[gmx-users] problem with gromacs

[Sylwia Chmielewska]

Hello,
Thanks for the advice. For one moment everything was ok, but at some point appeared an error.

$ 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.Abraham at anu.edu.au>
Do: "Discussion list for GROMACS users" <gmx-users at 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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