RE: AMBER: make install error

From: Ross Walker <>
Date: Fri, 10 Sep 2004 15:41:02 -0700

Dear Abd,

> - i try to run my minimization in my server and then i found
> that it took

Have you run the test suite? You should to ensure things are running

> only 49% of my cpu's power.. why is it happen? why the job
> did not used
> 100% of my cpu's power?

You don't specify any details about your machine. Is it a dual processor
machine? I suspect that it is and that top if just reporting that your
machine is using 1 cpu. Some operating systems report this as 100% per cpu -
so a dual cpu job on a dual cpu machine would use 200% cpu and a single cpu
job 100%. Other operating systems, however, report it as a total
utilisation. Thus a dual cpu job on a dual cpu machine would be 100%
utilisation. A single cpu job (as you have compiled amber for here) would
use only one of the cpu's and so "half" of the total cpu "power" and thus
would be reported as 50% cpu usage. Hence what you are seeing above -
perfectly normal behaviour. If your machine is NOT dual cpu then you have a
problem (or you are running more than one job) but I suspect that it has 2
cpus. Try running two minimisations simultaneously - it should then report
100% cpu usage (one job on each cpu).
> - i do 'ln -sf Machines/Machine.g77_mpich MACHINE
> - and the i try to make install in /sander but i got this
> error msg :-
> root.alpha sander]# make install
> ( SYSDIR=`../sysdir dir` ; echo sysdir is $SYSDIR ; \
> cd $SYSDIR ; make sys.a )
> sysdir is ERROR:/usr/local/amber6/amber6/src/MACHINE-NOT-A-FILE
> /bin/sh: line 1: cd:
> ERROR:/usr/local/amber6/amber6/src/MACHINE-NOT-A-FILE:
> No such file or directory
> make[1]: Entering directory `/usr/local/amber6/amber6/src/sander'
> make[1]: *** No rule to make target `sys.a'. Stop.
> make[1]: Leaving directory `/usr/local/amber6/amber6/src/sander'
> make: *** [syslib] Error 2

I suspect your link line above was incorrect. Check that
$AMBEROME/src/MACHINE points to the file you expect - try vi
$AMBERHOME/src/MACHINE. I don't have a copy of amber 6 installed so I can't
take a look to see if the Machine file you specify is the correct one so you
need to verify this as well.

If vi $AMBEROME/src/MACHINE brings up the machine file as you expect then
please email me back. I suspect however that your link is invalid.
Especially as you specify in the beginning of your email that you did:

> - i do "export AMBERHOME=/usr/local/amber/amber6

NOTE THE /amber/amber6 whereas the ERROR message above states

NOTE the /amber6/amber6

Did you mistype the path?

Try again from a fresh copy of amber 6 and go through the process slowly
checking that you are entering the correct paths / valid links etc.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Fri Sep 10 2004 - 23:53:00 PDT
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