AMBER Archive (2008)

Subject: AMBER: Compilation of amber8 patched with ramd

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jun 24 2008 - 09:32:54 CDT

I am trying to compile (serial) amber8 - patched with contributed
software RAMD - on a UMA type dual opetron machine, Debian Linux lenny
amd64.

The RAMD patch, which only modifies sander
(http://projects.eml.org/mcm/software), has to be applied before any
bugfix is applied to amber8 (although, perhaps, bugfix not related to
sander might have been applied; not tried; I just tried bugfix.all and
it prevented the RAMD patch to be applied)

Now
$ ./configure ifort
AMBERHOME set to /usr/local/amber8
Setting up for architecture ifort
MKL_HOME is set to /opt/intel/mkl/10.0.1.014/
Using MKL libraries from /opt/intel/mkl/10.0.1.014/lib/32
Using parallel communication library: none
config.h created successfully

$ make serial

gave error:
ifort -o addles lesmain.so addspace.o readprm.o writprm.so readcrd.o
writcerd.o pick.o rline.o nxt.o intgr.o find.o of.o geti.o unit.o
getc.o alert.o echo.o get4c.o getd.o wlesprm.o lesprm.o les2prm.o
checksz.o ../lib/random.o ../lib/mexit.o ../lib/nxtsec.o
-L/opt/intel/mkl/10.0.1.014//lib/32 -lvml -lmkl_lapack64 -lmkl -lguide
-lpthread

ld: skipping incompatible
/opt/intel/mkl/10.0.1.014/lib/32/libmkl_intel.so when searching for
libmkl_intel.so

ld: cannot find libmkl_intel,so. Actually this is present where it was
searched. Thus incompatibility?

serial error 2

Is it known (or imaginable) if the the problem is raised by having
patched sander with ramd, or these mkl libraries (which I used for
both amber10 and dock6.2) are too new for amber8 (not bugfixed)
anyway? In the first case I could try by commenting out MKL_HOME in my
.bashrc.

I am in contact with the German group for RAMD, too. However,
presently there is no one capable of adapting RAMD to current times.

It is clear that my only interest with amber8 if to have it running
patched with RAMD. Otherwise I have both amber10 and amber9 installed.
In a way, my question is a jump into the past.

Thanks

francesco pietra
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