Skip to Content.
Sympa Menu

charm - Re: [charm] [ppl] namd 2.7 on XE6 ?

charm AT lists.cs.illinois.edu

Subject: Charm++ parallel programming system

List archive

Re: [charm] [ppl] namd 2.7 on XE6 ?


Chronological Thread 
  • From: Abhinav S Bhatele <bhatele AT illinois.edu>
  • To: Viraj Paropkari <vrparopkari AT lbl.gov>
  • Cc: Phil Miller <mille121 AT illinois.edu>, charm AT cs.uiuc.edu
  • Subject: Re: [charm] [ppl] namd 2.7 on XE6 ?
  • Date: Tue, 8 Feb 2011 13:40:17 -0600
  • List-archive: <http://lists.cs.uiuc.edu/pipermail/charm>
  • List-id: CHARM parallel programming system <charm.cs.uiuc.edu>

Hi Viraj,

I downloaded the development version of charm and NAMD and they compiled just fine.
Here are the steps I followed:

module swap PrgEnv-pgi PrgEnv-gnu

Compile charm as:
./build charm++ mpi-crayxt -j8 -g

Compile namd as:
./config CRAY-XT-g++ --without-tcl --without-fftw

To get NAMD to link, I had to remove -lrca from charm/src/arch/mpi-crayxt/conv-mach.sh

And then I successfully ran NAMD on 24 cores.

- Abhinav


On Wed, Jan 26, 2011 at 2:52 PM, Viraj Paropkari <vrparopkari AT lbl.gov> wrote:
NAMD 2.7 and charm 6.2.2

On Tue, Jan 25, 2011 at 5:16 PM, Phil Miller <mille121 AT illinois.edu> wrote:
On Tue, Jan 25, 2011 at 19:09, Viraj Paropkari <vrparopkari AT lbl.gov> wrote:
> Hi Abhinav,
>                      Here is what I tried..
>
> I had trouble to build the latest version of NAMD 2.7 on Hopper II, so I
> built a bit older cvs version of NAMD on it instead. This cvs version was
> built in the exactly same way as building cray-xt5 on Hopper Phase I, and it
> runs fine. The problem is NAMD 2.7 code compiles fine, but the binary
> doesn't run because the Charm++ couldn't get the multi-thread support level
> correctly (do not have log of exact error messages right now). This was with
> latest version of charm++...
>
> If you want more information of exact build line etc , let me know.

This is exactly what Abhinav was asking for. Also, when you say "the
latest version of charm++", do you mean the 6.2.2 release, or
something gotten from Git? If the latter, what commit id?

> Also let me know if there is an update for your effort on XE6.
>
> Thanks.
>
>
>
>
> On Tue, Jan 25, 2011 at 4:48 PM, Abhinav S Bhatele <bhatele AT illinois.edu>
> wrote:
>>
>> What charm and NAMD build did you try? And what error messages are you
>> seeing when building Charm?
>> - A
>>
>> On Tue, Jan 25, 2011 at 6:45 PM, Viraj Paropkari <vrparopkari AT lbl.gov>
>> wrote:
>>>
>>> Hi Abhinav,
>>>                      Any updates on this one ? I also wanted to ask if
>>> charm++ has been ported on XE6 ? We are seeing some issues while building
>>> NAMD 2.7 on XE6 which seem to be coming from charm++. Error messages are
>>> about wrong level of multi thread support. Although namd2 binary from CVS
>>> version works.
>>>
>>> Thanks.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Thu, Jan 6, 2011 at 5:06 PM, Abhinav S Bhatele <bhatele AT illinois.edu>
>>> wrote:
>>>>
>>>> Hi Viraj,
>>>> As far as I know Cray has tried NAMD on some XE6's before they sold
>>>> them. We haven't tried running it yet but I am planning to in the next few
>>>> weeks.
>>>> - Abhinav
>>>>
>>>> On Thu, Jan 6, 2011 at 7:01 PM, Viraj Paropkari <vrparopkari AT lbl.gov>
>>>> wrote:
>>>>>
>>>>> Hi PPLers,
>>>>>                    Just wondering if group has tried running NAMD 2.7
>>>>> on Cray XE6 ?
>>>>>
>>>>>                   Thanks.
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------
>>>>> Viraj R. Paropkari
>>>>>
>>>>> HPC Engineer
>>>>> NERSC, Lawrence Berkeley National Lab
>>>>> One Cyclotron Road, MS 943-256
>>>>> Berkeley, CA  94720-8043
>>>>> 510.486.4520 voice
>>>>> 510.486.4316 fax
>>>>> VRParopkari AT lbl.gov
>>>>> ------------------------------------------------------------
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> ppl mailing list
>>>>> ppl AT cs.uiuc.edu
>>>>> http://lists.cs.uiuc.edu/mailman/listinfo/ppl
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Abhinav S Bhatele, Ph. D.
>>>> Webpage: www.bhatele.org
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------
>>> Viraj R. Paropkari
>>>
>>> HPC Engineer
>>> NERSC, Lawrence Berkeley National Lab
>>> One Cyclotron Road, MS 943-256
>>> Berkeley, CA  94720-8043
>>> 510.486.4520 voice
>>> 510.486.4316 fax
>>> VRParopkari AT lbl.gov
>>> ------------------------------------------------------------
>>>
>>>
>>
>>
>>
>> --
>> Abhinav S Bhatele, Ph. D.
>> Webpage: www.bhatele.org
>
>
>
> --
> ------------------------------------------------------------
> Viraj R. Paropkari
>
> HPC Engineer
> NERSC, Lawrence Berkeley National Lab
> One Cyclotron Road, MS 943-256
> Berkeley, CA  94720-8043
> 510.486.4520 voice
> 510.486.4316 fax
> VRParopkari AT lbl.gov
> ------------------------------------------------------------
>
>
>
> _______________________________________________
> ppl mailing list
> ppl AT cs.uiuc.edu
> http://lists.cs.uiuc.edu/mailman/listinfo/ppl
>
>



--
------------------------------------------------------------
Viraj R. Paropkari

HPC Engineer
NERSC, Lawrence Berkeley National Lab
One Cyclotron Road, MS 943-256
Berkeley, CA  94720-8043
510.486.4520 voice
510.486.4316 fax
VRParopkari AT lbl.gov
------------------------------------------------------------





--
Abhinav S Bhatele, Ph. D.
Webpage: www.bhatele.org



Archive powered by MHonArc 2.6.16.

Top of Page