AMBER Archive (2006)

Subject: Re: AMBER: Compiling AMBER 9 on windows XP using cygwin

From: Emilio Xavier Esposito (emilio.esposito_at_ndsu.edu)
Date: Thu Jul 06 2006 - 11:08:34 CDT

Hi Gobind
Are you trying to use the Intel compilers and MKL for Windows? I
compiled Amber 9 with g95. As, David Case and Gustavo Seabra have
mentioned make sure that the development files/tools for cygwin are
installed. It doesn't look like you do and this is causing one of your
problems.

Also, as David suggests, try compiling Amber without the MKL libraries.

Emilio

Gobind Bisht wrote:
> Hi Emilio,
> the method is not working. The following error were reported
> 1.) patch command not found
> 2.) ./configure: line 264[:C:Program:Binary Operator expected
> MKL libraries were not found!
> This is inspite the fact that the system environment variables are
> set to the MKL library path.
> 3.) make: command not found
>
> Can u plzz help...
> thanx a lot
> bye
>
> On 7/6/06, *Emilio Xavier Esposito* <emilio.esposito_at_ndsu.edu
> <mailto:emilio.esposito_at_ndsu.edu>> wrote:
>
> Hi Gobind
> I used the following commands to compile the serial version of Amber 9
> on my Windows XP box using cygwin and g95 (pmemd was not compiled). The
> test sets completed with minimal deviations. I only use the Windows
> version to set up simulations (remember to use dos2unix once you've
> moved the data to the *nix machine) and analyze trajectories.
>
> You should also read David Case's comments about running Amber on
> Windows http://amber.scripps.edu/mswindows.html .
>
> Hope this helps
> Emilio
>
>
> 1. go to ftp.g95.org <http://ftp.g95.org> and download latest set of
> binaries (cygwin x86
> tarball) into c:/temp
> (link to the g95 compilers:
> none_at_ftp.g95.org/g95-x86-cygwin.tgz">ftp://anonymous%40g95%2Eorg:none_at_ftp.g95.org/g95-x86-cygwin.tgz )
> 2. open a cygwin bash shell (startx type)
> 3. cd / (cygwin root)
> 4. tar zxvf /cygdrive/c/temp/g95-x86-cygwin.tgz
> 5. cd /cygdrive/c
> 6. tar zxvf /cygdrive/e/amber9.tgz (e is my CD drive)
> 7. export AMBERHOME=/cygdrive/c/amber9
> 8. cd $AMBERHOME
> 9. wget http://amber.scripps.edu/bugfixes/9.0/bugfix.all (latest amber9
> update)
> 10. patch -p0 -N -r patch_rejects <bugfix.all
> 11. cd src
> 12. ./configure -p4 -cygwin g95
> 13. make serial
> 14. ../test
> 15. make test.serial
>
>
> Gobind Bisht wrote:
> > hi all,
> > can anyone sugest how to compile AMBER9 in windows XP. I used
> cygwin
> > but it's not able to find the MKL libraries inspite of the fact
> that the
> > 'lib' path in system environment variables was set to the right
> location
> > of MKL libraries. I had also set LD_LIBRARY_PATH to the mkl
> libraries in
> > the user variablels but the error continues.Whoat should i do?
> Also the
> > "make serial" command is not recognised by cygwin. what command
> has to
> > be used to compile AMBER after making the config.h file?
> > Please help
> > thanx in advance
> >
> > --
> > Gobind Singh Bisht
> > Department Of Biotechnology
> > IIT Kharagpur, Kharagpur-721302
> > West Bengal,
>
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