RE: AMBER: Cygwin error

From: Ross Walker <>
Date: Thu, 9 Aug 2007 11:52:36 -0700

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

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| <> | 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: [] On Behalf Of
Lili Peng
Sent: Thursday, August 09, 2007 11:13
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?


On 8/8/07, Gustavo Seabra <
<> > wrote:

On 8/8/07, Lili Peng < <> >
> I think I figured it out. I have to run:
> or
> 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
> a problem with csh. I didn't have it installed, so now I'm going back
> 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
  $ 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.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Aug 12 2007 - 06:07:38 PDT
Custom Search