AMBER Archive (2009)

Subject: Re: [AMBER] Testing parallel amber10: no

From: M. L. Dodson (
Date: Wed Apr 08 2009 - 11:06:09 CDT

I really hesitate to get involved in this, but I sense reply-fatigue
on the list so I will stick in my 2 cents to give others a rest. But
my patience is limited as well.

On Apr 8, 2009, at 10:14 AM, Francesco Pietra wrote:

[elided for clarity]

> mkdir /usr/local/amber10/bin /usr/local/amber10/lib /usr/local/
> amber10/include
> mkdir: cannot create directory `/usr/local/amber10/bin': File exists
> mkdir: cannot create directory `/usr/local/amber10/lib': File exists
> mkdir: cannot create directory `/usr/local/amber10/include': File
> exists
> make: [install] Error 1 (ignored)
> (cd ucpp-1.3 && make install )
> make[1]: Entering directory `/usr/local/amber10/src/ucpp-1.3'
> Makefile:35: warning: overriding commands for target `.c.o'
> ../config.h:99: warning: ignoring old commands for target `.c.o'
> icc -c -wd117,177,266,880,1011 -DBINTRAJ -DSTAND_ALONE nhash.c
> /usr/include/limits.h(125): catastrophic error: could not open source
> file "limits.h"
> # include_next <limits.h> ^
> compilation aborted for nhash.c (code 4)
> make[1]: *** [nhash.o] Error 4
> make[1]: Leaving directory `/usr/local/amber10/src/ucpp-1.3'
> make: *** [install] Error 2
> ======================
> which limits.h
> limits: /usr/include/limits.h
>> From "echo:$PATH"
> /usr/include


When compiling, limits.h being on the PATH is irrelevant.
Executable files are found using the PATH in Unix, not C include files.

The compiler command line is were you would place /usr/include, as in


HOWEVER, the compiler should find this directory without the -I/usr/
being necessary (on any Unix I have ever used, although to be fair I am
not very much of a Linux user, only using it on my compute nodes). I
suspect a problem with the C compiler installation is the real problem
here. But you might try editing config.h to place -I/usr/include in

Bud Dodson

M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one

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