Re: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers

From: Philip Peartree (
Date: Wed Dec 12 2007 - 16:54:09 CST

Hi Brian,

I believe it's a 3Com GigE switch (I realised I'd forgotten to put the specs of my cluster on) I've used your tip from the Wiki which seems to have worked, I think there is a setting in conv-mach.h to change from gnu-malloc to the system malloc, will this help, I don't know if you've seen my other posts but I posted some times from megatest which to me seemed slow, but I don't actually know.

Philip Peartree

P.S. It is the portland group compiler version 6.0

----- Original Message -----
From: "Brian Bennion" <>
To: "Philip Peartree" <>
Sent: 12 December 2007 21:08:05 o'clock (GMT) Europe/London
Subject: Re: namd-l: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers

Which compiler are you using? Is it the portland group compiler?
What switches are on your cluster?
Basically if you are using an mpi layer then you need to tell charm++
to let the system handle memory allocation not gnu-malloc.
So if you can give more information on your setup I might be able to
fine tune my hints.


At 07:20 AM 12/12/2007, you wrote:
>I'm having some issues compiling Charm++/NAMD on our opteron based
>cluster. I've read somewhere that it is best to use the fastest
>compiler. I think I've just about got Charm++ working, and it works
>fine with the simplearrayhello, and I've compiled the megatest
>program.. the only error I got was an error from pgCC saying that
>-rdynamic is an unknown switch. If I run on 4 procs I get the following output:
>Megatest is running on 4 processors.
>test 0: initiated [groupring (milind)]
>test 0: completed (45.86 sec)
>test 1: initiated [nodering (milind)]
>test 1: completed (45.36 sec)
>test 2: initiated [varsizetest (mjlang)]
>test 2: completed (0.27 sec)
>test 3: initiated [varraystest (milind)]
>test 3: completed (0.32 sec)
>test 4: initiated [groupcast (mjlang)]
>test 4: completed (1.57 sec)
>test 5: initiated [nodecast (milind)]
>test 5: completed (0.96 sec)
>test 6: initiated [synctest (mjlang)]
>**ERROR: in routine alloca() there is a
>stack overflow: thread 0, max 535822332KB, used 2KB, request -1082359024B
>Could anyone elaborate on what's wrong here, I heard that the
>Megatest program tests things that are fairly crucial to NAMD's running?
>Philip Peartree

Biosciences and Biotechnology Division
Lawrence Livermore National Laboratory
Phone: 925-422-5722
Fax: 925-424-4334

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