[gmx-users] error message during make after gtomacs configuration

[Mark Abraham]

On 10/03/2012 5:52 PM, Dialing Pretty wrote:
> Dear All,
> My command is ./configure --disable-threads

Thanks. You do need --disable-threads, as noted by the Cygwin 
installation guide. Your earlier errors looked consistent with not 
having used it.
> The error message are as following. I am looking forward to getting a 
> message from you on how to avoid the error message.

I do observe intermittent issues with builds on Cygwin that look 
somewhat similar to the ones you suggest. Re-running make eventually 
succeeds. I expect this is some upstream issue that has nothing to do 
with GROMACS.

Mark

> Cheers,
> Dialing
> /bin/sh ../../../libtool --tag=CC--mode=compile 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 -MT sdot.lo -MD 
> -MP -MF .deps/sdot.Tpo -c -o sdot.lo sdot.c
> make[4]: execvp: /bin/sh: Bad address
> ../../../libtool: fork: retry: Resource temporarily unavailable
> ../../../libtool: fork: retry: Resource temporarily unavailable
> ../../../libtool: fork: retry: Resource temporarily unavailable
> ../../../libtool: fork: retry: Resource temporarily unavailable
> ../../../libtool: fork: Resource temporarily unavailable
> Makefile:338: recipe for target `sdot.lo' failed
> make[4]: *** [sdot.lo] Error 254
> make[4]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib/gmx_blas'
> Makefile:599: recipe for target `all-recursive' failed
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib'
> Makefile:302: recipe for target `all-recursive' failed
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
> Makefile:238: recipe for target `all' failed
> make[1]: *** [all] Error 2
> make[1]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
> Makefile:347: recipe for target `all-recursive' failed
> make: *** [all-recursive] Error 1
>
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Saturday, 10 March 2012 2:07 PM
> *Subject:* Re: [gmx-users] error message during make after gtomacs 
> configuration
>
> On 10/03/2012 2:50 PM, Dialing Pretty wrote:
>> Dear All,
>> After I run the Gromacs 4.5.5 configuration (in this step there is no 
>> error), I run make, but I meet the following error messages.
>> Will you please give me some suggestions on how to avoid these error 
>> messages?
>
> No. You haven't told us your configure command, so we're not going to 
> guess what you're doing wrong.
>
> Mark
>
>> Cheers,
>> Dialing
>> 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 
>> `/cygdrive/d/GROMACSNEW/GROMACS455/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 
>> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/gmxlib'
>> Makefile:302: recipe for target `all-recursive' failed
>> make[2]: *** [all-recursive] Error 1
>> make[2]: Leaving directory 
>> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
>> Makefile:238: recipe for target `all' failed
>> make[1]: *** [all] Error 2
>> make[1]: Leaving directory 
>> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
>> Makefile:347: recipe for target `all-recursive' failed
>> make: *** [all-recursive] Error 1
>>
>>
>
>
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