[gmx-users] gromacs installation in IBM BLUEGENE
fiona at epcc.ed.ac.uk
Wed Nov 28 17:37:17 CET 2007
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.
> 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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