AMBER: RE: AMBER9 Installation Help

From: Ross Walker <ross.rosswalker.co.uk>
Date: Thu, 20 Sep 2007 07:48:12 -0700

Hi Sebastien,
 
Unfortunately I can't reproduce the problem you are seeing on my system. The
specs of my system are:
 
IBM P655 running AIX 5.2. The xlc compiler is: IBM(R) XL C/C++ Enterprise
Edition V8.0 for AIX(R)
The xlf90 compiler is IBM(R) XL Fortran Enterprise Edition V10.1 for AIX(R)
 
I ran configure with the options: ./configure xlf90_aix
 
analyze.c is compiled with:
 
        xlc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -DCLINK_PLAIN
-o analyze.o analyze.c
 
This completes without error.
 
>From what you are showing it looks like the compiler is getting confused and
thinking the first entry for safe_malloc is actually a prototype rather than
use of an external function.
 
I would check that you have a correct version of analyze.c that is not
corrupted. The details around line 470 of $AMBERHOME/src/ptraj/analyze.c is:
 
    if(2*nevec <= nelem){
      ncv = 2*nevec;
      vout = (double *) safe_malloc(nelem * ncv * sizeof(double));
    }
 
Is yours the same?
 
You could also try explicitly adding the prototype for safe_malloc to
analyze.c
 
Immediately before
 
 int
analyzeTest(analyzeInformation *analyze, stackType *sp, int mode)
 
add
 
extern void * safe_malloc();
 
And see if this makes any difference.
 
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 |

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: Sébastien Kozlowskyj [mailto:kseb.averell.umh.ac.be]
Sent: Thursday, September 20, 2007 05:25
To: Ross Walker
Subject: RE: AMBER9 Installation Help



Hi Ross,

 

Many thanks for your reply.

 

Yes, I installed all the patch and the problem is not fixed.

 

I am looking forward from you for your kind and valuable suggestions.

 

Regards,

 

Sébastien Kozlowskyj.

 

 

 

 

 

 


  _____


From: Ross Walker [mailto:ross.rosswalker.co.uk]
Sent: mercredi 19 septembre 2007 14:36
To: Sébastien Kozlowskyj
Subject: RE: AMBER9 Installation Help

 

Hi Sebastien,

 

My apologies for not replying to this email earlier. It seems to have got
lost at the end of my inbox.

 

I think the problem you are seeing should be fixed by bugfix.1. Have you
applied all the amber9 bugfixes?

 

http://amber.scripps.edu/bugfixes90.html

 

Try this first of all and see if it fixes the problem. If not get back to me
and I'll look at my compiler versions, configure scripts etc.

 

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 |

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: Sébastien Kozlowskyj [mailto:kseb.averell.umh.ac.be]
Sent: Wednesday, August 22, 2007 06:38
To: rcw.sdsc.edu
Subject: AMBER9 Installation Help

Dear Ross Walker,

 

Nice meeting you through mail. I am Sébastien Kozlowskyj working in
University of Mons Hainaut, Laboratory for Chemistry of Novel Materials.

I am trying to install amber9 in our IBM machines whos' specifications are
as follows,

 

IBM p655 running on IBM Aix version 5.2. Processor - IBM Power PC. When I
issued the command,

 

>make serial

-o actions.o actions.c

        xlc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -DCLINK_PLAIN
-o analyze.o analyze.c

" analyze.c", line 470.70: 1506-046 (S) Syntax error.

"analyze.c", line 471.25: 1506-282 (S) The type of the parameters must be
specified in a prototype.

"analyze.c", line 471.22: 1506-343 (S) Redeclaration of safe_malloc differs
from previous declaration on line 65 of " utility.h".

"analyze.c", line 471.22: 1506-050 (I) Return type "double*" in
redeclaration is not compatible with the previous return type "void*".

"analyze.c", line 471.15 : 1506-275 (S) Unexpected text 'double'
encountered.

"analyze.c", line 474.26: 1506-046 (S) Syntax error.

"analyze.c", line 474.29: 1506-045 (S) Undeclared identifier get.

"analyze.c ", line 479.26: 1506-046 (S) Syntax error.

"analyze.c", line 493.9: 1506-046 (S) Syntax error.

make: 1254-004 The error code from the last command is 1.

 

 

Stop.

make: 1254-004 The error code from the last command is 2.

 

I see on your internet site that you have successfully installed amber9 in
your IBM machines and running it, even in parallel (whit what mpi library?
).

I feel your suggestions would take us through this compilation problem. I am
looking forward from you for your kind and valuable suggestions. Many thanks
in advance.

 

Sébastien Kozlowskyj.

 

 

 

****************************************************************************
****
Sébastien Kozlowskyj
Administrateur Système
Service de Chimie des Matériaux Nouveaux
Centre de Recherche en Electronique et Photonique Moléculaires
Université de Mons-Hainaut
Place du Parc, 20
B-7000 Mons (Belgique)
e-mail: kseb.averell.umh.ac.be

Tel.: ++32-(0)65-373866
Fax: ++32-(0)65-373861
****************************************************************************
****

 




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Received on Sun Sep 23 2007 - 06:07:28 PDT
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