[gmx-users] Installing mdrun-gpu Using Gromacs-4.5.3

Rossen Apostolov rossen at kth.se
Mon Nov 15 23:13:06 CET 2010


Did you run CMake in a fresh directory? If not try

$ rm CMakeCache.txt
$ make mdrun


On 11/14/10 5:58 PM, Solomon Berman wrote:
> Good day friends,
> I am trying to install mdrun-gpu on my MacBook Pro, using Mac OS X Snow Leopard v. 10.6.5.
> I typed the following commands into the terminal screen while in the gromacs-4.5.3 source directory.
> make mdrun
> The following error messages are produced:
> [ 63%] Building C object src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o
> /gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c: In function ‘nb_kernel400nf_x86_64_sse’:
> /gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: ‘gmx_invsqrt_exptab’ undeclared (first use in this function)
> /gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: (Each undeclared identifier is reported only once
> /gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: for each function it appears in.)
> /gromacs-4.5.3/src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c:629: error: ‘gmx_invsqrt_fracttab’ undeclared (first use in this function)
> make[3]: *** [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_x86_64_sse/nb_kernel400_x86_64_sse.c.o] Error 1
> make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
> make: *** [mdrun] Error 2
> I am not sure how to troubleshoot these error messages.  I know this is a new implementation, where we were originally given precompiled binaries for download, so this may or may not be unique to the switch over.
> Any help anyone would be willing to provide, I would be greatly appreciative. Thank you!
> Best,
> Solomon Berman
> Department of Chemistry
> Boston University--
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