[gmx-users] Gromacs installation question: Where is my Gromacs?

[bestenborstel]

Did run sudo make install again, but before I executed configure with prefix=/usr/local/gromacs and I did mkdir gromacs in /usr/local before manually. Content in the gromacs folder: bin	include	lib	share

Gromacs finished again with:

GROMACS is installed under /usr/local/gromacs.
Make sure to update your PATH and MANPATH to find the
programs and unix manual pages, and possibly LD_LIBRARY_PATH
or /etc/ld.so.conf if you are using dynamic libraries.

Please run "make tests" now to verify your installation.

If you want links to the executables in /usr/local/bin,
you can issue "make links" now.


Shall I execute now 'sudo make links' or 'make links', please? Sorry, I also don't really know how to update my PATH variable. 
Do I have to execute 'make test' as the Gromacs page says test set is broken?
Finally, is there something like 'make clean'  to allow for a proper, clean re-installation?

I thought I better ask again.
Sorry.
Gudrun


Am 16.03.2012 um 20:05 schrieb David van der Spoel:

> On 2012-03-16 21:03, bestenborstel wrote:
>> Sorry, David, not sure what you mean. Yes, I am the admin of my pc. I can do whatever I can :-)
>> What do you ask me please to do?
> sudo make install
> and check on the screen where the stuff is copied to.
> 
>> 
>> Am 16.03.2012 um 19:54 schrieb David van der Spoel:
>> 
>>> On 2012-03-16 20:49, bestenborstel wrote:
>>>> Thank you for your quick reply.
>>>> 
>>>> 'make links' produces:
>>>> 
>>>> Saturn:gromacs-4.5.5 gudrun$ make links
>>>> cd /usr/local/gromacs/bin&&   programs=`ls`&&   cd /usr/local/bin&&   \
>>>> 	for i in $programs; do \
>>>> 	   (test ! -f $i&&   ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
>>>> 	done
>>>> /bin/sh: line 0: cd: /usr/local/gromacs/bin: No such file or directory
>>>> make: *** [links] Error 1
>>>> 
>>>> I have a /usr/local/ but there is no gromacs. Not even after running again 'sudo make -n install'
>>>> Sorry, I am not sure where to post this lengthy output.
>>>> 
>>> -n means "not really"
>>> run it without to install.
>>> But do you have permission to write in /usr/local?
>>> 
>>>> Thank you for your help.
>>>> Kind regards
>>>> Gudrun
>>>> 
>>> 
>>> 
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell&  Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> -- 
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