[gmx-users] Gromacs installed , but no directory /bin under it

[Justin A. Lemkul]

On 5/23/12 9:37 PM, aiqunhuang at knights.ucf.edu wrote:
> Hi Justin, thanks a lot for replying.
> Regarding your question, in the beginning there were errors like this in config.log:
>
> " cc: error: unrecognized option '-V'
> cc: fatal error: no input files
> compilation terminated.
> configure:4343: $? = 4
> configure:4332: cc -qversion >&5
> cc: error: unrecognized option '-qversion'
> cc: fatal error: no input files
> .......
> configure:6186: checking how to run the C preprocessor
> configure:6217: mpicc -E -I/home/Program/fftw-3.3.1/include conftest.c
> configure:6217: $? = 0
> configure:6231: mpicc -E -I/home/Program/fftw-3.3.1/include conftest.c
> conftest.c:21:28: fatal error: ac_nonexistent.h: No such file or directory
> compilation terminated.
> mpicc: No such file o! r directory
> configure:6231: $? = 1
> configure: failed program was:
> .......
>
> Thread model: posix
> gcc version 4.6.1 (Ubuntu/Linaro 4.6.1-9ubuntu3)
> configure:9684: $? = 0
> configure:9673: mpicc -V >&5
> gcc: error: unrecognized option '-V'
> gcc: fatal error: no input files
> compilation terminated.
> configure:9684: $? = 4
> configure:9673: mpicc -qversion >&5
> gcc: error: unrecognized option '-qversion'
> gcc: fatal error: no input files
> compilation terminated
> .....
>
> fatal error: libxml/parser.h: No such file or directory "
>
> I searched a little and found this page
> http://verahill.blogspot.com/2012/01/debian-testing-64-whee!
> zy-compiling_20.html
> <http://verahill.blogspot.com/2012/01/debian-testing-64-wheezy-compiling_20.html> to
> run this command
> /sudo apt-get install libxml2-dev /
> /and fixed the last fatal error: /libxml/parser.h: No such file or directory
> but I did't do anything about the other errors
>

libxml is an optional package.

> In the first beginning I tried to install 4.5.5, but I didn't succeed. I got
> something like this"*** No rule to make target `../gmxlib/libgmx_mpi.la', needed
> by `libmd_mpi.la'"
> I tried both enable shared and disable shared for cofiguring Gromacs4.5.5. It
> didn't succeed.
>

This comes from the above error regarding mpicc not being found.  I see you 
installed lam previously.  Don't use it.  There are newer and better packages, 
and likely you can easily install an Ubuntu package for a modern version of 
OpenMPI that will be automatically configured for your environment.

> Ok, since there are more threads, I won't use mpi. can I ask you that what do
> you mean by " not
>  > install Gromacs within the source tree "? Can I create a new folder like
> /home/program and install FFTW and Gromacs and everything needed in the
> /home/program?
>

You can install programs wherever you like.  What I was saying was to choose an 
installation such that binaries are not installed as a subdirectory of the 
source code.  If you're not planning on doing any development, the source just 
gunks up disk space, since all you're after is the executables.

For instance, you may find it useful to install all your programs in some 
subdirectory within $HOME.  Just be careful to specify the locations correctly. 
  After sending my last message, I noticed a number of inconsistencies in your 
commands that likely refer to nonexistent directories.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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