* Francesco Pietra [2009 04 06, 16:51]:
> cd cytosine && ./Run.cytosine
> The authenticity of host deb64 (which is the hostname) (127.0.1.1)
> can't be established.
> RSA fingerprint .
> connecting ?
This is a warning from ssh, not from OpenMPI; probably it is the first
time the system tries
As I was unable to compile the parallel code Amber10 with openmpi
1.3.1 (fully tested) and intel compilers and mkl version 10 on debian
amd64 lenny, I'll try with the intels version 11. If it does not work
in my hands, I'll move to gnu compilers.
Question: to recompile openmpi 1.3.1. on intels 11
With amd64 etch, intel compilers 10, and openmpi 1.2.6 I had no
problem in compiling amber10.
Having changed to amd64 lenny, amber10 did no more pass installation
tets. I was unable to recompile amber10.
I upgraded openmpi 10 1.3.1, which passed all its tests, but again was
unable to recompile am
On Apr 8, 2009, at 5:08 AM, Francesco Pietra wrote:
As I was unable to compile the parallel code Amber10 with openmpi
1.3.1 (fully tested) and intel compilers and mkl version 10 on debian
amd64 lenny, I'll try with the intels version 11. If it does not work
in my hands, I'll move to gnu compiler
On Apr 6, 2009, at 6:22 PM, Steve Lowder wrote:
When I run the MPI version and set --mca opal_signal 6,7,11 the code
doesn't abort on underflow. I'd like to know if I'm interpreting this
behavior correctly, it appears that the mpi versus no mpi cases handle
underflow differently. I'm assuming O
On Wed, Apr 8, 2009 at 12:59 PM, Jeff Squyres wrote:
> On Apr 8, 2009, at 5:08 AM, Francesco Pietra wrote:
>
>> As I was unable to compile the parallel code Amber10 with openmpi
>> 1.3.1 (fully tested) and intel compilers and mkl version 10 on debian
>> amd64 lenny, I'll try with the intels versio
On Apr 8, 2009, at 8:00 AM, Francesco Pietra wrote:
> I test Intel v10 compilers frequently; they work fine with Open MPI.
>
> As far as we know, Intel v11 compilers work fine with Open MPI as
well.
Installing these over version 10 or doing a preparation before?
I'm not sure I understand
Hi Francesco, list
As Jeff suggested, the problem is not likely to be on the
Intel compilers or on OpenMPI.
I would guess it is the way information is being passed to the Amber
configuration script that may be the cause.
I am not familiar to Amber (we don't do computational Chemistry here),
so it
Hi Prentice,
after some tests I've concluded that is not an environment problem;
following you can see the env printed by a job. And seems correct.
I've seen if that the library /usr/local/lib/openmpi/mca_plm_lsf is in the
appropriate location the job fail:
> mpirun: symbol lookup error: /usr/local
On Wed, Apr 8, 2009 at 6:10 PM, Gus Correa wrote:
> Hi Francesco, list
>
> As Jeff suggested, the problem is not likely to be on the
> Intel compilers or on OpenMPI.
> I would guess it is the way information is being passed to the Amber
> configuration script that may be the cause.
> I am not fami
On Apr 7, 2009, at 6:05 AM, Bernhard Knapp wrote:
[bknapp@quoVadis04 testSet]$ mpirun -np 8 -machinefile /home/bknapp/
scripts/machinefile.txt mdrun -np 8 -nice 0 -s
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -c
1fyt_PKYVKQNTLELAT_bindingRe
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