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

Solomon Berman smberman at bu.edu
Sun Nov 14 17:58:50 CET 2010

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!


Solomon Berman
Department of Chemistry
Boston University

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