[gmx-users] installation problem of gromacs 4.0.7 on Rocks cluster

[Mark Abraham]

On 13/02/2012 9:56 PM, Parul tew wrote:
> Dear Gmx Users,
>
> I am facing problem while installing gromacs 4.0.7 on the rocks cluster
>
> 1. command:
> ./configure --enable-float --enable-threads --enable-sse --enable-mpi

If you were using an up-to-date version of GROMACS (and it is likely 
that you should do so), then you would not be able to compile with 
threads and with MPI. However this GROMACS version silently ignores the 
request for threads, because it wasn't implemented back then.

> we got the following error:
>
> checking for cc... cc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether cc accepts -g... yes
> checking for cc option to accept ISO C89... none needed
> checking for style of include used by make... GNU
> checking dependency style of cc... gcc3
> checking dependency style of cc... gcc3
> checking for mpxlc... no
> checking for mpicc... no
> checking for mpcc... no
> checking for hcc... no
> checking whether the MPI cc command works... configure: error: Cannot 
> compile and link MPI code with cc
>
> 2. command
> ./configure --enable-float --enable-threads --enable-sse --enable-mpi 
> --program-suffix=_mpi MPICC="/usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx"

mpicxx is intended to be a C++ compiler. This may or may not work 
correctly as a C compiler.

>
> we got the following error:
> checking whether we are using the GNU C compiler... yes
> checking whether cc accepts -g... yes
> checking for cc option to accept ISO C89... none needed
> checking for style of include used by make... GNU
> checking dependency style of cc... gcc3
> checking dependency style of cc... gcc3
> checking for mpxlc... /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx
> checking whether the MPI cc command works... yes
> checking for catamount... no
> checking for pthreads... yes
> checking how to run the C preprocessor... 
> /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx -E
> checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts -O3... yes
> checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts 
> -funroll-all-loops... yes
> checking whether /usr/mpi/gcc/mvapich-1.2.0/bin/mpicxx accepts  -O3 
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused 
> -funroll-all-loops... yes
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for ANSI C header files... no
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking whether byte ordering is bigendian... no
> checking for int... yes
> checking size of int... configure: error: cannot compute sizeof (int)
> See `config.log' for more details.
>
> though the installation completes without the --enable mpi
> the gcc compiler version used is 4.1.2.

Something is wrong with the setup of your MPI compiler - perhaps what I 
suggested above. You should verify that these work before attempting to 
troubleshoot GROMACS installation further.

See 
http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites 
where you are advised not to use this version of GCC.

I don't know for sure, but this version of MVAPICH could be too old to 
be useful.

Mark

>
> i will be grateful if  someone can help us out on how to resolve this 
> issue.
>
> thanking you,
>
> Parul Tewatia
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120213/c1dbc5cf/attachment.html>