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
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
