Re: compiling amber on a linux box using DMEM-ALLOC

From: Florian Barth <>
Date: Sat 7 Sep 2002 00:13:31 +0200


I also tried to use the DMEM-ALLOC flag but then sander was not
running anymore (Mandrake 8.2, gcc 3.1).
Obviously the DMEM-ALLOC flag does not apply to Linux Machines but
only to other Unix derivates. So I guess all you can do is changing
the limits in sizes.h and compile again.


       Florian Barth

rkdr> Dear amber users
rkdr> I am trying to install amber7 on a linux box with red hat 7.3. I
rkdr> followed the instructions on INSTALL file and I used the Machine.g77
rkdr> machine file. The compilation was ok, but doing the benchmarks I got an
rkdr> error message about sizes of pair list. Reading the manual one can see
rkdr> that if the compilation is done using DMEM-ALLOC flag the limits in
rkdr> sizes.h are ignored. So, I tried to compile including that machine flag
rkdr> but I got another error message when it try to compile sander.f, something
rkdr> about trajen routine can not be compiled.
rkdr> Does anybody has experience on how to compile amber7 in order to
rkdr> ignore the limits of sizes.h and could give some hints on how to do this?
rkdr> Thank you in advance.

rkdr> ________________________________________________________________________________
rkdr> Ramon Kleber da Rocha, MSc. VOICE +55-31-3499-5765
rkdr> e-mail FAX +55-31-3499-5700

rkdr> Laboratorio de QSAR e Modelagem Molecular
rkdr> Nucleo de Estudos em Quimica Medicinal - NEQUIM -
rkdr> Departamento de Quimica - Universidade Federal de Minas Gerais - (DQ/ICEx/UFMG)
rkdr> ---
rkdr> The World is my Fatherland, Science is my Religion. Christiaan Huygens 1629-1695
rkdr> ________________________________________________________________________________


Florian Barth
Institute of Technical Biochemistry
University of Stuttgart
Allmandring 31
70569 Stuttgart
phone: +49-711-6857481
fax: +49-711-6853196
Received on Fri Sep 06 2002 - 15:13:31 PDT
Custom Search