OpenMPI's MPI 2.0 support is broken. It's not an AMBER issue. Try again
with mvapich2 or mpich2...
On Wed, Aug 22, 2012 at 8:00 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Hello,
>
> I have just built Amber 12 cuda on Ubuntu 12.04 with Intel 12.1.3 and
> NVCC 4.2 V0.2.1221 and then invoked the test suite on a Tesla C2075.
>
> The test below did not produce output for about 40 minutes (I then
> killed the pmemd.cuda process):
>
> > cd gb_ala3/ && ./Run.irest1_ntt2_igb1_ntc2 SPDP
> /apps11/bioinfp/amber12_centos58_intel1213_openmpi16/amber12/include/netcdf.mod
> >
> > Killed
> > ./Run.irest1_ntt2_igb1_ntc2: Program error
>
> With "did not produce output" I mean that it did not change the mdout
> file anymore. These are the last lines in the mdout file before and
> after killing the process:
>
>
> > | Intermolecular bonds treatment:
> > | no_intermolecular_bonds = 1
> >
> > | Energy averages sample interval:
> > | ene_avg_sampling = 1
> >
> >
> --------------------------------------------------------------------------------
> > 3. ATOMIC COORDINATES AND VELOCITIES
> >
> --------------------------------------------------------------------------------
> >
> > ACE
> > begin time read from input coords = 1050.000 ps
>
> The tests before this one (about 20 of them) PASSED. While I am writing
> this email, the test suite proceeds. However, it currently hangs at
>
> > cd myoglobin/ && ./Run_md_myoglobin
>
> for already about 15 minutes which is suspicious, right?
>
> If I will have to kill this one, too, and maybe others, I will rerun the
> tests and see if the same tests are hanging or if they are hanging
> randomly. I'll then get back to you.
>
> Have you seen such behavior before?
>
> Any suggestion would be helpful.
>
> Thanks,
>
> Jan-Philip
>
>
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Received on Wed Aug 22 2012 - 09:00:03 PDT
