Notes on compiling NAMD 2.6
- Run
./config Linux-amd64-MPI.postfixto create an installation. - The new Charm++ and NAMD 2.7 use different platform names (e.g.
Linux-x86_64-OpenMPIfor NAMD 2.7, butLinux-amd64-MPIfor NAMD 2.6. This causes problems when looking for the Charm++ installation, so editMake.charmin NAMD directory:Code Block CHARMBASE = /share/apps/charm-6.2.0/mpi-linux-x86_64-mpicxx - Then edit
Makearchin theLinux-amd64-MPI.postfixdirectory as follows, by changing theCHARM=...line:Code Block include .rootdir/Make.charm include .rootdir/arch/Linux-amd64-MPI.arch CHARM = $(CHARMBASE) NAMD_PLATFORM = $(NAMD_ARCH)-MPI include .rootdir/arch/$(NAMD_ARCH)$(NAMD_SUBARCH).base - Try
makein the installation directory.
Using the queue system
All programs run on Darius must use the queue system. Users can submit their jobs using the qsub command:
...
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#!/bin/bash
#PBS -k o
#PBS -N apoa
#PBS -l nodes=1:ppn=4,walltime=12:00:00
#PBS -j oe
cd /home/musolino/namd/apoa1
h4. Notes on compiling NAMD 2.6
# Run {{./config Linux-amd64-MPI.postfix}} to create an installation.
# The new Charm++ and NAMD 2.7 use different platform names (e.g. {{Linux-x86_64-OpenMPI}} for NAMD 2.7, but {{Linux-amd64-MPI}} for NAMD 2.6. This causes problems when looking for the Charm++ installation, so edit {{Make.charm}} in NAMD directory:
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CHARMBASE = /share/apps/charm-6.2.0/mpi-linux-x86_64-mpicxx
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# Then edit {{Makearch}} in the {{Linux-amd64-MPI.postfix}} directory as follows, by changing the {{CHARM=...}} line:
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include .rootdir/Make.charm
include .rootdir/arch/Linux-amd64-MPI.arch
CHARM = $(CHARMBASE)
NAMD_PLATFORM = $(NAMD_ARCH)-MPI
include .rootdir/arch/$(NAMD_ARCH)$(NAMD_SUBARCH).base
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# Try {{make}} in the installation directory.
/usr/mpi/gcc/openmpi-1.4.1/bin/mpirun /share/apps/NAMD_2.7b2_Source/Linux-x86_64-OpenMPI/namd2 apoa1.namd
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