Dear Bertrand,
It looks like when you are running the make command it is stripping the
AMBERHOME environment variable.
First try just typing "make" in the test directory rather than "make
test.serial"
This should not make any difference but it is still possible.
Secondly check if you have anything strange setup on your machine that
controls the way jobs are run. For example any distributed computing
software such as Mosix. Or some kind of queing system that passes commands
through a filter rather than running them directly. In this case it may not
be copying across the environment variables.
Next add:
export AMBERHOME=/path_to_amber9/
to /etc/bashrc
and
setenv AMBERHOME=/path_to_amber9/
to /etc/csh.cshrc
That way the environment variable should be set for everybody.
Finally login as a user other than root - It is very dangerous to be running
programs such as amber as root. Best to errr on the side of caution.
Check with
echo $AMBERHOME
if this is okay then try:
cd $AMBERHOME/test
make
And see if this works. If you still get problems please after the test
command completes type 'env' and post the output to the mailing list.
All the best
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 |
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
bertrand russell
Sent: Friday, March 23, 2007 13:06
To: amber.scripps.edu
Subject: AMBER: Error - must define AMBERHOME environment variable
Dear Amber9 users,
I am trying to compile amber9 in my HP-work station xw4200 running in FC3.I
hope that I following all the instructions properly during my installation
procedure. But, if run
> make test.serial I am getting the following error.
############################################################################
##############################################################
ptraj: test ptraj on averaging les trajectory to normal trajectory
diffing hef_averaged.crd.save with hef_averaged.crd
PASSED
==============================================================
cd leap; ./Run.tleap
Error - must define AMBERHOME environment variable
make: *** [ test.leap] Error 1
[root.electron test]#
############################################################################
##############################################################
But I am sure that I set the AMBERHOME environment variable corrrectly.
When I issue
############################################################################
##############################################################
ptraj: test ptraj on averaging les trajectory to normal trajectory
diffing hef_averaged.crd.save with hef_averaged.crd
PASSED
==============================================================
cd leap; ./Run.tleap
Error - must define AMBERHOME environment variable
make: *** [test.leap ] Error 1
[root.electron test]# echo $AMBERHOME
/usr/local/insprogrms/amber/amber9
[root.electron test]#
############################################################################
##############################################################
My path is as follows,
############################################################################
##############################################################
ptraj: test ptraj on averaging les trajectory to normal trajectory
diffing hef_averaged.crd.save with hef_averaged.crd
PASSED
==============================================================
cd leap; ./Run.tleap
Error - must define AMBERHOME environment variable
make: *** [ test.leap] Error 1
[root.electron test]# echo $AMBERHOME
/usr/local/insprogrms/amber/amber9
[root.electron test]# echo $PATH
/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/b
in:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin:/usr/local/insprogrms/amber/a
mber9/exe
############################################################################
##############################################################
I don't know what I am doing wrong? Could anyone tell me, why I am getting
this error even when I have exported the AMBERHOME variable correctly. I am
compiling with g95 and I couldn't notice any error while compiling or while
making.
Many thanks in advance.
--
Live Life; Don't pass it
Bertrand.P.S.Russell
+91-9894398441
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Received on Sun Mar 25 2007 - 06:08:12 PDT
