AMBER Archive (2008)


From: Ross Walker (
Date: Thu Nov 06 2008 - 12:37:04 CST

Hi Albrite,


Such questions should be sent to the amber mailing list, not to me directly
so I am copying this reply there. Please see for details
on how to subscribe to this list.


With regards to the problems you are seeing you are getting errors like:


"cat command not found"

"mkdir command not found"


These are basic unix commands and I find it very unlikely that you don't
have them installed so I can only guess that your environment is messed up
in some way or you have trashed your path variable. Note when you add things
to the path environment variable you should make sure you append the
existing path. E.g. for bash:


export PATH=/foo/bar:$PATH


if you modified your path without doing this then you will have trashed your
login shell so even basic commands like ls can't be found.


Note I think you also have other problems to deal with - e.g. you specify
ifort but then when you issue make it tries to use f77. This suggests the
config.h file was not created and it is using some old config.h file that is
lying there - probably for an SGI. This is probably a function of your Unix
shell not being functional though.


Good luck



From: fitsum tesfa []
Sent: Thursday, November 06, 2008 7:45 AM
Subject: QUERRY?



i gor yr email while i was checking infos as far as amber8 installation is
concerned.I followed all the instructions in the manual;this was the final
output that i got:
After i enter the command:./configure -p4 ifort
AMBERHOME is set to /home/fkt/Desktop/AMBERH/

Setting up Amber configuration file for architecture: ifort
Using parallel communications library: none
MKL_HOME is set to /opt/intel/mkl
MKL libraries were not found !
./configure: line 917: cat: command not found

The configuration file, config.h, was successfully created.

again when i enter:make serial
Starting installation of Amber8 (serial) at .
mkdir ../exe
make: mkdir: Command not found
make: [serial] Error 127 (ignored)
cd lib; make install
make[1]: Entering directory `/home/fkt/Desktop/AMBERH/amber8/src/lib'
f77 -c -o new2oldparm.o new2oldparm.f
make[1]: f77: Command not found
make[1]: *** [new2oldparm.o] Error 127
make[1]: Leaving directory `/home/fkt/Desktop/AMBERH/amber8/src/lib'
make: *** [serial] Error 2
from the information i got in the net, they refer to modify the
config.h...surprizingly, the file refused to be opened.No am stuck what to
do...Have you come across the same problem?if you have any hints on this
regard,may i hear from you please.
thanks a lot IN ADVANCE.
OS;SUSE 10.1



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