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

From: Philip Peartree (
Date: Wed Dec 12 2007 - 17:47:59 CST

I had tried the pthreads bit, and it didn't make much difference. That was with me mistakenly running 4 processes on 2 processors on one (head) node... I can try running across multiple nodes if that helps?


----- Original Message -----
From: "Brian Bennion" <>
To: "Philip Peartree" <>
Sent: 12 December 2007 23:01:57 o'clock (GMT) Europe/London
Subject: Re: namd-l: Compilation of Charm++ then NAMD 2.6 on Opteron with Portland compilers

Yes the threads bit is important to and it was my next suggestion.

The timings are indeed slow. Can you run a 8 cpu megatest and see
what you get. I have just recently finished a tortuous compile for
our clusters here, hence the wiki entry.
I am assuming the megatest data that you just emailed was on 1node with 2cpus?


At 02:54 PM 12/12/2007, you wrote:
>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:
> >Hi,
> >
> >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

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

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