AMBER Archive (2006)

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

From: Gobind Bisht (gsbisht1_at_gmail.com)
Date: Thu Jul 06 2006 - 10:36:28 CDT

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> 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 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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-- 
Gobind Singh Bisht
Btech II yr, Department Of Biotechnology
IIT Kharagpur, Kharagpur-721302
West Bengal,

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