[gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8

Justin A. Lemkul jalemkul at vt.edu
Mon May 23 22:04:57 CEST 2011

Peter C. Lai wrote:
> On 2011-05-23 02:37:54PM -0500, Matthew Bick wrote:
>> Dear Gromacs community.  I am attempting to install the latest version
>> of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8).  I
>> have successfully installed FFTW following the instructions provided
>> on the Gromacs installation page.
>> "./configure --with-fft=fftw3" appears to work properly, but when I
>> perform  "Make" I get the following errors:
>> ld: symbol(s) not found
>> collect2: ld returned 1 exit status
>> make[4]: *** [libgmx.la] Error 1
>> make[3]: *** [all-recursive] Error 1
>> make[2]: *** [all-recursive] Error 1
>> make[1]: *** [all] Error 2
>> make: *** [all-recursive] Error 1
>> I did configure my shell (bash) environment, as per the Gromacs
>> installation instructions.  "Make" runs for about 10 minutes before I
>> get these errors.  I have searched the mailing list, and have seen
>> people report problems similar to mine, but couldn't determine how
>> those problems were resolved.  Also from the mailing list, I
>> understand that the errors I've listed above aren't that informative.
>> If it helps, I repeatedly get the following warnings during "Make":
>> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
>> function ‘tMPI_Atomic_add_return’:
>> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46:
>> warning: implicit declaration of function ‘__sync_add_and_fetch’
>> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
>> function ‘tMPI_Atomic_fetch_add’:
>> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51:
>> warning: implicit declaration of function ‘__sync_fetch_and_add’
>> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
>> function ‘tMPI_Atomic_cas’:
>> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57:
>> warning: implicit declaration of function
>> ‘__sync_bool_compare_and_swap’
>> If anyone has any suggestions, they would be greatly appreciated.
>> Thanks.
> Some things to watch out for:
> single vs. double precision (the library versions must match between
> fftw and what you passed to ./configure for gromacs (--enable-float
> is single precision,--disable-float is double).

If incorrect FFTW libraries were found, configuration would have failed.

> Maybe you need --enable-shared and specify correct LDFLAGS...
> The warnings section seems to imply this is happening in the threads/MPI
> section, Justin can correct me if I'm wrong, but maybe you need to explicitly
> disable mpi with --disable-mpi in the configure?

The thread_mpi library corresponds to the internal threading built into Gromacs 
and doesn't have anything to do with external MPI libraries.  The --disable-mpi 
option is the default behavior, anyway, and is only used in case of an MPI 
(non-threading) build.  It is worth noting that in a single installation step, 
threading and MPI cannot be mixed; you use one or the other.  A full 
configuration command would be necessary to see what's going on.


> Gromacs 4.5.4 is also in MacPorts, which contains a simplified options 
> framework (and will install gcc45 for you if you want as well) for all the
> popular configure variations:
> http://www.macports.org/ports.php?by=name&substr=gromacs
> (I would probably go with +gcc45, +gsl, +no_x11 [avoids openmotif]
> and +optimize [for gsl])
> Once you do get it working, watchout for overheating on that thing :)


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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