloc.c:246:22: error: expected ‘;’ before ‘CurrentProcessorNumber’
numa_malloc.c:285:5: warning: implicit declaration of function
‘smalloc_GetCurrentProcessorNumberEx’
numa_malloc.c:285:42: error: ‘CurrentProcessorNumber’ undeclared (first use in
this function)
numa_malloc.c:287:5: warning: implicit declaration of function
‘smalloc_GetNumaProcessorNodeEx’
numa_malloc.c:324:9: warning: implicit declaration of function
‘HeapSetInformation’
Makefile:332: recipe for target `numa_malloc.lo' failed
make[4]: *** [numa_malloc.lo] Error 1
make[4]: Leaving directory `/home/Sylwia/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/Sylwia/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/Sylwia/gromacs-4.5.5/src'
Makefile:238: recipe for target `all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:347: recipe for target `all-recursive' failed
make: *** [all-recursive] Error 1
make install
Once something goes wrong, trying to press forward is normally fruitless.
There's a bug with threading that shows up with version 4.5.5 on Cygwin. Use
"configure --disable-threads" (and whatever else you need to use).
Mark
the same thing:
cc -DHAVE_CONFIG_H -I. -I../../../src -I/usr/include/libxml2 -I../../../include
-O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -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
.libs/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__’
before ‘smalloc_GetNumaProcessorNodeEx’
numa_malloc.c:122:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘smalloc_GetCurrentProcessorNumberEx’
numa_malloc.c: In function ‘InitNumaHeapSupport’:
numa_malloc.c:151:5: error: ‘smalloc_GetCurrentProcessorNumberEx’ undeclared
(first 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
(first use in this function)
numa_malloc.c:151:79: error: expected ‘;’ before ‘GetProcAddress’
numa_malloc.c:152:5: error: ‘smalloc_GetNumaProcessorNodeEx’ undeclared (first
use in this function)
numa_malloc.c:152:39: error: ‘func_GetNumaProcessorNodeEx_t’ undeclared (first
use 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
function)
numa_malloc.c:246:22: error: expected ‘;’ before ‘CurrentProcessorNumber’
numa_malloc.c:285:5: warning: implicit declaration of function
‘smalloc_GetCurrentProcessorNumberEx’
numa_malloc.c:285:42: error: ‘CurrentProcessorNumber’ undeclared (first use in
this function)
numa_malloc.c:287:5: warning: implicit declaration of function
‘smalloc_GetNumaProcessorNodeEx’
numa_malloc.c:324:9: warning: implicit declaration of function
‘HeapSetInformation’
Makefile:332: recipe for target `numa_malloc.lo' failed
make[3]: *** [numa_malloc.lo] Error 1
make[3]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/gmxlib/thread_mpi'
Makefile:599: recipe for target `install-recursive' failed
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src/gmxlib'
Makefile:302: recipe for target `install-recursive' failed
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/Sylwia/gromacs-4.5.5/src'
Makefile:347: recipe for target `install-recursive' failed
make: *** [install-recursive] Error 1
$ source /usr/local/gromacs/bin/GMXRC
-bash: /usr/local/gromacs/bin/GMXRC: No such file or directory
Thanks for any help.
Sylwia Chmielewska
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