[gmx-users] gromacs installation in IBM BLUEGENE

Mark Abraham Mark.Abraham at anu.edu.au
Wed Dec 5 06:11:41 CET 2007

Fiona Reid wrote:
> 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
> _nss_*
> Adding -lnss_files -lnss_dns -lresolv -lc -lnss_files -lnss_dns -lresolv
> to LDFLAGS should solve this problem.
> Hope this helps.
> Fiona

Thanks very much for that Fiona. I've added the information to the 
GROMACS Wiki here http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene


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