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
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