Hey Jason,
I followed the directions on your wiki for installing amber 12,
running ./patch_amber.py --update-tree until it returns that Amber12
and AmberTools12 are up to date.
The error messages from the supercomputer I'm using are,
"[compute-f17-1.deepthought.umd.edu:21064] [[44012,1],39]
ORTE_ERROR_LOG: Data unpack would read past end of buffer in file
runtime/orte_init.c at line 132
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: orte_init failed
--> Returned "Data unpack would read past end of buffer" (-26)
instead of "Success" (0)
--------------------------------------------------------------------------
*** The MPI_Init() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[compute-f17-1.deepthought.umd.edu:21061] Abort before MPI_INIT
completed successfully; not able to guarantee that all other processes
were killed!"
which I thought were generic openmpi error messages. For your
reference, the version of openmpi I am using is openmpi16-gnu.
I have also attempted to use the openmpi143-gnu version of openmpi,
obtaining the error message,
"[compute-f16-26.deepthought.umd.edu:30072] mca: base: component_find:
unable to open /cell_root/software/openmpi/1.4.3/gnu46/sys/lib/openmpi/mca_btl_openib:
perhaps a missing symbol, or compiled for a different version of Open
MPI? (ignored)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 14 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them."
My REMD simulation is 50 replicas at different temperatures in NVT
ensembles attempting exchanges every 5 ps. The template for my mdin
files is
replica exchange
&cntrl
imin=0, irest=1, ntx=5,
ntt=3, temp0=XXXXX, gamma_ln=2.0, ig=-1,
nstlim=2500, dt=0.002,
ntb=1, ntc=2, ntf=2,
ntr=0, ntp=0,
ntwr=100000, ntwx=2500, ntpr=2500,
cut=12,
numexchg=1000,
/
&wt type='END'
/
Hopefully this answers your questions, thanks,
David
On Mon, Mar 11, 2013 at 6:56 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Mar 11, 2013 at 6:34 PM, David Winogradoff <dwino218.gmail.com>wrote:
>
>> I am currently working on a project using amber in parallel to conduct
>> a long REMD run. A few weeks ago, using the same input file that
>> worked before (modified to start from where the previous simulation
>> ended), my parallel run failed with a generic openmpi error message.
>> After some initial hesitation, I decided to delete my installation of
>> amber 12 and recompile and rebuild. I have run 'make test'
>> successfully with my new serial and parallel versions of amber 12, but
>> my REMD simulation still won't run. After many unsuccessful attempts
>> to run, I decided to look at some of my previous output files. To my
>> surprise, the older output files had amber 11 at the top. Even though
>> my new simulations won't run, they do write the header, which says
>> amber 12.
>>
>> I did see that it is possible to have some combination of amber 11 and
>> amber 12, but I never installed amber 11 and do not have the tar files
>> to do so. Is there any way to install amber 11 with amber 12 tar files
>> (accidentally)? My hypothesis is that some requirement, such as my
>> version of gnu, was out of date during my previous installation,
>> preventing the complete installation of amber 12. I have tried to
>> recreate the mistake, since I didn't think I could make files meant
>> for amber 11 to work with amber 12, without success. The only solution
>> I can think of right now is to purchase amber 11 and create a hybrid
>> form of amber 11 and amber 12 that will hopefully run my simulations
>> once more.
>>
>
> When Amber 12 was released, it actually still said "Amber 11" at the top.
> That was updated in bugfix.2 for Amber 12. Do you have all bug fixes
> applied?
>
> What error messages are you getting? And what exactly are you doing? The
> better way forward, IMO, is to fix Amber 12... What kind of REMD are you
> doing?
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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Received on Wed Mar 13 2013 - 10:30:03 PDT
