AMBER Archive (2005)

Subject: AMBER: Installation problem. .

From: Sukjoon Yoon (yoonsj_at_sookmyung.ac.kr)
Date: Thu Jun 16 2005 - 09:49:19 CDT

Dear Andreas,

This was a great advice. I finally installed AMBER 8 in my machine
(64bit Xeon Cpus with FC3) following your instruction. However, my "make
test" was not successful. So please let me ask you one more question.

One more thing: On my machine, All "Run.(...)" scripts must start with
#!/bin/csh -f (mind the '-f'), otherwise sander and colleagues don't
find the needed shared libs. This might not be a problem on other
machines (?).

As you mentioned above, I ended up with following message.

************************************************************************
**********************
[root_at_bioinfo test]# make test
cd dmp; ./Run.dmp
../../exe/sander: error while loading shared libraries: libvml.so:
cannot open shared object file: No such file or directory
  ./Run.dmp: Program error
make: *** [test.sander.no_lmod] Error 1
************************************************************************
**********************

My "Run.(...)" files already had "#!bin/csh -f "......... Does anybody
know how to fix this problem?

Thank you.

Sukjoon

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Andreas Svrcek-Seiler
Sent: Wednesday, June 15, 2005 9:32 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Installation problem. .

Hi,
> 2.6 Linux kernel is already installed in my PC.
..That's the default, probably even since FC2 (?)

> My intel fortran compiler for linux is version 8.1. Was this the
> critical problem in installing AMBER 8?
..No problem at all (more or less).
The best way for the intel compiler and opterons:
do a:
/configure -p4 ifort

then edit config.h:
Optimization recommended for athlon 64 CPUs are '-O3 -ip -xW' '-xW'
turns on specific optimizations for Intel pentium4s and compatible
processors (e.g. Athlon 64).
Then (if present) set the path to the correct MKL library
(e.g. /opt/intel/mkl721/lib/em64t on my machine).

Now, everything should work like a charm (not charmm :-).
When compiling xleap, I found one issue: In one Makefile, /usr/X11R6/lib
should be changed to /usr/X11R6/lib64, otherwise
compilation fails.

There's one caveat: If you want 64 bit, choose the right compiler. Many
people might have 32 and 64 bit compilers installed (me, too). Just make
sure to source the right ${BLA}/bin/ifortvars.csh. Per default, 64 bit
compilers are under /opt/intel_fce_80 (fortran) and opt/intel_cce_80.

One more thing: On my machine, All "Run.(...)" scripts must start with
#!/bin/csh -f (mind the '-f'), otherwise sander and colleagues don't
find the needed shared libs. This might not be a problem on other
machines (?).

I've attached 'my' config.h, which leads to a flawless 'make test'.

> Version 9.0 will be available for free from Auguest based on
> anouncement in Intel website.
>
..The C/C++ compiler is already available (and works - giving a
noticeable performance gain in the benchmarks I did, again on an athlon
64). Curiously, the install script doesn't allow installation, but a
manual install works just fine. I wonder whether that happened on
purpose (assuming it might take users till August to
find out how to do the installation manually) or someone simply messed
things up.

>
> I would really appreciate if anybody give me an advice to intall AMBER

> 8 in a 64bit machine with FC3 x86_64 or FC4 x86_64. I don't want to
> buy a compiler just to install AMBER...
..No need to, obviously. I'd just recommend *not* to install FC4 right
now. FC3 with all updates and bug fixes might be the better choice until
FC4 has matured a little bit - but that's solely my personal
opinion.

Good luck,
Andreas 

-- 

             )))))
             (((((
            ( O O )
-------oOOO--(_)--OOOo--------------------------------------------------
---
               o        Wolfgang Andreas Svrcek-Seiler
               o        (godzilla)
                        svrci_at_tbi.univie.ac.at
       .oooO            Tel.:01-4277-52733
       (   )   Oooo. 
-------\ (----(
)--------------------------------------------------------
         \_)    ) /
               (_/

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu