On 29/03/2010 10:24 PM, DreamCatcher wrote:
Hello gmx-users,
I am trying to install a MPI version of Gromacs that I come
across some problems as follows:
[cele...@celeste gromacs-4.0.7]$ sudo ./configure
--prefix=/home/programmes/gromacs --disable-float --enable-mpi
Don't use sudo for configure. It doesn't need it and you risk trashing
your system if something in configure doesn't work quite right. Use sudo
for the "make install" step only. This is not the cause of your problem,
however.
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
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
I have installed MPICH2 in my PC and export the PATH where the
mpicc is.Yet,as a matter of fact,the prompts above indicates that there
isn't an mpicc in my PC.Could anybody tell me what the hell the problem
is. How can I fix it?
Does "which mpicc" immediately before a failing configure show the
correct executable? If it does, if you're setting the PATH manually, the
only think I can think is that your shell environment in which the
configure stuff gets executed is over-writing PATH in the dotfiles, not
appending to it. Thus, you lose the effect of your PATH setting. So you
could check for and/or fix that. Alternatively, try "./configure
--blahblahblah MPICC=/path/to/mpicc"
Another question, I am use a PC with dual-CPU, is it neccissary to
install an MPI version? Will the difference between a gmx with or
without a MPI in such a system be big enough to save our CPU time when
implement a molecular dynamics? My system may contains about 10000 or
more atoms.
Yes. MPI is the only way you can derive any advantage, which will be
considerable.
Mark
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