AMBER Archive (2006)

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

From: Gobind Bisht (gsbisht1_at_gmail.com)
Date: Fri Jul 07 2006 - 09:13:37 CDT

Hi Emilio,
             I did install all the development tools/files as u told but
after that it began giving some other problem and used only g95:
after the command :make serial
the following happened:

--------------------------------------------------------------------------------------
Starting installation of AMBER 9
cd lib; make install
make [1]:Entering directory 'home/user/amber9/src/lib'
g95 -o new2oldparm.o nxtsec.o
my new2oldparm.exe ../../exe
/bin/rm _*.f
/bin/rm: cannot remove '_*.f':nNo such file or directory
make[1]: [instal] Error 1,ignore.
make[1]: leaving directory..............................
cd addles ; make install
make[1]; make install
make[1]: Entering directory '/home/user/amber9/src/addles'
cd../lib; ./Makelist../lib/random.o../lib/mexit.o../lib/nxtsec.o
/bin/sh:./Makelist :/bin/csh:bad interpreter: no such file or directory
make[1]: ***[libobj] Error 126
make [1]: leaving directory................
make: ****[serial] Error 2
-------------------------------------------------------------------------------------------------
what should i do next? Please help.

On 7/6/06, Emilio Xavier Esposito <emilio.esposito_at_ndsu.edu> wrote:
>
> 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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> 

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

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