Hi Robert,
This is a quirk of using cygwin. Essentially most implementations of Unix
include a csh shell. More commonly this is in the form of the more modern
tcsh but the OS is setup in such a way that /bin/csh points to /bin/tcsh in
cygwin this is not always done by default. So:
1) Check that /bin/tcsh.exe exists. If it doesn't then run the cygwin
setup.exe prog and find the option for tcsh and install it.
2) create a link for csh that points to tcsh.exe.
cd /bin
ln -s tcsh.exe csh
Then hopefully things will work correctly - I suspect up to the compilation
of xleap where it may stop with a header not found error implying that you
need to install the X11 development libraries for cygwin - again not
installed by default.
Good luck.
Ross
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|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Hopkins, Robert
Sent: Friday, October 05, 2007 11:32
To: amber.scripps.edu
Subject: RE: AMBER: Problems with 'make'
Thanks Ross!
Your prompt and perceptive analysis was right on. After wiping the egg off
my face, it hit me that I had been trying to proceed from the $AMBERHOME/exe
directory after I'd misinterpreted the step in the Install Readme that says,
"d. compile and install the binaries into $AMBERHOME/exe:".
With your suggestions, the 'make serial' command hummed along beautifully,
creating & assembling '.o' files, up to a point. However, the following
output then came up:
(In $AMBERHOME/src/addles):
'
' All apparently OK
'
'
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 '/usr/local/amber9/src/addles'
make: *** [serial] Error 2
At this point the output stopped and the prompt returned to $AMBERHOME/src.
I looked at the Makelist file and noticed the first line reads:
#!/bin/csh -f
It appears this should be, but might not be, interpreted as a remark.
Indeed, there is no csh program in /bin. With my limited UNIX/Linux
experience, I'm not sure if this is even relevant. Again, I'd greatly
appreciate any suggestions.
Thanks,
Bob Hopkins
_____
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Ross Walker
Sent: Thursday, October 04, 2007 3:55 PM
To: amber.scripps.edu
Subject: RE: AMBER: Problems with 'make'
Dear Robert,
Just to check are you in $AMBERHOME/src when you are typing make or just in
$AMBERHOME?
In the later case you will see "make: *** No rule to make target `serial'.
Stop." because there is no makefile in the amber9 root directory. The
makefile is under the src directory so you need to do:
cd $AMBERHOME/src/
make clean
make serial
See if that works, if not and you are definately in the src directory please
check that you have a file called "Makefile" present in that directory.
Good luck...
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Hopkins, Robert
Sent: Thursday, October 04, 2007 12:08
To: amber.scripps.edu
Subject: AMBER: Problems with 'make'
Amber Users:
I'm new to Amber and relatively new to UNIX/Linux. Nonetheless, I'm trying
to install Amber9 on a laptop running Windows XP. I've successfully
installed the Cygwin environment as well as g95. After unpacking the Amber
files, setting the environment variables & path, applying all of the Bug
fixes and running the configuration script, all successfully, I hit a brick
wall trying to 'make serial'. Although a 'make' utility was supplied with
the old g77, there was none with g95, so I installed the 'make' utility for
Cygwin. However, this version neither recognizes 'make serial' nor 'make
clean' - a similar error is reported in each case:
make: *** No rule to make target 'serial'. Stop.
Although I've searched the mail archives at both the Scripps and UK Amber
sites, I haven't found an answer to this problem. It may be that I'm
overlooking something, but it appears that many others have had some type of
problem with the 'make' command. I would greatly appreciate any help or
suggestions in regard to this impasse.
Thanks,
Bob Hopkins
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Received on Sun Oct 07 2007 - 06:07:48 PDT
