AMBER Archive (2007)

Subject: Re: AMBER: Cygwin error

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Thu Aug 09 2007 - 15:30:19 CDT

Lili,

You will need to download and install 'g95' (http://ftp.g95.org/)
first. Then, you can use the -cygwin flag in Amber's configure
program, to create the config.h for cygwin. Just follow the same
procedure as for installing Amber in other computers.

Now, if you only want some programs (I for one only installed
leap/xleap and ptraj locally), you can just comment the lines related
to other programs in the '$AMBERHOME/src/Makefile'.

Gustavo.

On 8/9/07, Lili Peng <lilipeng_at_gmail.com> wrote:
> Hi Dr. Walker,
>
> I was previously running xleap via SDSC's Teragrid server, but I was
> encouraged to run it locally on my own computer in efforts to reduce
> computational time. Now I'm trying to run xleap on my Windows desktop.
>
> How should I go about recompiling it? I Googled "compile xleap windows" but
> nothing relevant came up.
>
> Thanks,
> Lili
>
>
> On 8/9/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> >
> >
> > Hi Lili,
> >
> > Typically when you receive a message saying "cannot execute binary file"
> it means the executable was compiled on a different system/architecture to
> the one you are trying to run it on.
> >
> > Are you certain Leap was compiled in cygwin on the same architecture you
> are currently trying to run it on? If not you'll need to recompile it.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
> >
> >
> >
> > ________________________________
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Lili Peng
> > Sent: Thursday, August 09, 2007 11:13
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: Cygwin error
> >
> >
> >
> > Dear all,
> >
> > Thanks all for your helpful comments. I've installed the tcsh package in
> Cygwin. However, I've encountered another problem. When I try to run xleap
> by typing "$AMBERHOME/exe/xleap -s -f
> $AMBERHOME/dat/leap/cmd/leaprc.ff99SB" I just end up
> getting the following message:
> >
> > "/cygdrive/h/amber9/exe/xaLeap: /cygdrive/h/amber9/exe/xaLeap: cannot
> execute binary file"
> >
> > I've also tried the following:
> > $ xleap
> > /cygdrive/h/amber9/exe/xaLeap: /cygdrive/h/amber9/exe/xaLeap: cannot
> execute binary file
> >
> > $ xaLeap
> > ./xaLeap: ./xaLeap: cannot execute binary file
> >
> > I wondered whether it was a permissions problem, so I tried:
> > $ ls -ll xaLeap
> > -rwx------+ 1 Lili None 3467265 Mar 29 15:54 xaLeap
> >
> > ...Obviously I have read, write, and execute access, so it can't be a
> permissions issue..
> >
> > Does anyone have insights on the problem?
> >
> > Thanks,
> > Lili
> >
> >
> > On 8/8/07, Gustavo Seabra <gustavo.seabra_at_gmail.com > wrote:
> > > On 8/8/07, Lili Peng <lilipeng_at_gmail.com > wrote:
> > > > I think I figured it out. I have to run:
> > > >
> > > > cd "$AMBERHOME"
> > > > or
> > > > ls "$AMBERHOME"
> > > >
> > > > cd or ls don't work without the quotes.
> > >
> > > That's weird, it works fine for me. Which shell are you using? The
> > > default in cygwin in bash, which is the one I use, and just "cd
> > > $AMBERHOME" works just fine.
> > >
> > > > Still, this doesn't solve the problem with running xleap, but I think
> that's
> > > > a problem with csh. I didn't have it installed, so now I'm going back
> into
> > > > the Cygwin setup file and installing the csh file.
> > >
> > > Well, that's another thing. This is unrelated to the error you
> > > reported before, but yes, you need csh. In Cygwin, "csh" is actually a
> > > symlink to "tcsh":
> > >
> > > $ which csh
> > > /usr/bin/csh
> > > $ ls -l /usr/bin/csh
> > > lrwxrwxrwx 1 adm None 8 Jun 7 15:47 /usr/bin/csh -> tcsh.exe
> > >
> > > The problem is that tcsh is not installed by default. You need to run
> > > setup.exe again and explicitly select it from the "shells" menu. The
> > > link from csh is created automatically.
> > >
> > > Gustavo.
> > >
> -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> >
> >
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu