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


Chronological Thread 
  • From: Jim Phillips <jim AT ks.uiuc.edu>
  • To: Abhinav S Bhatele <bhatele AT illinois.edu>
  • Cc: Viraj Paropkari <vrparopkari AT lbl.gov>, charm AT cs.uiuc.edu
  • Subject: Re: [charm] [ppl] namd 2.7 on XE6 ?
  • Date: Tue, 8 Feb 2011 14:53:24 -0600 (CST)
  • List-archive: <http://lists.cs.uiuc.edu/pipermail/charm>
  • List-id: CHARM parallel programming system <charm.cs.uiuc.edu>


Can we automate including it when it is needed somehow, or at least take it out so the typical case works out of the box?

-Jim

On Tue, 8 Feb 2011, Abhinav S Bhatele wrote:

rca is used to get physical coordinates for each physical node using the
rca_get_meshcoord call.
This need not be linked in since the code is not turned on by default.

- Abhinav


On Tue, Feb 8, 2011 at 2:35 PM, Jim Phillips
<jim AT ks.uiuc.edu>
wrote:


Thanks. Anybody know what -lrca does? -Jim


On Tue, 8 Feb 2011, Abhinav S Bhatele wrote:

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




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





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