[gmx-users] gromacs installation in IBM BLUEGENE

Fiona Reid fiona at epcc.ed.ac.uk
Wed Nov 28 17:37:17 CET 2007

Dear Anupam,

I also obtained a similar error to you when trying to install GROMACS 
on Blue Gene. I posted a message to the list on Monday but have since
found a solution.

> `/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
> rm -f kernel-stamp
> ./mknb   -software_invsqrt
> >>> Gromacs nonbonded kernel generator (-h for help)
> >>> Generating single precision functions in C.
> >>> Using Gromacs software version of 1/sqrt(x).
> Error: Cannot open nb_kernel010_c.c for writing.

Essentially the problem is that the executable ./mknb is compiled for the 
compute nodes on Blue Gene and when the make process attempts to run this 
executable on the front-end (login nodes running Linux) it fails.

I've managed to solve this problem by running ./mknb with the appropriate 
options, e.g. "./mknb -software_invsqrt" for your example on the backend 
on a single processor. This enables the required kernel****_c.c files to be 
created. Once the kernel files have been created you can continue the 
make process. At the final link stage you might encounter a number of 
undefined symbols, e.g. _nss_files_getaliasent_r and others beginning with

Adding -lnss_files -lnss_dns -lresolv -lc -lnss_files -lnss_dns -lresolv
to LDFLAGS should solve this problem.

Hope this helps.


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