On Aug 26, 2009, at 3:45 AM, Alan wrote:
> It's because apbs-mpi.info is replacing /sw/bin/apbs instead of
> putting
> another binary called, e.g., /sw/bin/apbs_mpi
Is renaming the binary sufficient, or is it a different binary? (I
have to stop reading email in the middle of the night.)
Sorry guys,
I found another problem with apbs-mpi.
It's because apbs-mpi.info is replacing /sw/bin/apbs instead of putting
another binary called, e.g., /sw/bin/apbs_mpi then when running apbs (with
mpi) the output dx file will be appended with -PE0, no matter what one
defines in the apbs.in input
I think it's fixed at least with openmpi since apbs-mpi is working as
expected AFAIK.
Cheers,
Alan
On Mon, Aug 17, 2009 at 03:57, William G. Scott
wrote:
> Hi Alan:
>
> Sorry, I was away in the most inaccessible part of Utah I could find. I
> think Jack Howarth fixed it in my absence, but if no
Hi Alan:
Sorry, I was away in the most inaccessible part of Utah I could find.
I think Jack Howarth fixed it in my absence, but if not, please let me
know. Sorry for this continuing nightmare.
Bill
On Aug 14, 2009, at 12:35 AM, Alan wrote:
> Starting to answer myself, I did this test wi
Thanks Jack, I am using you files anyway. Excellent job.
Alan
On Sat, Aug 15, 2009 at 03:47, Jack Howarth wrote:
> Alan,
> I have uploaded a first pass of new apbs-mpi
> packaging which builds apbs properly against openmpi.
> It probably still needs work to make compatible with
> the lammpi var
Still, is it possible to make openmpi with a handle for xgrid? It should be
as simple as openmpi-static and openmpi-shared. Of course that it's not
urgent since xgrid support is broken in openmpi 1.3.x series so far.
Cheers,
Alan
On Sat, Aug 15, 2009 at 18:35, Daniel Macks wrote:
> On Sat, Aug
On Sat, Aug 15, 2009 at 01:30:47PM -0400, Jack Howarth wrote:
> Daniel,
>I added static library support to openmpi because of complaints from
> folks trying to build static binaries via fink for distributing their
> programs. I would rather leave that in as my philosophy is that fink
> should d
Daniel,
I added static library support to openmpi because of complaints from
folks trying to build static binaries via fink for distributing their
programs. I would rather leave that in as my philosophy is that fink
should do whatever possible to discourage users from installing their
own copies
Alan,
I have uploaded a first pass of new apbs-mpi
packaging which builds apbs properly against openmpi.
It probably still needs work to make compatible with
the lammpi variant. The packaging is on fink tracking
at...
https://sourceforge.net/tracker/index.php?func=detail&aid=2838001&group_id=17
Starting to answer myself, I did this test with a custom compiled version of
apbs:
~/Programmes/apbs-1.1.0-source% ./configure --enable-fast
--with-openmpi=/usr
make all
cd examples/actin-dimer
/usr/bin/mpirun -c 8 ../../bin/apbs apbs-mol-parallel.in
WORKED!
Than I realise that "--with-openmpi="
Hi There,
So I installed apbs-mpi-openmpi and it seems to work fine but when trying
this link to run in multi-core machine:
http://apbs.wustl.edu/MediaWiki/index.php/How_do_I_run_a_calculation_that%27s_too_big_for_my_computer%3F
I got this message and nothing done.
[snip]
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