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.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.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Andreas Svrcek-Seiler
Sent: Wednesday, June 15, 2005 9:32 PM
To: amber.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.tbi.univie.ac.at
.oooO Tel.:01-4277-52733
( ) Oooo.
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)--------------------------------------------------------
\_) ) /
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Received on Thu Jun 16 2005 - 15:53:01 PDT
