[gmx-users] q question related to gromacsinstallation by cygwin

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 10 09:41:07 CET 2012

On 10/01/2012 5:45 PM, Dialing Pretty wrote:
> Dear Mark,
> If "--disable-threads ", how it will influence the function of GROMACS?

By preventing you from running mdrun with a separate execution thread in 
parallel on each physical processor that your machine has. If you need 
parallel functionality, compile with MPI enabled.

> Secondly, for the webpage you introduced to me 
> "http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO", 
> "Edit your login files to source /usr/local/gromacs/bin/GMXRC (or 
> manually add /usr/local/gromacs/man to the MANPATH and check that 
> /usr/local/bin is in the PATH)" is a little difficult to me. What is 
> "GMXRC"? What is the login files? How to find the MANPATH? How do I 
> know whther  /usr/local/bin is in the PATH is in the path? How can 
> source /usr/local/gromacs/bin/GMXRC?

That page contains the strongly-worded advice to check the normal 
GROMACS installation instructions, which has a fuller discussion of this 
"getting access to GROMACS" issue. Please search the web for tutorials 
and discussion of how UNIX PATH environment variables function.


> I am looking forward to getting a reply from you.
> Dialing
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tuesday, 10 January 2012 12:29 PM
> *Subject:* Re: [gmx-users] q question related to gromacsinstallation 
> by cygwin
> On 10/01/2012 12:24 PM, Dialing Pretty wrote:
>> Dear All,
>> I have tried to install gromacs-4.5.5 by cygwin but I meet the 
>> following problems.
>> I am looking forward to getting your suggestions on how to solve the 
>> problem.
>> Dialing
>> $ make
>> Making all in include
>> make[1]: Entering directory `/cygdrive/d/GROMACS2/gromacs-4.5.5/include'
>> Making all in .
>> make[2]: Entering directory `/cygdrive/d/GROMACS2/gromacs-4.5.5/include'
>> make[2]: Nothing to be done for `all-am'.
>> make[2]: Leaving directory `/cygdrive/d/GROMACS2/gromacs-4.5.5/include'
>> Making all in types
>> make[2]: Entering directory 
>> `/cygdrive/d/GROMACS2/gromacs-4.5.5/include/types'
>> make[2]: *** No rule to make target `all'. Stop.
>> make[2]: Leaving directory 
>> `/cygdrive/d/GROMACS2/gromacs-4.5.5/include/types'
>> Makefile:479: recipe for target `all-recursive' failed
>> make[1]: *** [all-recursive] Error 1
>> make[1]: Leaving directory `/cygdrive/d/GROMACS2/gromacs-4.5.5/include'
>> Makefile:347: recipe for target `all-recursive' failed
>> make: *** [all-recursive] Error 1
> The actual error occurred further up, so we cannot give specific help. 
> Be sure you are following the instructions here 
> http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO, 
> in particular --disable-threads.
> Mark
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